Office of Graduate StudiesUniversity of South Florida

Tampa, Florida

CERTIFICATE OF APPROVAL__________________

Ph.D. Dissertation__________________

This is to certify that the Ph.D. Dissertation of

YA-LI YAO

with a major in Medical Sciences has been approvedfor the dissertation requirement on April 9, 2001

for the Doctor of Philosophy degree.

Examining Committee:

_________________________________________________Major Professor : Edward Seto, Ph.D.

_________________________________________________Member : Burt Anderson, Ph.D.

_________________________________________________Member: Peter Medveczky, M.D.

_________________________________________________Member: Richard Jove, Ph.D.

REGULATION OF YY1, A MULTIFUNCTIONAL TRANSCIPTION FACTOR

by

YA-LI YAO

A dissertation submitted in partial fulfillmentof the requirements for the degree of

Doctor of PhilosophyDepartment of Medical Microbiology and Immunology

College of MedicineUniversity of South Florida

May 2001

Major Professor: Edward Seto, Ph.D.

DEDICATION

To my parents, Ta-Chung (Righteous and Magnanimous) and Shiao-Hung (Little

Rainbow).

ACKNOWLEDGEMENTS

I am eternally grateful to my Lord, Who gave me the chance to fulfill my

dream of earning a Ph.D. degree. I would like to thank my mentor, Dr. Edward Seto,

for his endless support and guidance. Without him I would never have accomplished

my goal. My gratitude also extends to my committee members, who gave me

invaluable advice and helped me meet the requirements of the department. My

special acknowledgement goes to my husband, Dr. Wen-Ming Yang, whose help and

encouragement accompanied me when I needed them the most.

I thank Dr. Nancy Olashaw for critical reading and the core facilities at the

Moffitt Cancer Center as well as the Protein Chemistry Core at the University of

Florida for technical support. I would also like to express my gratitude to Kathy

(Mom), Linda, Susan, Cheryl, Sally, and B.J. They made my life as a graduate

student much easier and happier.

i

TABLE OF CONTENTS

LIST OF FIGURES iv

ABSTRACT viii

INTRODUCTION 1

Transcription is an important step in gene regulation. 1

Transcription in prokaryotes. 2

Transcription in eukaryotes. 3

RNA polymerase II and the eukaryotic promoter. 4

Activators and transcriptional activation. 6

Repressors and transcriptional repression. 8

Chromatin and transcription. 9

Chromatin remodeling. 10

Histone acetyltransferases as co-activators. 11

Histone deacetylases as co-repressors. 13

YY1 is a transcriptional regulator. 13

General characteristics of YY1. 14

YY1 and transcriptional initiation. 15

OBJECTIVES 17

MATERIALS AND METHODS 20

Isolation of YY1 genomic clones. 20

ii

Plasmids. 20

Sequencing of the human YY1 promoter. 22

Primer extension. 22

Cell line, transfection, luciferase assays, and CAT assays. 23

Recombinant proteins. 23

In vitro acetylation reactions. 24

Immunoprecipitation and western blot analysis. 24

In vitro protein-protein interaction assays. 25

Histone deacetylation assays. 25

Immunofluorescence analysis. 26

Electrophoretic mobility shift assays. 26

Gel filtration analysis of YY1. 27

Purification of a YY1 complex by anion exchange and immobilized-

metal affinity chromatography. 27

Coomassie staining and silver staining. 27

Purification of a YY1 complex by anion exchange and antibody-

affinity chromatography. 28

Purification of the F-YY1 complex. 28

Radioimmunoprecipitation analysis (RIPA) of F-YY1. 28

Accession number. 29

RESULTS 30

Determination of the transcriptional start site of the human YY1

gene. 30

iii

Transcriptional analysis of the human YY1 promoter. 31

Sequence analysis of the human YY1 promoter. 33

E1A-mediated repression of the human YY1 promoter. 35

YY1 does not autoregulate its own promoter. 37

YY1 is acetylated by p300 and PCAF. 38

Lysine-to-arginine mutations within YY1 residues 170-200

significantly reduce the transcriptional repression activity of YY1. 45

Acetylation of YY1 residues 170-200 increases YY1 binding to

HDACs. 46

HDAC1 and HDAC2 deacetylate YY1 170-200 but not the C-

terminal region of YY1. 46

HDACs bind YY1 at multiple regions. 52

YY1 contains associated histone deacetylase activity, which localizes

to C-terminal residues 261-333 of YY1.

52

Acetylation of YY1 at the C-terminal zinc finger domain decreases

the DNA-binding activity of YY1.

54

YY1 exists in a high molecular weight protein complex. 57

Purification of native YY1 complexes. 57

Purification of a Flag-tagged YY1 complex. 65

DISCUSSION 70

REFERENCES 80

ABOUT THE AUTHOR End Page

iv

LIST OF FIGURES

FIG. 1. Step-wise assembly of the transcriptional initiation complex. 5

FIG. 2. Regulation of transcription: a model. 7

FIG. 3. Determination of the 5’ end of the human YY1 transcript. 30

FIG. 4. Expression of luciferase enzymatic activity driven by the

human YY1 promoter in transiently transfected cells. 32

FIG. 5A. DNA sequences upstream of the translational start codon of

the human YY1 gene. 33

FIG. 5B. Comparison of the YY1 promoter DNA sequences between

mouse and human. 34

FIG. 6. Adenovirus E1A proteins repress the YY1 promoter. 36

FIG. 7. The YY1 protein does not autoregulate the YY1 promoter. 37

FIG. 8. Multiple functional domains of transcription factor YY1. 38

FIG. 9A. Acetylation of YY1 by PCAF. 39

FIG. 9B. Acetylation of YY1 by p300. 40

FIG. 9C. Acetylation of YY1 is dependent on p300 or PCAF. 41

FIG. 9D. YY1 is acetylated in vivo. 42

FIG. 9E. Identification of regions of YY1 acetylated in vivo. 43

FIG. 9F, G. Determination of the number of acetylated lysines by mass

spectrometry. 44

v

FIG. 10. The effect of acetylation of YY1 residues 170-200 on the

transcriptional repressor activity of YY1. 45

FIG. 11. Increased HDAC-binding to YY1 residues 170-200 by

acetylation. 47

FIG. 12A. YY1 peptide deacetylation by HDACs. 48

FIG. 12B. YY1 protein deacetylation by HDACs. 49

FIG. 12C. Deacetylation of YY1 serial deletion proteins by HDAC1. 50

FIG. 13. Mapping of the HDAC-interaction domains of YY1. 51

FIG. 14A. Histone deacetylase activity of endogenous YY1 in HeLa

cells. 52

FIG. 14B, C. Identification of amino acid 261-333 as the histone

deacetylase activity domain of YY1. 53

FIG. 14D. Expression of F-YY1 deletion mutants. 54

FIG. 14E. Sub-cellular localization of F-YY1 deletion constructs. 55

FIG. 15A, B. The effect of acetylation on YY1’s sequence-specific DNA-

binding activity. 56

FIG. 16. Gel filtration analysis of YY1 in HeLa cells. 57

FIG. 17A, B. Purification of a native YY1 complex from HeLa cells using

anion exchange chromatography and IMAC. (A) A

Coomassie-stained SDS-polyacrylamide gel of the Q

Sepharose fractions. (B) Western blot analysis of the Q

Sepharose fractions. 58

FIG. 17C, D. Purification of a native YY1 complex from HeLa cells using

vi

anion exchange chromatography and IMAC. (C). EMSA of

the Q Sepharose fractions using the AAV P5+1 YY1 binding

sequence as a probe. (D). Histone deacetylation assay of the

Q Sepharose fractions. 59

FIG. 17E, F. Purification of a native YY1 complex from HeLa cells using

anion exchange chromatography and IMAC. (E) Western

blot analysis of the Ni2+ column fractions. (F) EMSA of the

300 mM imidazole-eluted fractions using the AAV P5+1

YY1 binding sequence as a probe. 60

FIG. 17G. Purification of a native YY1 complex from HeLa cells using

anion exchange chromatography and IMAC. (G) Silver-

staining analysis of the second fraction from the 300 mM

imidazole-eluted fractions. 61

FIG. 18A, B. Purification of a native YY1 complex from HeLa cells using

anion exchange chromatography and antibody-affinity

chromatography. (A) A Coomassie-stained SDS-

polyacrylamide gel of the Q Sepharose fractions. (B)

Western blot analysis of the Q Sepharose fractions. 62

FIG. 18C, D. Purification of a native YY1 complex from HeLa cells using

anion exchange chromatography and antibody-affinity

chromatography. (C) EMSA of the Q Sepharose fractions

using the AAV P5+1 YY1 binding sequence as a probe. (D)

Histone deacetylation assay of the Q Sepharose fractions. 63

vii

FIG. 18E. Purification of a native YY1 complex from HeLa cells using

anion exchange chromatography and antibody-affinity

chromatography: (E) Silver-staining analysis of fractions

from the anti-YY1 H-10 column (lane 2) and the protein G

control column (lane 1). 64

FIG. 18F. Purification of a native YY1 complex from HeLa cells using

anion exchange chromatography and antibody-affinity

chromatography. (F) Histone deacetylation assay from the

protein G control column (protein G) and the anti-YY1 H-10

column (H-10) against the H4 peptide. 65

FIG. 19A. Silver-staining analysis of the second fractions from the

Flag-alone (lane 1) column and the F-YY1 column (lane 2). 66

FIG. 19B. Histone deacetylation analysis of the second fractions from

the Flag alone column and the F-YY1 column against the H4

peptide. 67

FIG. 20A. A representative autoradiograph showing proteins bound to

Flag alone or F-YY1. 68

FIG. 20B. A representative autoradiograph showing proteins bound to

different F-YY1. 69

FIG. 21 Summary of regulation of YY1 by acetylation and

deacetylation. 72

viii

REGULATION OF YY1, A MULTIFUNCTIONAL TRANSCRIPTIONAL

FACTOR

by

YA-LI YAO

An Abstract

of a dissertation submitted in partial fulfillmentof the requirements for the degree of

Doctor of PhilosophyDepartment of Medical Microbiology and Immunology

College of MedicineUniversity of South Florida

May 2001

Major Professor: Edward Seto, Ph.D.

ix

Yin Yang 1 (YY1) is a sequence-specific DNA binding transcription factor that plays

an important role in development and differentiation. It activates or represses many

genes during cell growth and differentiation and is also required for the normal

development of the mammalian embryo. Moreover, it has been shown that YY1 may

function as a transcriptional initiator. In this dissertation, regulation of human YY1 is

analyzed systematically at three levels: At the genomic level, one major

transcriptional initiation site of the YY1 gene was mapped to 478 bp upstream of the

ATG translational start site. The YY1 promoter was localized to within 277 bp

upstream of the major transcriptional initiation site and was shown to contain multiple

binding sites for transcriptional factor Sp1 but lack a consensus TATA box. Over-

expression of the adenovirus E1A protein represses expression of the YY1 promoter.

At the polypeptide level, the activity of YY1 is regulated through acetylation by p300

and PCAF and deacetylation by HDACs. YY1 was acetylated in two regions: both

p300 and PCAF acetylated the central glycine/lysine-rich domain of residues 170-

200, and PCAF also acetylated YY1 at the C-terminal DNA-binding domain.

Acetylation of the central region was required for the full transcriptional repression

activity of YY1 and targeted YY1 for active deacetylation by HDACs. However, the

C-terminal region of YY1 could not be deacetylated. Rather, the acetylated C-

terminal region interacted with HDACs, which resulted in stable histone deacetylase

activity associated with the YY1 protein. Furthermore, acetylation of the C-terminal

domain decreased the DNA binding activity of YY1. At the protein complex level,

YY1 was shown to form a complex with up to four different proteins consistently

throughout different purification methods. These proteins are likely to have important

x

regulatory roles in the transcriptional activity of YY1. Taken together, these findings

will provide valuable information to our understanding of the regulatory mechanisms

of transcription in general.

Abstract Approved: ______________________________________________Major Professor: Edward Seto, Ph.D.Associate Professor, Interdisciplinary Oncology Program

Date Approved: _______________________________

1

INTRODUCTION

Transcription is an important step in gene regulation. The Big Bang of

our knowledge on gene regulation happened in 1961, with the debut of the concept of

the prokaryotic operon (77, 78). Monod and Jacob pictured the perfect regulatory

circuitry of making proteins out of genes using an amplifiable intermediate, which

they called the messenger RNA (mRNA). In this model, genes of the same

biochemical pathway are grouped into an operon, which is immediately preceded by a

regulatory DNA element called the operator. A repressor protein binds the operator

and keeps the operon in the “off” position. Upon proper environmental cues, an

inducer molecule binds the repressor protein, inducing an allosteric modification. In

this configuration, the repressor no longer binds the operator, thus causing the operon

to switch to the “on” position. When the operon is “on,” mRNA is being made. This

process is referred called transcription. mRNA, the product of transcription, is the

template recognized by the ribosomes for making proteins (17, 50). This linear

relationship among DNA, mRNA, and proteins is so important that it is called the

Central Dogma of Biology, and transcription has been recognized as an important step

in gene regulation.

Much of the original operon model proposed by Monod and Jacob still holds

true today. However, some modifications are needed. For example, we now know

that all operons are not regulated by repression/de-repression. Some operons are

regulated by activation, and some operons are under control of multiple regulatory

2

mechanisms. Moreover, transcription regulation can occur at multiple stages,

including initiation, which was essentially what Monod and Jacob initially described,

as well as elongation and termination, two steps subsequent to the initiation stage.

Nevertheless, the concept that mRNA is made according to precisely regulated

interplay among DNA regulatory elements, repressors and activators remains as the

true essence of transcriptional regulation, and the importance of understanding how

genes are regulated will likely to continue rising with the complete sequencing of the

human genome.

Transcription in prokaryotes. The initial operon model soon expanded to

full understanding of transcriptional control in prokaryotes (for a historical review,

see reference 107). In prokaryotes, such as bacteria, transcription is catalyzed by an

enzyme called RNA polymerase. The RNA polymerase is a four-unit protein

consisted of two α subunits and two β subunits. During transcriptional initiation,

RNA polymerase scans the length of the bacterial DNA. When it encounters a

specific sequence about 35 bp upstream from the transcriptional initiation site, it

becomes associated with a specific protein called σ factor and anchors on the DNA.

Then it spreads along the DNA until it finds another sequence, which usually lies

about 10 bp upstream from the initiation site. This -10 sequence tells the polymerase

where to lay down the first nucleotide, and the polymerase faithfully unwinds the

DNA and starts incorporating nucleotides to make RNA. The σ factor then falls off,

and the polymerase becomes dedicated to the next phase of transcription, elongation.

Both the protein players, including the polymerase and the σ factor, and the DNA

sequences, including the -35 and -10 sequences, have tremendous influence on where,

3

when, and how often transcription starts. Regulation of transcriptional initiation

largely relies on manipulation of this system. For example, a repressor usually blocks

the binding of the RNA polymerase to either the -35 or the -10 sequence, and no

transcription can occur in this configuration. An activator may augment the

association between DNA and the RNA polymerase, causing more frequent firing of

the polymerase and higher levels of transcription. These findings significantly

enriched our understanding of transcriptional control. In the mean time, with the

continuous efforts from numerous researchers, it became apparent that transcription in

eukaryotes is regulated in very similar fashions. The differences between prokaryotic

transcription and eukaryotic transcription, in fact, are the complex layers and flavors

in regulations that are unique to eukaryotes.

Transcription in eukaryotes. The most significant difference between

prokaryotes and eukaryotes is the nucleus. The nucleus by itself provides excellent

regulation because mRNA export in eukaryotes is a highly regulated process (49, 79).

However, the consequences of having a nucleus are far beyond mere physical

barriers: In eukaryotic nuclei, DNA is packaged into chromatin (151). Even though

the basic layouts of transcription in eukaryotes are the same as those in prokaryotes,

chromatin inevitably inhibits access of the RNA polymerase to the DNA. Therefore,

as opposed to gene-specific activators/repressors observed in prokaryotes, genes in

eukaryotes are repressed in general due to the way DNA is organized. Furthermore,

prokaryotes are unicellular organisms, but many eukaryotes are multi-cellular

organisms with complex body plans. Prokaryotic gene regulators activate or repress

transcription in a swift fashion because prokaryotes need to respond to the

4

environmental changes quickly. Cells in complex eukaryotes, however, are

committed to specific functions after differentiation, and only a certain fraction of the

genome is active in a certain place at a certain time. As a result, transcriptional

control in eukaryotes is characterized by developmentally timed up- and down-

regulations of specific subsets of genes whose accessibility is determined by the

chromatin structure. The beauty of eukaryotic transcriptional control, therefore, lies

in the intricate connections among the RNA polymerase, activators, repressors, and

the DNA promoter elements organized within the chromatin along the temporal and

spatial axes.

RNA polymerase II and the eukaryotic promoter. The RNA polymerase

responsible for making mRNA in eukaryotes is the RNA polymerase (Pol) II. Pol II

enzyme in yeast is a multi-subunit protein complex comprising 12 polypeptides (174).

Pol II needs additional protein factors to recognize promoters and initiate

transcription; these protein factors are termed general transcription factors (reviewed

in references 32, 175). It has been suggested that the general transcription factors for

Pol II, designated TFIID, -B, -F, -E, and -H, cooperate with Pol II in a highly

coordinated fashion to form the transcriptional initiation complex (20, 175) (Figure

1): First, TFIID recognizes the promoter by virtue of its TBP subunit binding to the

TATA box in the promoter. The TATA box is analogous to the -10 sequence in

prokaryotes, and TBP is analogous to the σ factor. Upon recognizing the TATA box,

TBP bends DNA and creates a binding surface for TFIIB, which associates with Pol II

and recruits Pol II to the promoter. TFIIF associates with both Pol II and TFIIB.

Through multiple interactions with TFIID, TFIIB, and TFIIF, Pol II is accurately

5

positioned on the promoter. Under some circumstances, this minimal complex can

initiate transcription without TFIIE and TFIIH.

The association of TFIIE with the polymerase is required for the subsequent

recruitment of TFIIH. TFIIH possesses an ATP-dependent helicase activity, which

unwinds DNA around the transcriptional initiation site and triggers transcriptional

initiation. It is thought that TFIIE and TFIIH are key players in converting the

process of transcription from the initiation phase to the elongation phase, an event

sometimes called promoter clearance.

Pol II

TFIIB

TBP

TFIID

TATA+1

TFIIE

TFIHTFIIF

TFIIA

TFIIE

TFIH

Pol II

TFIIB

TBP

TFIID

TATA+1

TFIIF

TFIIA

Pol II

TFIIB

TBP

TFIID

TATA+1

TFIIA

TFIIF

FIG. 1. Step-wise assembly of the

transcriptional initiation complex. A

thick line represents DNA. A bent

arrow depicts the direction of

transcription. The transcriptional

initiation site is indicated by “+1.”

TATA represents the TATA box

(adapted from reference 20).

6

Activators and transcriptional activation. Activators are usually DNA-

binding proteins with modular structures of activation domains that can be defined by

fusing to a heterologous DNA-binding motif. Typical activation domains have been

characterized as acidic (reviewed in reference 56), glutamine rich, or proline rich

(reviewed in reference 113) . Detailed structural and mutagenesis studies suggest that

the mechanisms of activation domains might involve ionic and hydrophobic

interactions between the repeated amino acids within the activation domains and their

target general transcription factors (37, 44, 157). However, in vitro, transcriptional

activation cannot occur without participation of another protein complex called the

Mediator (reviewed in reference 14). In yeast, the Mediator complex contains 20

subunits, many of which have been shown to be important in transcriptional control in

vivo (118). For example, inactivation of SRB4 (suppressor of RNA polymerase B 4)

immediately causes cessation of transcription by Pol II (156). Interestingly, a human

Mediator complex was also isolated as a co-activator complex specifically associated

with ligand-bound nuclear hormone receptors (53). Subsequent efforts of purification

demonstrate significant similarities between the human and the yeast Mediator

complexes (reviewed in reference 59). The consensus at this moment is that

transcriptional activators directly interact with components of the Mediator complex,

which in turn cause the polymerase to initiate transcription more often than the basal

level (Figure 2).

The Mediator complex is thought to tether directly to the C-terminal domain

of Pol II (85, 155). Affinity purification involving components of the Mediator

complex suggests that in vivo, the Mediator complex exists in a form of a RNA

7

polymerase holoenzyme containing Pol II, general transcription factors, the Mediator,

and proteins involved in chromatin remodeling (reviewed in references 87, 125, 169).

It has been further suggested that interactions between activators and any components

of the holoenzyme can lead to transcriptional activation (27). This view implies that

the holoenzyme represents a single target of transcriptional activation in vivo, and

perhaps repression as well, since an SRB complex purified as part of the holoenzyme

has been shown to act as a co-repressor (reviewed in reference 118). This view also

AcAc

TFs

Mediator

GeneralTranscription

Factors

co-activator complex

co-repressor complex

Pol II

FIG. 2. Regulation of transcription: a model. The basic unit of chromatin, the

nucleosome, is depicted as a flat cylinder of histone octamers wrapped around by

two turns of DNA. DNA-binding transcription factors (TFs) that activate

transcription have been shown to interact with the Mediator proteins, which in turn

associate with the general transcription machinery, causing increased levels of

transcription. TFs also interact with co-activators or co-repressors. Some co-

activators have HAT activity, and some co-repressors have HDAC activity

(adapted from reference 89).

8

directly contradicts the ordered-assembly view of the transcriptional initiation

complex formation. Recent evidence supports the idea of a stable holoenzyme

complex; however, it has not been proven that the ordered-assembly view is wrong.

Therefore, the detailed kinetics of transcriptional activation in vivo remains unclear.

Repressors and transcriptional repression. Transcription of eukaryotic genes

is also regulated by repressors, which turn off transcription. The mechanism of

repression is even less well understood than that of activation. Traditionally, it is

thought that repressors employ the following strategies to repress transcription: (1) by

competing with an activator for its binding site in DNA, such as competition of

transcription factor YY1 with serum-response protein for binding to the serum

response element in α-actin gene (28); (2) by physical interactions with the activator,

which result in either masking of the activation domain or dimerization leading to

inactivation of the activator. Examples include interactions between MDM2 and p53

(115) as well as MyoD dimerization with Id proteins (12); (3) by post-translational

modification of the activator, such as acetylation of HMG-1, which renders it unable

to activate IFN-β (reviewed in reference 150); (4) by interfering with the formation of

a functional initiation complex. Examples include the yeast SRB10 protein, which

phosphorylates the C-terminal domain of Pol II prior to initiation and marks the

polymerase incapable of transcriptional initiation (reviewed in reference 118). Recent

understanding of transcriptional repression adds another class of transcriptional

repressors: those involved in modification of chromatin by deacetylation, which

establishes a transcriptionally repressive chromatin environment.

9

Chromatin and transcription. Although it had long been suspected that

chromatin played a role in transcription, it was the proposal more than 25 years ago

that the eukaryotic chromatin is based on repeating units of nucleosomes first laid

down the ground stone for subsequent elucidation of the relationship between

chromatin and transcription (88). Nucleosomes, the basic units of chromatin, are

organized by DNA wrapping around a histone octamer, which composes of two

copies of histone proteins, namely H2A, H2B, H3 and H4 (83, 90, 132). Micrococcal

nuclease digestion reveals that these four histones are closely associated with 146

base pairs of DNA, forming the core particle of nucleosomes (123). A short stretch of

DNA, called linker DNA, connects two nucleosomes. Histone proteins have two

general structural domains: the globular histone fold domain and the flexible N-

terminal tails. The X-ray crystal structure of the core particle suggests that while the

DNA winds around the surface of the histone core, it winds two turns with grooves

aligned, creating a gap where the N-terminal tails of H2B and H3 pass through to the

outside of the core particle. The tails of H2A and H4 also extend from the flat

surfaces of the core particle to the outside (108). These exposed tails are thought to

contact neighboring core particles and can be critical in mediating higher-order

structures of chromatin beyond the nucleosomal level. In vivo and in vitro studies

show that these histone tails also contact DNA (39, 120, 166). However, the high

ionic crystal environment and the lack of linker DNA preclude direct observation of

histone tail-DNA contact (108, 166). Interestingly, nucleosomes have intrinsic

plasticity suggested by the observation that the twist of DNA around histone core is

slightly altered, and the lost of about 1 base per turn is readily accommodated at

10

various locations within the core particle (108). This structural plasticity also

suggests that nucleosomes can be subjected to remodeling.

Nucleosomes have a general inhibitory effect on transcription. In vitro studies

show that transcriptional initiation is stalled by packaging of promoters into

nucleosomes (86, 106). Early genetic studies in yeast also demonstrated that histone

proteins are important in transcriptional repression: When synthesis of normal core

histone H2B or H4 is repressed, promoters of inducible genes become accessible to

the general transcription machinery (52). Deletions of histone H2A/H2B genes (170)

and point mutations in H3 (67) have been identified as suppressor mutations in

switch-independent (SIN) genes, which allow inducible gene transcription in yeast

strains deficient for switch (SWI) genes or sucrose nonfermenting (SNF) genes, two

general activators in yeast (68, 122, 129). Most researchers agree that gene regulation

by modifying chromatin structures occurs in two flavors, chromatin remodeling and

histone acetylation/deacetylation, which are often found in the same protein

complexes.

Chromatin remodeling. Genetic studies suggest that two classes of activator

proteins, SWI and SNF, act to antagonize the negative effects of chromatin on

transcription (reviewed in references 13, 170). Subsequently, a multi-protein complex

containing the SWI/SNF proteins was purified and shown to remodel chromatin (25,

35, 74). Since then, the yeast SWI/SNF complex has become the paradigm of the

ATP-dependent chromatin remodeling complexes, which utilize energy from ATP

hydrolysis to change the chromatin structure and are often required for the full

functioning of a variety of transcription factors (22). To date, two families of ATP-

11

dependent chromatin remodeling complexes have been purified: the SWI/SNF family

and the ISWI family. The SWI/SNF family of chromatin remodeling machines

contains large protein complexes. They destabilize nucleosomes by disrupting the

contacts between DNA and histones, resulting in increased accessibility of

nucleosomal DNA to DNase I, restriction enzymes, or DNA-binding transcription

factors (35, 74, 105). In contrast, the ISWI family of chromatin remodeling machines

contains smaller protein complexes, which uses ISWI (imitation SWI) protein as the

ATPase (76, 159, 162). ISWI chromatin remodeling complexes enable sliding of

histone octamers to adjacent positions on the same strand of DNA (33, 58, 94).

Purification of these ATP-dependent chromatin remodeling complexes suggest that

the nucleosome is a dynamic structure subject to intricate modulations, and that

transcription and chromatin structure are tightly linked in vivo.

Histone acetyltransferases as co-activators. Several lysine residues in the

core histones can be acetylated at the ε-amino positions. This kind of histone

modification has been associated with various biological processes, one of them

transcriptional control (4, 65, 140, 163). It has been postulated that charge

neutralization caused by lysine acetylation reduces the affinity of histone tails to DNA

and increases the accessibility of regulatory elements to transcription factors (69).

Some researchers believe that lysine acetylation does not influence the strength of

interaction between histone tails and DNA but rather opens up the higher-order

structure of the chromatin by disrupting the interaction between histone tails

protruding from nucleosomes within the chromatin fiber (89). Nevertheless, there is a

positive correlation between the extent of histone acetylation and gene activity. For

12

example, the transcriptional inactive heterochromatin is associated with

hypoacetylated histones (65, 163).

The enzymes catalyzing the addition of acetyl groups to histones are histone

acetyltransferases (HATs). The first definitive link between transcriptional activation

and histone acetylation came with the identification that the yeast Gcn5 protein,

which is a transcriptional co-activator of many genes, is a HAT (19). Most

significantly, the HAT activity of Gcn5 is required for its transcriptional activation

activity (91), and there is a general increase in histone H3 acetylation in the promoter

of a Gcn5-regulated gene upon induction (21). Since then, many transcription factors

have been identified as HATs, including the TAFII250 subunit of TFIID (114),

p300/CBP (8, 124), PCAF (173), and SRC-1 (148). p300/CBP and SRC-1 family

members were first identified as transcriptional co-activators. They do not bind

specific DNA elements but potentiate transcriptional activation when associated with

an activator. An attractive model has emerged in which sequence-specific

transcriptional activators activate transcription by associating with HATs (Figure 2).

However, there is no direct evidence demonstrating that histone acetylation per se

activates transcription. Recently many transcription factors have been shown to be

acetylated, including p53 (54) as well as the basal transcription factors TFIIE and

TFIIF (75). It is possible that acetylation of transcription factors contributes to

transcriptional activation (or repression), in addition to acetylation of the core

histones. Recent studies, both biochemical and genetic, also suggest that core histone

acetylation and chromatin remodeling act in concert to activate transcription (34,

13

101). However, the temporal sequence of these two biological activities is still under

intense debate.

Histone deacetylases as co-repressors. Similar to the discovery that many

transcriptional co-activators are HATs, many transcriptional co-repressors are found

to possess histone deacetylase (HDAC) activity (171) (Figure 2). HDACs identified

to date are classified into families. The Class I Rpd3 family of HDACs, including

HDAC1, HDAC2, and HDAC3, has been shown to be important in transcriptional

repression (153, 171, 172). These HDACs are found in multi-protein complexes,

including many co-repressor complexes (reviewed in reference 36). Moreover, they

also associate with DNA-binding repressor proteins such as YY1 (171), Mad (93),

Ume6 (81), and nuclear hormone receptor co-repressors (3, 66, 121). Although

association with HDAC complexes may not account for all cellular repression

activities, more and more repressors appear to utilize this mode of transcriptional

repression. It will be extremely informative to test whether HDACs as co-repressors

only act in a gene-specific manner, or they also participate in epigenetic control of

gene repression.

YY1 is a transcriptional regulator. Transcription factor YY1 (Yin Yang 1)

represents a valuable system to study various aspects of eukaryotic transcriptional

control. YY1 was first discovered in a biochemical assay analyzing the activity of

the P5 promoter of the adeno-associated virus (AAV) (144). AAV is a defective

parvovirus; it cannot replicate without co-infection of adenovirus. The P5 promoter

of AAV is silent in the absence of adenovirus co-infection. In the presence of the

adenoviral E1A protein, which is normally introduced as a result of adenovirus

14

infection, the P5 promoter is activated and the lytic cycle of AAV begins. Using this

P5 promoter element, a cellular protein was discovered as the target of E1A-directed

promoter activation. This protein was named Yin Yang 1 for its dual transcriptional

activity: in the absence of E1A, it represses transcription from P5. In the presence of

E1A, YY1 activates transcription from P5. Yin and Yang represent the repression

and activation properties of YY1.

Independent of the analysis of the AAV P5 promoter, other experimental

systems also discovered YY1 as a transcriptional regulator. δ, the mouse homolog of

YY1, was identified as an activator of certain ribosomal protein genes (61). YY1,

also identified as NF-E1, represses transcription by binding to the immunoglobulin κ

3’enhanber (126). YY1 was also known as UCRBP, which binds to the upstream

conserved regions of the Moloney murine leukemia virus (MuLV) and represses

MuLV promoter activity (41). Since then, YY1 has been shown to be instrumental in

the regulation of many cellular and viral gene promoters, many of which have

important functions in cell growth and differentiation (reviewed in reference 143).

General characteristics of YY1. YY1 binds a specific DNA sequence

(CGCCATNTT) in the promoters by 4 C2H2 zinc fingers, which are located at the C-

terminus of the protein (reviewed in references 143, 154). Deletional and domain-

swapping experiments (5, 23, 24, 97, 99, 100, 144, 171) show that the C-terminal zinc

finger region of YY1 accounts for one of the two repression domains of YY1. The

other repression domain resides in the middle glycine/alanine-rich segment of YY1.

The N-terminal region of YY1 is identified as the activation domain of YY1,

suggesting that YY1 possesses transcriptional activation activity independent of its

15

repression activity. The human YY1 protein contains 414 amino acid residues with a

predicted molecular weight of 44 kDa. However, YY1 has an apparent size of about

65 kDa on SDS-polyacrylamide gels, suggesting that YY1 might have a unusual

structure. The amino acid sequence of YY1 is highly conserved among human,

mouse, and Xenopus, and a Drosophila homologue of YY1 has also been discovered

(144, 18, 41, 61, 126, 130). Knockout studies show that deletion of YY1 results in

peri-implantation lethality in mice (38), further demonstrating the importance of YY1

in fundamental biological processes such as development.

YY1 and transcriptional initiation. In addition to being a transcriptional

regulator, YY1 has also been suggested to be a transcriptional initiator. In vitro

studies show that YY1 binds directly to the initiator (Inr) element of the AAV P5

promoter (144), and YY1 binding to this Inr element is necessary for transcriptional

initiation (142). In a reconstituted transcription assay, purified YY1, TBP, and Pol II

are sufficient to initiate transcription from a supercoiled template (160). Crystal

structure studies of the zinc finger domain of YY1 bound to the Inr element of P5

suggest intrinsic directionality of YY1-mediated transcriptional initiation: YY1 binds

both the template strand and the non-template strand of DNA upstream of the Inr

element but only the template strand downstream of Inr, providing structural basis for

the correct direction of transcription (70).

In addition to the AAV P5 promoter, YY1 binds to the Inr elements of many

gene promoters, including the cytochrome oxidase Vb subunit promoter (10), DNA

polymerase β promoter (64), PCNA promoter (92), and the mouse Surf-1 promoter

(42, 43). However, the mechanistic basis for the initiator activity of YY1 is still

16

unclear. It has been shown that YY1 physically interact with TFIIB and Pol II both in

vitro and in vivo (30, 161). YY1 also interacts with TBP and TAFII55 (5).

Sedimentation studies further confirm that YY1 co-purifies with components of the

general transcription machinery (109, 139). These lines of evidence suggest that

YY1, when bound to the Inr element, recruits Pol II to the transcriptional initiation

site, and this may account for the initiator activity of YY1.

17

OBJECTIVES

As we began to appreciate the unique properties of YY1, it became apparent

that we knew very little about how the activity of YY1 is regulated. For example,

when does YY1 function as a transcriptional activator and when as a repressor? How

does the role of YY1 as a transcriptional initiator reconcile with that as a

transcriptional regulator? Understanding how the activity of YY1 is regulated will

help us answer those questions and tremendously enhance our knowledge about the

basic mechanisms of transcription. Therefore, it is important that we understand how

the activity of YY1 is regulated.

It has been shown that YY1 is a stable phosphorylated protein expressed

ubiquitously regardless of cell cycle position or the differentiation status of the cell

(5). However, several lines of evidence also suggest that YY1 is regulated. For

example, expression of YY1 mRNA in NIH3T3 cells is affected by cell density and

growth factors such as insulin-like growth factor (IGF)-1 (40). The activity of YY1

also changes during myoblast differentiation and during aging (1, 98). Furthermore,

the DNA-binding activity of YY1 decreases during differentiation in human

teratocarcinoma cells (104).

A wide variety of transcription factors have been shown to associate with

YY1, suggesting that the activity of YY1 could be controlled by protein-protein

interactions. These YY1-interacting proteins include proteins of the basal

transcription machinery, such as TBP (5), TFIIB (160); sequence-specific DNA-

18

binding transcriptional activators, such as Sp1 (96, 141), c-Myc (145), ATF/CREB

(178), C/EBP (11); and various transcriptional co-regulators, such as E1A (100),

TAFII55 (30), p300/CBP (5, 95), and HDAC1, HDAC2, and HDAC3 (171, 172).

The YY1-p300/CBP and YY1-HDACs interactions are of particular interest. In

certain circumstances, the transcriptional activation activity of YY1 directly depends

on its association with p300/CBP (95). In contrast, it has been shown that the

transcriptional repression activity of YY1 is mediated by association of HDAC2 with

residues 170-200 of YY1, which corresponds to one of the repression domains of

YY1 (171). It is conceivable that by selectively associating with either HATs or

HDACs, YY1 becomes an activator or a repressor. However, it has not been shown

definitively that such an active selection system exists for YY1. Recently p300, CBP,

and another HAT, PCAF (p300/CBP associated factor), have been shown to acetylate

transcription factors in addition to their histone substrates (reviewed in reference 150).

Importantly, acetylation was a key regulatory mechanism for the regulation of those

transcription factors. Because YY1 interacts with both p300/CBP and HDACs, it is

possible that the activity of YY1 is regulated by acetylation and deacetylation.

Association between YY1 and p300/CBP or HDACs also suggests that YY1

might interact with cellular proteins to form protein complexes. It has been

discovered that many chromatin-modifying activities, including chromatin-

remodeling and histone acetylation/deacetylation, exist in forms of multi-subunit

protein complexes. For example, the yeast Gcn5 co-activator, which possesses HAT

activity, exists in two protein complexes: SAGA (Spt-Ada-Gcn5 acetyltransferase)

and ADA (48). HDAC1 and HDAC2 also exist in two major histone deacetylase

19

complexes: NuRD and SIN3 (reviewed in reference 2). The formation and

recruitment of these protein complexes have important influence on the biological

activities of the constituent proteins. It is possible that YY1 is also regulated in the

context of a protein complex in vivo.

Taken these lines of evidence together, this dissertation study was initiated to

test the hypothesis that the activity of YY1 is regulated by multiple mechanisms. Three

aims have been proposed:

Aim 1 is focused on regulation of YY1 at the genomic level, which includes

cloning and analysis of the human YY1 promoter.

Aim 2 is devoted to regulation of YY1 at the polypeptide level, which is

regulation of YY1 by acetylation and deacetylation.

Aim 3 is intended to study YY1 in a context of protein complexes, which

involves purification of a YY1 protein complex.

20

MATERIALS AND METHODS

Isolation of YY1 genomic clones. A human liver genomic library (ATCC

37333) in Charon 4A was screened with a 32P-labeled human YY1 cDNA fragment

(nt 1-315) using a standard protocol (136). λ phage DNA was purified from two

positive clones, digested with restriction enzymes, and analyzed by Southern blotting

(136). A 4.5 kb EcoRI fragment was subcloned into a pGEM7zf(+) vector (Promega)

for subsequent analyses.

Plasmids. An EcoRI/NcoI fragment was isolated from the 4.5 kb human YY1

λ clone described above, treated with Klenow to blunt ends, and ligated into pGL2-

Basic vector to create p-3600Luc. pGL2-Basic (Promega) contains a firefly luciferase

gene as a reporter and lacks eukaryotic promoter and enhancer sequences. p-3600Luc

was subsequently digested with NsiI/StuI and subjected to exonuclease III digestion to

create 5’ progressive deletions of the YY1 promoter linked to the luciferase reporter

gene. pRL-TK (Promega) was used as a control for normalization in co-transfection

experiments. pRL-TK contains a Renilla luciferase genes under control of the herpes

simplex virus thymidine kinase promoter.

Glutathione S-transferase was expressed from pGSTag (133). GST-YY1 (1-

414) was expressed from pGST-YY1 (171), and deletion constructs of GST-YY1

were generated by restriction enzyme digestion and re-ligations of pGST-YY1. GST-

p53 expression plasmid has been described (72). GST-p300 and GST-PCAF were

21

expressed from plasmids pGEX2T-p300 (aa 1195 to 1810) and pGEX5X-PCAF (aa

352 to 832), respectively (26).

Gal4-YY1 was expressed from pM1-YY1, which was constructed by inserting

the full-length YY1 cDNA in-frame with the Gal4 DNA-binding domain in pM1

(134). pM1-YY1 (K170-200R) was prepared using adapter oligonucleotides

containing AAG (lysine) to AGG (arginine) mutations within YY1 aa 170 to 200 of

pM1-YY1. pG5CAT-Control was constructed by inserting five Gal4 DNA-binding

sites into the BglII site of pCAT-Control (Promega), which contains the

chloramphenicol acetyltransferase (CAT) gene downstream of the SV40 promoter and

enhancer sequences. Flag-YY1 was expressed from pCEP4F-YY1, which was

generated by inserting the full-length YY1 cDNA into the pCEP4F vector (179).

Serial Flag-YY1 deletion constructs were made by restriction enzyme digestion and

re-ligations of pCEP4F-YY1. pET15b-YY1, which expressed non-tagged full-length

YY1 in E. coli in an inducible system, was constructed by cloning the full-length YY1

cDNA into pET15b (Novagen). pGEM7Zf3X-HD1, which was used to generate in

vitro translated HDAC1, was made by subcloning full length HDAC1 into the

pGEM7Zf3X vector.

Plasmids pCMV12S, pCMV13S, and pCMV-YY1 have been described

previously (7, 171). pCMV12S directs expression of the E1A 243R protein, and

pCMV13S expresses the E1A 289R protein. The following plasmids have also been

previously described: pBJ5-HD1F (153), which expresses HDAC1 C-terminally

tagged with a Flag epitope; pBJ5.1-HD1F (H199F) HDAC1 point mutant (63);

pME18S-FLAG-HDAC2, which expresses Flag-tagged HDAC2 (93).

22

Sequencing of the human YY1 promoter. The dideoxy chain-termination

sequencing method was employed to obtain the complete sequence of one strand of

the human YY1 promoter using p-3600Luc and its deletion derivatives as templates

and GLprimer 1 (Promega) as primer. Custom-designed oligodeoxynuclotide primers

and GLprimer 2 (Promega) were used to obtain the sequence of the complementary

strand.

Primer extension. Primer extension was performed essentially as described

previously with minor modifications (136). An antisense oligonucleotide

corresponding to the human YY1 promoter sequence from position +76 to +100 was

synthesized and end-labeled with [γ-32P]ATP and T4 polynucleotide kinase. HeLa

total RNA was isolated using the acid phenol-guanidinium thiocyanate method (31).

10 µg of the HeLa total RNA or yeast total RNA was mixed with 105 cpm of the

labeled oligonucleotide primer and the mixture was ethanol-precipitated. The DNA-

RNA mixture was then re-dissolved in 30 µl of hybridization buffer [40 mM PIPES

(pH 6.4), 1 mM EDTA (pH 8.0), 0.4 M NaCl and 80% formamide], denatured at 85oC

for 10 min, and annealed at 30oC overnight. The annealed hybridization mixture was

then ethanol-precipitated, washed, and re-dissolved in 20 µl of reverse transcriptase

buffer [50 mM Tris-HCl (pH 7.6), 60 mM KCl, 10 mM MgCl2, 1 mM each of dATP,

dCTP, dGTP and dTTP, 1 mM dithiothreitol (DTT), 1 U/µl RNase inhibitor and 50

µg/ml actinomycin D]. 50 U of avian myeloblastosis (AMV) reverse transcriptase

was then added, and the reactions were incubated at 37oC for 2 h. At the end of

incubation, the reactions were stopped with EDTA, treated with DNase-free RNase,

and phenol-chloroform extracted. Single-stranded DNA was recovered by ethanol

23

precipitation, washed, and dissolved in 4 µl of TE (pH 7.4). Samples were added with

6 µl of formamide loading buffer [80% formamide, 10 mM EDTA (pH 8.0), 1 mg/ml

xylene cyanol and 1 mg/ml bromophenol blue], heated at 95oC for 5 min, and

resolved on a 6% polyacrylamide/7 M urea gel. The gel was then dried and images

were obtained by autoradiography.

Cell line, transfection, luciferase assays, and CAT assays. HeLa cells were

maintained in Dulbecco’s modified Eagle’s media supplemented with 10% fetal

bovine serum and 100 mg/ml penicillin and streptomycin. For each transfection

reaction, 3x105 cells were seeded into a 60-mm tissue culture dish. Sixteen h later,

10 µg plasmids were transfected using the calcium phosphate co-precipitation method

(47). Forty-eight h after transfection, cells were harvested. For luciferase assays,

luciferase activity was determined using the Dual Luciferase Reporter Assay system

(Promega). For CAT assays, cells were harvested by scraping and lysed by repeated

freezing/thawing, and extracts were assayed for CAT activity by thin-layer

chromatography (46).

Recombinant proteins. The GST fusion constructs of p300, PCAF, p53, and

YY1 deletion mutants were expressed in E. coli DH5α, bound to glutathione-agarose

beads (Sigma), washed extensively in phosphate-buffered saline (PBS), and eluted

with 25 mM reduced glutathione. The eluate was then dialyzed against a buffer

containing 20 mM Tris-HCl (pH 8), 0.5 mM EDTA, 100 mM KCl, 20% glycerol, 0.5

mM dithiothreitol (DTT), and 1 mM phenylmethylsulfonyl fluoride (PMSF).

Non-tagged YY1 was expressed in E. coli BL21 (DE3), induced with 0.2 mM

IPTG, and captured by Ni2+ resin (ProBond, Invitrogen). Unbound bacterial proteins

24

were removed with 50 mM imidazole, and bound YY1 was eluted with 500 mM

imidazole. Flag-tagged YY1 used in electrophoretic mobility shift assays (EMSA)

was purified on an anti-Flag column (Sigma) under stringent conditions following the

manufacturer’s suggestions.

In vitro acetylation reactions. Purified GST-YY1 and serial deletion proteins

were incubated at 30oC for 30 min with 0.25 µCi [3H]acetyl coenzyme A (CoA)

(Amersham) and purified GST-p300 (0.2 µg) or GST-PCAF (1 µg) in 30 µl of

acetylation buffer containing 50 mM Tris-HCl (pH 8.0), 5% glycerol, 0.1 mM EDTA,

50 mM KCl, 1 mM DTT, 1 mM PMSF, and 10 mM sodium butyrate. Proteins were

resolved by SDS-polyacrylamide gel electrophoresis (SDS-PAGE). SDS-

polyacrylamide gels were fixed by Coomassie blue staining and subjected to signal

amplification (Amplify, Amersham) prior to exposing to X-ray film.

For subsequent mass spec analyses, 0.5 pmol of the YY1 peptide

(GRVKKGGGKKSGKKSYLSGGAGAAGGRGADP) was acetylated in acetylation

buffer for 2 hr with CAT-assay grade acetyl CoA (Amersham).

Immunoprecipitation and western blot analysis. Immunoprecipitation of

endogenous YY1 from HeLa cell extract was performed with H-10 anti-YY1 mAb

(Santa Cruz) and GammaBind protein G Sepharose (Amersham). Endogenous Max

and 14-3-3 were immunoprecipitated using anti-Max mAb (Pharmingen) and anti-14-

3-3 H-8 mAb (Santa Cruz), respectively. Immunoprecipitation of Flag-YY1 deletion

proteins was done using anti-Flag M2 affinity gel (Sigma) following the

manufacturer’s suggestions.

25

Western blot analyses were performed using standard protocols (62).

Immunoprecipitated proteins were detected with diluted primary antibodies [1:1000

of anti-acetyl lysine (Upstate), 1:5000 of H-10, 1:500 of anti-Max, 1:1000 of H-8,

1:5000 of anti-Flag M2 (Sigma), 1:1000 of anti-HDAC1, HDAC2, or HDAC3 rabbit

anti-serum (93, 158, 168)] followed by 1:7500 diluted alkaline phosphatase-

conjugated secondary antibodies (Promega). The blots were subsequently developed

with 5-bromo-4-chloro-3-indolyl phosphate and nitro blue tetrazolium (Promega).

In vitro protein-protein interaction assays. 35S-labeled HDAC1 was

generated from pGEM7Zf3X-HD1 using T7 RNA polymerase and the TNT

Reticulocyte Lysate System (Promega). GST-YY1 (170-200) was either acetylated

with cold acetyl CoA or mock acetylated and was then captured onto glutathione-

agarose beads. 5 µl of in vitro translated HDAC1 was mixed with the beads in the

presence of PBS plus 0.2% NP-40 at room temperature for 1 h. Beads were washed

extensively in PBS plus 0.2% NP-40. Bound proteins were eluted by boiling in

Laemmli sample buffer, separated by SDS-PAGE, and detected by Coomassie blue

staining and autoradiography.

Histone deacetylation assays. HeLa cells were transfected with 10 µg of

pCEP4F-YY1 deletion plasmids by the calcium phosphate co-precipitation method

(47). Forty-eight h after transfection, cells were harvested, lysed in PBS plus 0.1%

NP-40, and immunoprecipitated with anti-FLAG M2 affinity gel (Sigma). Histone

deacetylase activities of the immunoprecipitated Flag-YY1 were determined using a

peptide corresponding to residues 2 to 24 of histone H4 as described (153) except that

incubation was performed at room temperature overnight. 400 nM (final

26

concentration) of TSA (Sigma) or a 5 column-volume (cv) of Flag peptide (Sigma)

was added to the immunoprecipitate 30 min prior to addition of the H4 substrate

peptide, if appropriate. Histone deacetylation assays on chromatographic fractions

were performed using the same H4 peptide as substrate.

Immunofluorescence analysis. HeLa cells were grown on chamber slides

(Nalge Nunc International) for about twenty-four h and transfected with 10 µg of F-

YY1 deletion constructs. Two days later, cells were washed with ice-cold PBS, fixed

with 4% paraformaldehyde for 10 min, rinsed again with PBS, covered with 400 µl of

1% bovine serum albumin (BSA) in PBS for 1 h at room temperature, washed again

in PBS, and then treated with 1:200 dilution of anti-Flag FITC conjugate antibody

(Upstate) for 1 h at room temperature. Subsequently, cells were subjected to

extensive washing with PBS and cover slips were applied with one drop of anti-fade

mounting medium with DAPI (Vector) before analysis under a fluorescence

microscope.

Electrophoretic mobility shift assays. Single-stranded

oligodeoxynucleotides corresponding to a consensus YY1-binding site (142) or a p53

cognate sequence (54) were labeled individually with [γ32P]ATP and T4

polynucleotide kinase, heated together at 65oC, and allowed to anneal by slow cooling

to room temperature. Binding reactions were performed in a 12 µl reaction volume

containing 12 mM Hepes (pH 7.9), 10% glycerol, 5 mM MgCl2, 60 mM KCl, 1 mM

DTT, 0.5 mM EDTA, 50 mg/ml BSA, 0.05% NP-40, 0.1 mg poly(dI-dC),

approximately 1 ng of purified proteins or 5 µl of chromatographic fractions, and 5

fmol radiolabeled DNA. Reactions were incubated for 10 min at room temperature

27

and separated on 4% non-denaturing polyacrylamide gels. The gels were then dried

and exposed to film.

Gel filtration analysis of YY1. HeLa nuclear extract was prepared according

to the Dignam method and dialyzed into TM buffer [50 mM Tris-HCl (pH 7.9), 122.5

mM MgCl2, 1 mM EDTA, 10% glycerol, 1 mM DTT, 0.1 mM PMSF] plus 0.1 M

KCl. 2.5 mg of dialyzed HeLa nuclear extract was applied to a calibrated Superdex

200 HR 10/30 column (Pharmacia) and fractions were collected.

Purification of a YY1 complex by anion exchange and immobilized-metal

affinity chromatography (IMAC). Nuclear extract derived from 6 L of HeLa cells

was loaded on a Q Sepharose column (Pharmacia). Bound proteins were eluted in

buffer A [20 mM Hepes (pH 7.8), 5 mM MgCl2, 20% glycerol, 0.5 mM DTT, 0.2 mM

EDTA, 0.1 mM PMSF] with a linear gradient (5 cv) of KCl from 150 mM to 1 M.

The presence of YY1 was monitored with western blotting and EMSA. Fractions

containing YY1 were pooled, dialyzed into PBS (pH 7.4) containing 10% glycerol, 5

mM β-mercaptoethanol, and 1 mM PMSF, and loaded on a column with 1 mL bed

volume of Ni2+ resin (ProBond, Invitrogen). The column was washed extensively

with wash buffer [PBS (pH 7.4), 50 mM imidazole, 10% glycerol, 5 mM β-

mercaptoethanol, and 1 mM PMSF]. Bound YY1 complex was eluted with elution

buffer [PBS (pH 7.4), 10% glycerol, 5 mM β-mercaptoethanol, and 1 mM PMSF]

containing 300 mM imidazole.

Coomassie staining and silver staining. Detection of YY1 protein

complexes with Coomassie staining and silver staining was performed using standard

protocols (6).

28

Purification of a YY1 complex by anion exchange and antibody-affinity

chromatography. Nuclear extract derived from 6 L of HeLa cells was loaded on a Q

Sepharose column (Pharmacia). Bound proteins were eluted in buffer A [20 mM

HEPES (pH 7.8), 5 mM MgCl2, 20% glycerol, 0.5 mM DTT, 0.2 mM EDTA, 0.1 mM

PMSF] with a linear gradient (5 cv) of KCl from 150 mM to 1 M. The presence of

YY1 was monitored with western blotting and EMSA. Fractions containing YY1

were pooled, dialyzed into PBS (pH 7.4) containing 10% glycerol and 1 mM PMSF,

and loaded on a protein G column (GammaBind, Amersham). The flowthrough

fraction was collected and loaded onto an antibody column made by coupling H-10

anti-YY1 mAb (Santa Cruz) to protein G beads. The antibody column was then

washed extensively with PBS (pH 7.4) containing 10% glycerol, 100 mM KCl, and 1

mM PMSF. Bound proteins were either used directly in histone deacetylation assays

or eluted with 100 mM glycine (pH 2.5).

Purification of a Flag-tagged YY1 complex. 1.5x109 HeLa cells were

transiently transfected with plasmid pCEP4F-YY1 using the calcium phosphate co-

precipitation method (19). Cells were harvested, pooled, and lysed by sonication in

PBS (pH 7.4) plus 1 mM PMSF. Cell lysate was applied to an anti-Flag M2 column

(Sigma) and the adsorbed protein complex was washed extensively with PBS (pH 7.4)

containing 10% glycerol and 1 mM PMSF. Bound proteins were eluted with excess

Flag peptide (100 µg/ml) in 5 cv of PBS (pH 7.4) containing 10% glycerol and 1 mM

PMSF.

Radioimmunoprecipitation analysis (RIPA) of F-YY1. HeLa cells were

transiently transfected with full-length F-YY1 (pCEP4F-YY1) and its serial deletion

29

plasmids using the calcium phosphate co-precipitation method (47). Sixteen h later,

cells were labeled with [35S]methionine and cysteine (11.0 mCi/ml, NEN) for four h.

Labeled cells were harvested and lysed by sonication in PBS (pH 7.4) containing

0.1% NP-40 and 1 mM PMSF. Anti-Flag M2 agarose beads (Sigma) were added to

the cell lysates and washed extensively with PBS (pH 7.4) containing 0.1% NP-40

and 1 mM PMSF. The beads were boiled in Laemmli sample buffer and proteins

were separated by SDS-PAGE. Gels were then dried and exposed X-ray film.

Accession number. The nucleotide sequence data of the human YY1

promoter reported in this dissertation appears in GenBank, EMBL, and DDBJ

Nucleotide Sequence Databases under the accession number AF047455.

30

RESULTS

Determination of the transcriptional start site of the human YY1 gene.

To determine the transcriptional initiation site of the YY1 gene, primer extension was

performed using primers spanning the putative transcriptional start site and total HeLa

RNA. Identical reactions using yeast tRNA were performed side by side as negative

controls. One primer consistently yielded a strong signal indicating one strong

transcriptional start site. Alignment with a dideoxynucleotide sequence ladder from

FIG. 3. Determination of the 5’ end

of the human YY1 transcript.

Purified total RNA from HeLa cells

(lane 5) or tRNA from yeast (lane 6)

were used as templates in primer

extension analysis using a 25 bp 32P-

labeled antisense oligonucleotide

probe and AMV reverse transcriptase.

A sequencing ladder of the YY1

promoter was created in parallel and

is shown on the left with radiolabeled

nucleotides (lanes 1-4). The arrow

indicates the most likely start site of

transcription.

.

GATC HeLa t

otal R

NA

yeas

t tRNA

1 2 3 4 5 6

GAATCGAGAGGGCGAACGGGC

5'

3'

+1

31

the same primer showed that the strong signal corresponds to a G within a GC-rich

region of the YY1 promoter (Fig. 3) However, due to the cap structure of the mRNA,

the true transcription initiation site might be the A immediately preceding this G.

Transcriptional analysis of the human YY1 promoter. A 3.6 kb

EcoRI/NcoI fragment of the genomic clone containing sequences upstream of the

ATG codon in the YY1 cDNA was subcloned into pGL2-Basic and the resulting

plasmid was named p-3600Luc. The pGL2-Basic vector contains a firefly luciferase

gene but no eukaryotic promoter or enhancer sequences.

When transiently transfected into HeLa cells, p-3600Luc resulted in a 180-fold

increase in luciferase activity compared to pGL2-Basic alone (Fig. 4). To determine

the 5’ boundary of the YY1 promoter, serial deletion constructs of p-3600Luc were

generated and assayed for luciferase activities in HeLa cells after transient

transfection. As shown in Figure 4, deletion constructs p-2100Luc, p-1729Luc, p-

1514Luc, p-1248Luc, p-1110Luc, p-917Luc, p-478Luc, and p-277Luc exhibited

similar levels of luciferase activities to p-3600Luc. Deletion of the promoter to +54

drastically reduced the luciferase activity, suggesting the presence of a positive cis-

acting element between positions -277 and +54. However, a significant increase in

luciferase activity was observed between p-1514Luc and p-1248Luc, indicating a

negative cis-acting element was present between nt -1514 and -1248 of the YY1

promoter. Further deletions of the YY1 promoter to position +379 completely

abolished the luciferase activity to the background level (compared to pGL2-Basic).

These results suggest that a minimal sequence of 54 bp located downstream of the

32

transcriptional initiation site of the YY1 gene contains significant levels of the

promoter activity, and this activity is enhanced by the sequence between positions

-277 and +54.

-3600 Luciferase

-2100

-1514

-1248

-1110

-917

-478

+54

+379

0 100 200 300

relative luciferase activity

-1729

+475

-277

≈

≈

p-3600Luc

p-2100Luc

p-1729Luc

p-1514Luc

p-1248Luc

p-1110Luc

p-917Luc

p-478Luc

p-277Luc

p+54Luc

p+379Luc

pGL2-Basic

FIG. 4. Expression of luciferase enzymatic activity driven by the

human YY1 promoter in transiently transfected cells. The left panel

shows schematic drawings of various fragments of the human YY1

gene 5’ sequence subclones upstream of a luciferase reporter gene. A

bent arrow indicates the direction of transcription. Reporter constructs

were transfected into HeLa cells by the calcium phosphate co-

precipitation method, harvested, and assayed for luciferase activity.

All relative luciferase activities, as shown in the right panel, are

normalized with control Renilla luciferase expressions. Data shown

represent the average of three independent experiments with standard

deviations.

33

Sequence analysis of the human YY1 promoter. p-3600Luc and its serial

deletion derivatives were utilized to determine the promoter sequence of the human

YY1 gene. The complete DNA sequence of the human YY1 gene is shown in Figure

5A, which exhibits remarkable similarity to the mouse YY1 promoter (Fig. 5B). The

FIG. 5A. DNA sequences upstream of the translational start codon of

the human YY1 gene. The major transcriptional initiation site (+1) is

indicated by a bent arrow. Transcription factor binding sites are

underlined and indicated below each binding site sequence.

-1717 CCTCATTTCTCTTGCTCTCACAATTGGTGTTTATGGG -1681

-1680 GAAGTATCAACTACTTGCAGTGCCATTTCCCCATCAATTACTAGAGAGTGGGGAAAGTGAAATTTAAAAAGCATTAAGAC -1601

-1600 ATGTAAAAGTTCTCCCACAACTGGTTTCCATTCATGAAATATTTATGCAGAGTTTATAAGCTATAAAGCCAGAGATGACT -1521

-1520 TAATTCAACAGATTTGACTTTTCCAAACTGAGTGGGTGCAGTACTCCAAGGGGAATTATTCAGGTTTCAAAGCTCAGATT -1441

-1440 CAAAGAGAAAACGATCTAATTTGTCACTCCTTACACTAATATTCTCAAAAGTCAAGTCCAATGCGATTTAGCAATAAGAA -1361

-1360 GGGACTAGGATTTATAAAGTTGCCTTTTAATGAGAATGTATAGTCTACTTGTTTTAACAAGTTGAGCCTAAGATTAATGT -1281

-1280 ATTGCGTACAGTTCAGAAAATCATGGGCCTCAACTGCATGAACACTATTACAAAACAGTAAATGTTGATAATATTTAAGT -1201

-1200 TGAACAAATTCACAGAGGCGTTAAATCGGCCAAACGAGTACAACAAAGACACACCTTTCCAACTCTTCAATTTGTCATAG -1121

-1120 TTTCCTTAAAAATCAGGAAATCTTTGTTTTGCTTTAAGGCAAATTGTCAGGTCGACCAAAAGGACAGATAAGAGCAGAAA -1041

-1040 CACTTCGCTGCAATGTAACTCATTCAGGAAGGTTTAACTTGCCGCTAATCCGTGCCACAAAAAAAAATCTAGGCTCTGTT -961

-960 GCAGGTACAATGGAGGACACGGCTGAAAAAATTTGGAATTTTAAATGAGACAAATGCAAAACC TGGTGGGCGTAAAAAGG -881

-880 AGCACCTATGAAAGTGACAAATAGGGGGAAAGGGTGGGCAAGGGAAACAATGGCTGACTGGAG AGCAAAGAAGGGGAAGC -801

-800 TCAGGAGAAAATTTTAGAAAGCCGCCAGGACCCTGTAGTTCTAAGATCTACGGGGAAACAGGC ACCCAACGGCTGCGTCT -721

-720 CAGGTTTCCGCGGGTCACTAAAGAATAACGGACATCCTCCCAACGGTGGCCCTGGGGCTCCGC GGGCGCTTCCGCCGAGC -641

-640 TCGCGCCGACCCCGCGCTCGGCCCCGCACCCCGCCGGGCGCTCGCGGCGAGATACCGGACGCT GCCCGCGTCGCCCGATT -561

-560 TTGTCCGTTCGGTCCTCCACACTCACCCCGCGGCCATCGCTCGCCCGAAGCCAGGCGACAAGA ACAAACACCTCCCGACG -481

-480 CGAAAAAGGAAGCACAGGCGATTCTCGTCAAAGCAGACTTTATTGGGGCGACAGGGCCGCCCC GCACGCGCCAGCCGCTC -401

-400 CCCGCGCCGCCGGGCCGCCCACCCGCCTCAACCCCGCTCCCGGCCGGCCCCTCCCTCCCTTCT CCTCAGCTCCCGCCCCC -321

-320 GTGGTGCCCGGGGCCGCGCGGACCGCTCACCGGCTCCCAAGGCAGCGGCTGTAGCGGCGACGC CCGTTCCCGAGTGCGGC -241

-240 CCCGGCCCGAGGCGGCGGGTTTTGTGGCTGTGGCACCGCGAAGGGCGGCACGGCGCGACACCG GGAAGCGGGAGGCGGTG -161

-160 GCGGCGGCGGCGGCGCGCTGACGTCACGCGCCGGGCCAGCCAGGGCGCGTGCGAGCCGCCCCGCCCCCGGTCCCATCGGC -81

-80 CCCAATCCGGGAGGAGCCCGGCGAGTGGGCGGGGCCGCGGAGGCCAGCGGACAGATCGATTGGCCGAGAGGAGAATCGAG -1

1 AGGGCGAACGGGCGAGTGGCAGCGAGGCGGGGCGGGCTGAGGCCAGCGCGGAAGTCTCGCGAGGCCGGGCCCGAGCAGAG 80

81 TGTGGCGGCGGCGGCGAGATCTGGGCTCGGGTTGAGGAGTTGGTATTTGTGTGGAAGGAGGCGGAGGCGCAGGAGGAGGA 160

161 AGGGGGAAGCGGAGCGCGGCCCGGACGGGAGGAGGCGCGGCCAGGGCGGGCGGTTGCGGCGAGGCGAGGCGAGGCGGGGA 240

241 GCCGAGACGAGCAGCGGCCGAGCGAGCGCGGGCGCGGGCGCACCGAGGCGAGGGAGGCGGGAAGCCCCGCGCCGCCGCGG 320

321 CGCCCGCCCCTTCCCCCGCCGCCCGCCCCCTCTCCCCCCGCCCGCTCGCCGCCTTCCTCCCTCTGCCTTCCTTCCCCACG 400

401 GCCGGCCGCCTCCTCGCCCGCCCGCCCGCAGCCGAGGAGCCGAGGCCGCCGCGGCCGTGGCGGCGGAGCCCTCAGCATG 476

MZF1

Nkx-2

v-myb/c-myb

v-myb

CREB/ATF

Sp1

Sp1

Sp1

CDP/Cut

34

human YY1 promoter possesses a region rich in GC nucleotides (80% GC from -427

to +96) and lacks a TATA box, which is typical of the 5’ untranslated regions of

many transcription factors. Multiple GC boxes are located at positions -57, +29 and

+231, which are binding sites for the Sp1 family transcription factors (80). In

addition to the GC boxes, the human YY1 promoter also contains putative binding

sites for several ubiquitous and lineage-specific transcription factors. A binding site

for CDP/CUT, which functions as a transcriptional repressor (60), is found just 20 bp

upstream from the transcriptional start site. Further upstream is a binding site for

10 20 30 40 50 60hYY1 - AGGCACCCAACGGCTGCGTCTCAGGTTTCCGCGGGTCACTAAAGAATAACGGACATCCTC ::::::::::: : : : ::: ::::::::::::::: ::::::::::::::: ::mYY1 - AGGCACCCAACCGGCGGGGCTCCGGTTTCCGCGGGTCATAAAAGAATAACGGACACACTT 10 20 30 40 50 60

70 80 90 100 110hYY1 - CCAACGGTGGCCCTGGGGCTCCGCGGGC-GCTTCCGCCGAGCTCGCGCCGACCCCGCGCT ::::::::: :: :::: :::: :: :::::::: : :: :::: :mYY1 - CCAACGGTGAACCCTAGGCTGCGCGCGCCGCTTCCGC-----TTGC--------CGCGGT 70 80 90 100

120 130 140 150 160 170hYY1 - CGGCCCCGCACCCCGCCGGGCGCTCGCGGCGAGATACCGGACGCTGCCCGCGTCGCCCGA :: : :: :::::: :: :::: : : : : ::::: : :: :mYY1 - CGCCTTCGGCGCCCGCCACCGGCACGCGACCAAAGA---------GCCCGTGGAGCACA- 110 120 130 140 150

180 190 200 210 220 230hYY1 - TTTTGTCCGTTCGGTCCTCCACACTCACCCCGCGGCCATCGCTCG---CCCGAAGCCAGG ::::: : :: ::: : : :: : ::: :: ::: :: : :mYY1 - -----------CGGTCGGCTACGCTC---CGTCCGCTACCGCACGAGACCCCGAGTAACG 160 170 180 190 200

240 250 260 270 280 290hYY1 - CGACAAGAACAAACACCTCCCGACGCGAAAAAGGAAGCACAGGCGATTCTCGTCAAAGCA : ::: :::: : :: : ::::: ::::::::::: ::::::::: ::::mYY1 - AGTAAAGG-CAAAACGAACGGGAAACCAAAAATCAAGCACAGGCGTTTCTCGTCAGAGCA 210 220 230 240 250 260

300 310 320 330 340 350hYY1 - GACTTTATTGGGGCGACAGGGCCGCCCCGCACGCGCCAGCCGCTCCCCGCGCCGCCGGGC :::::::::: ::: ::::::: :: : : ::: ::::::: :mYY1 - GACTTTATTGCGGC---------------CACGCGC--GCGGTCGCACGCCCCGCCGG-C 270 280 290 300

360 370 380 390 400 410hYY1 - CGCCCACCCGCCTCAACCCCGCTCCCGGCCGGCCCCTCCCTCCCTTCTCCTCAGCTCCCG :: : :: ::: :: : ::: ::: :::::: :: :::::: :mYY1 - AGCACGCCAGCCCCAGGCGCGCGCCC---------------CCCTTCACCCCAGCTC--G 310 320 330 340

420 430 440 450 460 470hYY1 - CCCCCGTGGTGCCCGGGGCCGCGCGGACCGCTCACCGGCTCCCAAGGCAGCGGCTGTAGC ::::: :: ::: :::::::: : :: ::::::::: :::: : : :mYY1 - TTACCGTGC--GCCTGGGTCGCGCGGAAAGTTCGCCGGCTCCCGAGGCGTAAGGCGCACG 350 360 370 380 390 400

480 490 500 510 520 530hYY1 - GGCGACGCCCGT-TCCCGAGTGCGGCCCCGGCCC--GAGGCGGCGGGTTTTGTGGCTGTG : :::::::: ::: : ::: : ::::: ::: : : :::::: ::::mYY1 - GCCGACGCCCCACTCCTGTCAGCGACTGGGGCCCCGGAGACCGGCACTTTTGTCACTGTT 410 420 430 440 450 460

540 550 560 570 580 590hYY1 - GCACCGCGAAGGGCGGCACG--GCGCGACACCGGGAAGCGGGAGGCGGTGGCGGCGGCGG :::::::: : : ::: ::::::: ::: ::: : :: ::: ::::mYY1 - GCACCGCGGACGCCGGGGATTCGCGCGACGCCG---AGC----GCCGTAAGCGACGGC-- 470 480 490 500 510

600 610 620 630 640hYY1 - CGGCGCGCTGACGTCACGCGCCGGG---CCAGCCAGGGCGCGTGCGAGCCGCCCCGCCCC :: ::::::::::::::::::: :::::::: ::::::::: :::::: ::::::mYY1 - --ACGAGCTGACGTCACGCGCCGGGGGGCCAGCCAGCGCGCGTGCG-GCCGCCACGCCCC 520 530 540 550 560 570

650 660 670 680 690 700hYY1 - CGGTCCCATCGG-----CCCCAATCCGGGAGGAGCCCGGC---GAGTGGGCGGGGCCGCG : : ::: ::: :::::::: ::::::: :: :: :::: ::::::::: ::mYY1 - C--TACCAGCGGGGGCCCCCCAATC-GGGAGGACCCTGGTTGGGAGTAGGCGGGGCCCCG 580 590 600 610 620 630

710 720 730 740 750hYY1 - GAGGCCAGCGGACAGAT-CGATTGGCCGAGAGG-AGAATCGAGAGGGCGAACGGGCGAGT : : : : :: : ::::::: : :::: :: : :::::: :::: : :::::mYY1 - GCGCCTCGAGGGGCCCTGCGATTGGTAGCGAGGGAGGAGCGAGAGCCGGAACAG-CGAGT 640 650 660 670 680

760 770 780 790 800 810hYY1 - GGC--AGCGAGG-CGGGGCGGGCTGAGGCCAGCGCGGAAGTCTCGCGAGGCCGGGCCCGA :: : :: :: ::::::::: ::: : ::::::::::::::::::::: ::: ::mYY1 - GGGGAATCGGGGACGGGGCGGGGCGAGAGCCCCGCGGAAGTCTCGCGAGGCCGAGCCGGA 690 700 710 720 730 740

820 830 840 850 860hYY1 - GCAGAGTGTGGCGGCGGCGGCG------AGATCTGGGCTCGGG-TTGAGGAGTTGGTATT :::::::::::::::::::::: ::::::::::::::: ::::::::::::::::mYY1 - GCAGAGTGTGGCGGCGGCGGCGGCGGCGAGATCTGGGCTCGGGGTTGAGGAGTTGGTATT 750 760 770 780 790 800

870 880 890 900 910 920hYY1 - TGTGTGGAAGGAGGCGGAGGCGCAGGAGGAGGAAGGGGGAAGCGGAGCGC-GGCCCGGA- ::::::::::::::::::::::::::::: :::::: :::: : ::: ::::::::mYY1 - TGTGTGGAAGGAGGCGGAGGCGCAGGAGGC---AGGGGGCAGCGTAACGCCGGCCCGGAG 810 820 830 840 850 860

930 940 950 960 970hYY1 - --CGGGAGGAGGCGCGGCCA------GGGCGGGCGGTTGCGGCGAGGCGAGGCGAGGCGG :::::::::::::::::: :::: ::: : : :::::::::: : ::::::mYY1 - GGCGGGAGGAGGCGCGGCCACAGCCAGGGCAGGCAGCCGAGGCGAGGCGAAGGCAGGCGG 870 880 890 900 910 920

980 990 1000 1010 1020 1030hYY1 - GGAGCCGAGACGAGCAGCGGCCGAGCGAGCGCGGG-CGC----GGGCGCACCGAGGCGAG ::: : ::: :::::::::::::::::: : : ::: ::::::::::: : :mYY1 - GGAAGCAGGACAGGCAGCGGCCGAGCGAGCGAGCGACGCAGCGGGGCGCACCGAT-CTCG 930 940 950 960 970 980

1040 1050 1060 1070 1080 1090hYY1 - GGAGGCGGG-AAGCCCCGCGCCGCCGCGGCGCCCGCCCCTTCCCCCGCCGCCCGCCCCCT ::::::::: :::::::: ::::: ::::::::::::::::::::::::::::::::mYY1 - GGAGGCGGGGAAGCCCCG----GCCGCCGCGCCCGCCCCTTCCCCCGCCGCCCGCCCCCT 990 1000 1010 1020 1030 1040

1100 1110 1120 1130 1140 1150hYY1 - CTCCCCCCGCCCGCTCGCCGCCTTCCTCCCTCTGCCTTCCTTCCCCACGGCCGGCCGCCT :::::::::::::: ::: :::::::::::::::::::::::::::::::::::::::::mYY1 - CTCCCCCCGCCCGCCCGCTGCCTTCCTCCCTCTGCCTTCCTTCCCCACGGCCGGCCGCCT 1050 1060 1070 1080 1090 1100

1160 1170 1180 1190hYY1 - CCTCGCCCGCCCGCCC--------GCAGCCGAGGAGCCGAGGCCGCC-------GCGGCC :::::::::::::::: :::::: ::::::::: :::::: ::::::mYY1 - CCTCGCCCGCCCGCCCTCCCTCCCGCAGCCCAGGAGCCGACGCCGCCTGCCGCGGCGGCC 1110 1120 1130 1140 1150 1160

1200 1210hYY1 - GTGGCGGCGGAGCCCTCAGC---- ::::::::::::::::::::mYY1 - GTGGCGGCGGAGCCCTCAGCCATG 1170 1180

FIG. 5B. Comparison of the YY1 promoter DNA sequences between mouse

and human. The human YY1 promoter sequence [hYY1 (-74 to +476)] is

aligned with the mouse YY1 sequence [mYY1 (-751 to +434)] (135).

Identical nucleotide positions are indicated by double dots.

35

CREB/ATF (position -142) (57) as well as three Myb binding sites (51) in tandem

(positions -736 to -673). Far upstream at position -1522, a consensus binding site for

the mouse tinman homeodomain factor Nkx-2 is found. Nkx-2 has been shown to

antagonize the transcriptional repression activity of YY1 in the cardiac α-actin

promoter through competitive binding during myogenesis (28). There is a binding

site for MZF-1, a myeloid zinc finger transcription factor (116), at position -1640

close to the Nkx-2 site. Interestingly, the three Sp1 binding sites (GC boxes), the

CREB/ATF binding site, and the three Myb binding sties are conserved between the

mouse and the human YY1 promoters, suggesting that transcription factors that bind

to those sites might play an important role in the regulation of the mRNA level of

YY1.

E1A-mediated repression of the human YY1 promoter. YY1 is an

important regulator of the cardiac α-actin promoter, and the adenovirus E1A protein

blocks myogenesis as well as cardiac-specific gene transcription (119). It has also

been shown that E1A relieves YY1-mediated transcriptional repression of the AAV

P5 promoter (144). It is possible that E1A directly affects transcription of the YY1

gene. To test this possibility, E1A expression plasmids (pCMV12S or pCMV13S)

and a YY1 promoter construct (p-3600Luc) were transiently transfected into HeLa

cells to examine the effect of E1A on YY1 transcription. Transcription initiated from

the human YY1 promoter was significantly down-regulated by over-expressed E1A

12S and 13S proteins as measured in luciferase assays (Fig. 6A).

To further examine whether E1A represses YY1 promoter expression through

upstream cis-acting sequences or through basal transcriptional machinery, a minimal

36

YY1 promoter, p-277Luc, was utilized in co-transfection/reporter assays. Figure 6B

shows that the luciferase activity of p-277Luc was repressed by both E1A 12S and

13S proteins, suggesting that the mechanism of YY1 repression by E1A does not

involve upstream sequence-specific DNA binding factors. This E1A-mediated

.

0

20

40

60

80

100

120

0

20

40

60

80

100

120

rela

tive

luci

fera

se a

ctiv

ity

rela

tive

luci

fera

se a

ctiv

ity

p-3600 luc p-3600 luc + E1A 12S

p-3600 luc + E1A 13S

p-277 luc p-277 luc + E1A 12S

p-277 luc + E1A 13S

A B

FIG. 6. Adenovirus E1A proteins repress the YY1 promoter.

Luciferase assays were performed after transient

transfections into HeLa cells with p-3600Luc or p-277Luc

and pRL-TK plasmids in the presence or absence of

plasmids encoding the adenovirus 12S or 13S proteins.

Results were presented as the mean of three independent

transfections with standard deviations and normalized with

control Renilla luciferase expressions.

37

repression of the YY1 promoter most likely results from E1A modulating the activity

of the basal transcription elements surrounding the YY1 transcriptional initiation site.

YY1 does not autoregulate its own promoter. It is known that many

transcription factor autoregulate their own promoters. Some transcription factors bind

directly to DNA elements located in their own promoters and regulate their own

expression, while others activate or repress expression of a separate set of

transcription factors, which in turn modulate transcription from their gene promoters.

Although the human YY1 promoter does not appear to contain a YY1-binding

.

120

100

80

60

40

20

0p-3600Luc p-3600Luc

+pCMV-YY1

rela

tive

luci

fera

se a

ctiv

ity

FIG. 7. The YY1 protein does

not autoregulate the YY1

promoter. Luciferase assays

were performed after transient

transfections into HeLa cells

with p-3600Luc and pRL-TK

plasmids in the presence or

absence of a plasmid encoding

the YY1 protein. Results are

presented as the mean of three

independent transfections with

standard deviations and

normalized with control

Renilla luciferase expressions.

38

consensus sequence, YY1 might alter expression levels of other transcription factors

which are capable of binding the YY1 promoter and regulate expression of YY1.

Therefore, a YY1 expression plasmid (pCMV-YY1) was transfected into HeLa cells

to test if over-expression of YY1 had any effect on its own promoter (p-3600Luc).

Figure 7 shows that YY1 had no significant effects on the activity of its own

promoter. It is possible that the concentration of endogenously-expressed YY1 is

sufficiently high to negate any effects from over-expressed YY1 introduced by

transfection. However, our data suggest that YY1 most likely does not autoregulate

its own promoter.

YY1 is acetylated by p300 and PCAF. Acetylation has been shown to

FIG. 8. Multiple functional domains of transcription factor

YY1. YY1 has one transcriptional activation domain at the

N-terminus and two repression domains, one encompassing

residues 170 to 200 and the other one residing at the C-

terminus. The amino acid sequence of the central repression

domain (residues 170 to 200) is given with lysine residues

underlined. His, histidine-rich domain; GA,

glycine/alanine-rich domain; GK, glycine/lysine-rich

domain; Zn fingers, zinc fingers.

54 80 154 414200 295

transcriptionalactivation

domain

transcriptionalrepression

domain

transcriptionalrepression

domain

170

DNA-binding domain

Zn FingersSpacerAcidic GKGAHisAcidic

GRVKKGGGKKSGKKSYLSGGAGAAGGRGADP

39

regulate the activity of many transcription factors including sequence-specific DNA-

binding factors p53 (54), GATA-1 (15, 73), E2F (110, 111), and MyoD (137).

Analysis of the YY1 amino acid sequence reveals that YY1 contains multiple lysine

residues that are potential substrates for acetylation. Interestingly, within YY1’s

histone deacetylase interaction domain (residues 170-200), there are 6 lysines

arranged in pairs (Fig. 8). As described previously, YY1 interacts with the HAT p300

(5, 95) which interacts with another HAT, PCAF (173). Remarkably, both p300 and

PCAF catalyze the acetylation of transcription factors (reviewed in reference 150).

To determine if p300 or PCAF acetylated YY1, we performed in vitro acetylation

reactions using GST-tagged p300 and PCAF purified from E. coli as enzymes. YY1

serial deletion constructs were similarly purified from E. coli as GST-fusion proteins

..

97

68

43

29

GST1-

414

170-

200

∆ 170-

200

261-

333

MW(kD)

8 9 10 11 12

GST1-

414

398-

414

333-

414

260-

414

13 14 15 16 17

29

97

68

43

MW(kD)1-

200

1-26

11-

333

1-41

4

1-12

21-

396

1-17

0

1 2 3 4 5 6 7

97

68

43

MW(kD)

FIG. 9A. Acetylation of YY1 by PCAF. Serial GST-YY1

deletion proteins were incubated with GST-PCAF and

separated by SDS-PAGE. The gels were then exposed to X-

ray film to detect acetylated proteins. Arrows indicate

acetylated YY1 proteins. Auto-acetylated forms of PCAF

were detected as three bands around 68 kD.

40

and used as substrates. GST-PCAF acetylated various deletion constructs of YY1

(Fig. 9A, lanes 1-5, 8-11, 13, 15, 16) but not GST alone (lanes 12, 17). Unlike PCAF,

GST-p300 efficiently acetylated GST-YY1 (170-200) as well as GST-YY1 (1-200)

(Fig. 9B, lanes 3, 12, 15). GST alone was not acetylated by p300, showing that the in

vitro acetylation was specific to YY1 (Fig. 9B, lane 1). Moreover, acetylation of YY1

was dependent on p300 or PCAF and was not due to YY1 auto-acetylation (Fig. 9C).

Taken together, we found that PCAF acetylated YY1 at residues 170-200 and at its C-

terminus. p300, in contrast, efficiently acetylated YY1 only at residues 170-200 and

only when YY1 was in a C-terminal truncated form, implying that p300-mediated

acetylation of YY1 is dependent on the conformation of YY1.

..

97

68

43

29

GST1-

414

170-

200

∆ 170-

200

261-

333

∆ 261-

333MW

(kD)

1 2 3 4 5 6

1-41

420

0-26

1

260-

414

398-

414

7 8 9 10 11 12

170-

200

333-

414

97

68

43

29

MW(kD)

1-12

2

1-17

01-

200

1-26

11-

333

1-39

61-

414

13 14 15 16 17 18 19

MW(kD)

97

68

43

29

FIG. 9B. Acetylation of YY1 by p300. Serial GST-YY1 deletion

proteins were incubated with GST-p300. Arrows indicate YY1 proteins

acetylated by p300.

41

To determine if YY1 was acetylated in vivo, we immunoprecipitated

endogenous YY1 from HeLa cells and then western blotted the precipitated material

with anti-acetyl lysine antibody (Fig. 9D, lanes 2 and 3). Neither YY1 nor acetylated

YY1 was seen in experiments in which YY1 antibody was omitted from the

immunoprecipitation reaction (mock IP, lane 1). Unlike YY1, the transcription

factors Max and 14-3-3 were not acetylated in vivo (lanes 4 and 5). This finding

indicates that YY1 is acetylated in vivo, and protein acetylation is restricted to specific

proteins such as YY1.

To determine which region of YY1 was acetylated in vivo, we performed

similar IP-western experiments, this time using YY1 serial deletion constructs fused

to a Flag epitope. Flag-tagged YY1 (F-YY1) deletion constructs were transiently

transfected into HeLa cells and immunoprecipitated with anti-Flag antibody.

200

97

68

43

29

18

MW(kD)

YY1 (170-200)

YY1 (1-414)

p300

PCAF

Acetyl-CoA

+-

+

++++

+--

-

-

+

+

+-

-++

-

-

---

-

1 2 3 4 5

FIG. 9C. Acetylation of YY1 is

dependent on p300 or PCAF. In

vitro acetylation reactions were

performed in the presence or

absence of p300 or PCAF.

Arrows indicate that YY1 was

acetylated only in the presence

of p300 or PCAF.

42

Acetylated forms of F-YY1 were detected by western blotting with anti-acetyl lysine

antibody (Fig. 9E, top panel). To ensure that all F-YY1 deletions were expressed,

blots were also probed with anti-Flag antibody (Fig. 9E, bottom panel). The results of

these experiments show that YY1 is acetylated in vivo at residues 170-200 as well as

in the C-terminal residues 261-414. Taken together, our in vitro and in vivo

acetylation results suggest that there are two acetylation domains on YY1: residues

170-200, which are acetylated by both p300 and PCAF, and the C-terminus, which is

acetylated by PCAF only.

Because both p300 and PCAF acetylate YY1 at residues 170-200, we were

interested in determining the specificity of acetylation by these two enzymes. Using

GST-p300 or GST-PCAF, we in vitro acetylated a synthetic peptide corresponding to

FIG. 9D. YY1 is acetylated in vivo.

Endogenous YY1 (lanes 2 and 3), Max

(lane 4), and 14-3-3 (lane 5) were

immunoprecipitated from HeLa cells

and analyzed for acetylation by western

blotting using anti-acetyl lysine

antibody (bottom panels) or for

expression using their perspective

antibodies (top panels). "Mock IP"

indicates that no primary antibody was

used in immunoprecipitation reactions.

Arrows indicate highlighted protein

bands.

200

97

68

43

29

MW(kD) IP

α-YY1

Westernα-YY1α-Max

α-14-3-3

IP α-M

ax

IP α-1

4-3-

3

3 4 5

Westernα-acetyl lysine

200

97

68

43

29

mock

IP

IP α-Y

Y1MW(kD)

1 2

43

YY1 residues 170-200. We then compared the mass spectra produced by mass

spectrometry. Figure 9F shows that mock-acetylated YY1 peptide had a Mr of 2861

(panel A, 2861 m/z). When this peptide was acetylated with PCAF, another peak

emerged with a Mr of 2903 (panel B, 2903 m/z). Compared to the mock-acetylated

peptide, this additional peak had a mass corresponding to one additional acetyl group

(2903-2861=42), suggesting that the YY1 peptide was acetylated once by PCAF.

Interestingly, when we compared the spectrum from the p300-acetylated peptide with

FIG. 9E. Identification of regions of YY1 acetylated in

vivo. Flag-tagged YY1 serial deletion proteins were

transiently expressed in HeLa cells, immunoprecipitated

with anti-Flag antibody, and analyzed by western blotting

using anti-acetyl lysine antibody and anti-Flag antibody.

Arrows indicate immunoprecipitated YY1 proteins that

were acetylated.

MW 1-12

21-

170

1-20

0

1-26

11-

333

1-39

6

1-41

4

55-4

14

∆170-

200

∆261-

300

∆261-

333

333-

414

261-

414

170-

414

kD 1-17

026

1-33

3

∆261-

333

1-41

4

14

18

29

68

43

97200

14

18

29

68

43

97200

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

α-acetyl-lysine

α-Flag

44

that of the mock-acetylated peptide, we found 3 additional peaks at 2903, 2945, and

2987 m/z, which contained one, two, and three additional acetyl groups, respectively

(Fig. 9G). This result strongly suggests that YY1 can be acetylated by p300 at three

different lysines between residues 170 and 200.

.

Mass (m/z)

2900 3000 31002900 3000 3100

cou

nts

2800 2800

unmodifiedunmodified

monoacetylated

YY1 (170-200) PCAF acetylatedYY1 (170-200)

Mass (m/z)

2900 3000 3100 32002900 3000 31002800

unmodified unmodified

monoacetylated

diacetylated

triacetylated

YY1 (170-200) p300 acetylatedYY1 (170-200)

cou

nts

G

F

FIG. 9F, G. Determination of the number of acetylated lysines by mass

spectrometry. A YY1 peptide containing residues 170 to 200 was in vitro

acetylated by PCAF or p300 and subjected to mass spec analysis. Left panels

are spectra from mock-acetylated peptides. Right panels contain spectra from

acetylated as well as unacetylated peptides.

45

Lysine-to-arginine mutations within YY1 residues 170-200 significantly

reduce the transcriptional repression activity of YY1. To understand the effect of

acetylation on the transcriptional activity of YY1, we mutated the six lysines within

YY1 residues 170-200 to arginines. Arginine substitutions preserve the charges of the

affected amino acid residues but prevent acetylation in vivo by HATs. Both wild-type

and mutant YY1 were fused to a Gal4 DNA-binding domain and transfected into

HeLa cells in combination with a CAT reporter driven by the SV40 promoter

Gal4Gal4-YY1

Gal4-YY1 (K170-200R)

+--

+-

- +-- +

--

+-

- +--

Gal4-YY1

YY1

Western α-YY1

1 2 3 4 5 6

1 2 3 4 5 6

Gal4-YY1 (K170-200R)

FIG. 10. The effect of acetylation of YY1 residues 170-200

on the transcriptional repressor activity of YY1. HeLa cells

were transfected with Gal4 DNA-binding domain alone

(Gal4), Gal4-YY1 fusion construct (Gal4-YY1), or Gal4-

YY1 mutant with the 6 lysines mutated to arginines (Gal4-

YY1 (K170-200R)). Transcriptional activities were analyzed

by CAT assays using a CAT reporter containing five Gal4

binding sequences in tandem, and a representative

autoradiogram is shown. Western blot analyses were

performed to verify the expression levels of the effector

proteins.

46

containing five Gal4 binding sites. Consistent with previous findings (144, 171),

wild-type Gal4-YY1 was a potent transcriptional repressor (Fig. 10, top panel, lanes 2

and 5). However, when the six lysines were mutated and no longer able to be

acetylated, YY1 lost much of its repression activity (Fig. 10, top panel, lanes 3 and 6).

This finding suggests that acetylation of YY1 is necessary for the maximum

transcriptional repression activity of YY1. Western blot analysis showed that the loss

of repression was not due to lack of expression of the mutant YY1 proteins (Fig. 10,

bottom panel, compare lane 3 to lane 2, lane 6 to lane 5).

Acetylation of YY1 residues 170-200 increases YY1 binding to HDACs.

Using GST pull-down assays, we previously demonstrated that HDACs interact with

YY1 residues 170-200 (79). Therefore, we asked if acetylation of YY1 in this region

would affect YY1’s interaction with HDACs. Figure 11 shows that [35S] methionine-

labeled HDAC1 bound more efficiently to PCAF-acetylated and p300-acetylated

GST-YY1 (170-200) than to unacetylated GST-YY1 (170-200) (compare lane 1 to

lane 2, lane 3 to lane 4). The same amount of GST-YY1 (170-200) was used in all

reactions as shown by Coomassie staining. Similar results were obtained using in

vitro transcribed and translated HDAC2 (data not shown). In short, our data suggest

that acetylation of YY1 at residues 170-200 significantly increases the binding of

YY1 to HDACs.

HDAC1 and HDAC2 deacetylate YY1 170-200 but not the C-terminal

region of YY1. It is possible that the binding of HDACs to acetylated YY1 (170-

200) results in the subsequent deacetylation of YY1 (170-200). To test this

hypothesis, a synthetic peptide corresponding to YY1 residues 170-200 was

47

chemically labeled with [3H]sodium acetate and used as a substrate in deacetylation

assays. Figure 13A shows that immunopurified Flag-tagged HDAC1 and HDAC2 (F-

HDAC1 and F-HDAC2) deacetylated the YY1 (170-200) peptide. Deacetylation of

YY1 (170-200) by F-HDAC1 and F-HDAC2 was abolished by treatment with

tricostatin A (TSA), a potent inhibitor of HDAC1 and HDAC2. Furthermore, if F-

HDAC1 and F-HDAC2 were immunoprecipitated in the presence of an excess

competitor, Flag peptide, deacetylase activity was not observed on the YY1 peptide.

Similarly, endogenous HDAC1 and HDAC2 immunopurified from HeLa cells

FIG. 11. Increased HDAC-binding

to YY1 residues 170-200 by

acetylation. A representative

autoradiogram of in vitro translated

HDAC1 captured by acetylated or

mock-acetylated GST-YY1 (170-

200) is shown here. "Input"

represents one-tenth the amount of

HDAC1 used in each binding

reaction. Reaction mixtures were

separated by SDS-PAGE, and the

gels were stained with Coomassie

blue prior to exposure to film to

confirm that equal amounts of

GST-YY1 (170-200) were used in

the binding reactions.

.

HDAC1

1 2 3 4

input

97

68

43

29

MW(kD)

18

200

PCAF acet

ylate

d

mock

p30

0 ace

tylat

ed

p300 a

cety

lated

mock

PCAF ac

etyla

ted

GST-YY1(170-200)

GST-YY1(170-200)

Coomassie

48

(HDAC1 and HDAC2) also deacetylated the YY1 (170-200) peptide, and

deacetylation by endogenous HDAC1 and HDAC2 was also TSA-sensitive (Fig.

12A)..

F-HDAC1F-HDAC2

HDAC1HDAC2

200

400

600

800

1000

YY

1 (1

70-2

00)

dea

cety

lase

act

ivit

y (C

PM

)

Flag +----

+-

---

+

--

--

+

---

- +

----

-

----

competitorTSA

1200

1400

1600

--

-

-

---

-+

+

---

+-

---

+-

+-

---+-

--

+

--

--+-

+

--

--

+-

--

--

FIG. 12A. YY1 peptide deacetylation by HDACs.

Endogenous HDAC1 and HDAC2 and over-expressed

Flag-tagged HDAC1 and HDAC2 (F-HDAC1, F-

HDAC2) were immunoprecipitated from HeLa cells.

A YY1 (residues 170-200) peptide was labeled with

[3H]acetate and 20,000 cpm of the labeled peptide was

used in deacetylation reactions.

49

To provide further evidence that HDACs deacetylated YY1, we used an F-

HDAC1 immunoprecipitate to deacetylate full-length GST-YY1 and GST-YY1 (170-

200), both of which were in vitro acetylated with PCAF. As expected, YY1 (170-

.

Flag F-HDAC1 F-HDAC1H199F

1000

2000

3000

his

ton

e d

eace

tyla

se a

ctiv

ity

(cp

m)

2 3 4 5 6 7 81

9768

43

29

MW(kD)

PCAF acetylated YY1 (170-200)

HDAC1HDAC1(H199F)

p300 acetylated YY1 (170-200)

97

68

43

29

MW(kD)

Coomassie1 2 3 4 5 6 7 8

FIG. 12B. YY1 protein deacetylation by HDACs. Left panels: GST-

YY1 (170-200) was in vitro acetylated by p300 or PCAF. Half of the

acetylated GST-YY1 (170-200) was mixed with protein G beads alone

and the other half was mixed with immunoprecipitated wild type or

mutant (H199F) HDAC1. Samples were then separated by SDS-PAGE,

and the gels were subsequently stained with Coomassie blue and

exposed to film. Arrows indicate the position of GST-YY1 (170-200).

Right panel: Transiently expressed wild type and H199F mutant

HDAC1 were immunoprecipitated from HeLa cells and tested for their

histone deacetylase activity against a H4 peptide.

50

200) was efficiently deacetylated by HDAC1 (Fig. 12B, top panel, compare lane 1 to

lane 2). As a control, YY1 (170-200) was not deacetylated by an HDAC1 mutant that

was devoid of deacetylation activity ((24), Fig. 12B, right panel and top panel, lane

3). A Coomassie-stained gel (bottom panel) showed that the same amount of YY1

(170-200) was present in each reaction. Similarly, YY1 (170-200) acetylated by p300

was also deacetylated by HDAC1 (Fig. 12B, compare lane 5 to lane 6). To our

surprise, and in contrast to YY1 (170-200), full-length YY1 was not appreciably

deacetylated by HDAC1 (Fig. 12C, lane 1). This observation suggests that

200

97

68

43

29

MW(kD)

1 2 3 4 5 6 7 8Coomassie

200

97

68

43

29

MW(kD)

YY1 (1-414)YY1 (170-200)YY1 (261-333)YY1 (261-414)

HDAC1

+

-

-

+ -+

-+-+

-+

--

-- -

-

+

-

--

+

+

--

-+

--

--

+

--

+

-

---

1 2 3 4 5 6 7 8

FIG. 12C. Deacetylation of

YY1 serial deletion proteins by

HDAC1. Serial deletion

proteins of GST-YY1 were in

vitro acetylated by PCAF. Half

of the GST-YY1 proteins were

mixed with protein G beads and

the other half mixed with

HDAC1 immunoprecipitate.

Samples were then separated by

SDS-PAGE, and the gels were

subsequently stained with

Coomassie blue and exposed to

film. Arrows indicate the

positions of GST-YY1 deletion

proteins.

51

deacetylases only target specific regions of YY1. In support, we also found that

HDAC1 did not deacetylate two additional PCAF-acetylated GST-YY1 proteins, YY1

(261-333) and YY1 (261-414) (Fig. 12C, lanes 5 and 7). We conclude that only

residues 170-200 of YY1, and not the C-terminal zinc finger region of YY1, can be

deacetylated by HDAC1.

..

1-200

1-261

++

1-333 +1-396 +

+

261-333 ++261-414

333-414 -1-414 +

∆170-200

1-170 -

HDAC-binding domains170 200 261 333

56-414 +170-414 +

Flag -

1-17

01-

200

1-26

11-

333

1-39

6

1-41

455

-414

∆ 170-

200

HDAC1HDAC2HDAC3 IgH

1 2 3 4 5 6 7 8

MW(kD)

68

43

97

Flag

55-4

14

1-41

4

∆ 170-

200

333-

414

261-

414

170-

414

261-

333

9 12 131110 1514 16

α-HDAC2α-HDAC3

FIG. 13. Mapping of the HDAC-interaction domains of YY1. Serial

Flag-tagged YY1 deletion constructs were transfected into HeLa cells,

immunoprecipitated with anti-Flag antibody, and analyzed by western

blotting for the presence of HDAC1, HDAC2, and HDAC3 (lanes 1-8)

or HDAC2 and HDAC3 only (lanes 9-16). The bottom panel

summarizes the HDAC-binding domains of YY1. "+" indicates

positive interactions between YY1 and HDACs; "-" denotes the

absence of YY1-HDAC interactions.

52

HDACs bind YY1 at multiple regions. Based on our previous result that

YY1 interacts with HDACs at residues 170-200 in vitro (171), the inability of

HDAC1 to deacetylate the C-terminal zinc finger region of YY1 may arise from a

general failure of HDACs to interact with YY1 in the zinc finger region. To test this

possibility, we performed co-immunoprecipitation analyses to map the interaction

domain of YY1 with HDACs in vivo (Fig. 13). Surprisingly, our results showed that

in addition to residues 170-200, YY1 also interacted with HDACs at residues 261-333

in vivo. These results, together with those of our previous in vitro acetylation-

deacetylation experiment, suggest that YY1 interacts with HDACs at two domains:

residues 170-200, where bound HDACs deacetylate YY1, and the C-terminal residues

261-333, where bound HDACs do not result in deacetylation of YY1.

YY1 contains associated histone deacetylase activity, which localizes to C-

terminal residues 261-333 of YY1. After we precisely mapped the HDAC-binding

FIG. 14A. Histone deacetylase

activity of endogenous YY1 in HeLa

cells. Endogenous YY1 was

immunoprecipitated from HeLa cells

and assayed for deacetylase activity

against the H4 peptide. "+ TSA"

indicates addition of TSA to 400 nM

prior to addition of the peptide

substrate.

.

200

400

600

800

TSA +-

his

ton

e d

eace

tyla

seac

tivi

ty (

cpm

)

α-YY1 +- +-

53

domains in YY1, we sought to determine the functional effect of this interaction. We

found that immunoprecipitated endogenous YY1 from HeLa cells also contained

histone deacetylase activity, which was inhibited by TSA (Fig. 14A). Using serial F-

YY1 deletions, we determined the histone deacetylase activity domain of YY1, which

localized to residues 261-333 (Figs. 14B and 14C). This region of YY1 was

necessary and sufficient for the histone deacetylase activity associated with YY1

(Figs. 14B and 14C). Most strikingly, the YY1 histone deacetylase activity

domain completely overlapped with one of the HDAC-interacting domains of YY1.

Furthermore, the histone deacetylase activity associated with YY1 residues 261-333

.

vector

1-122

1-170

1-200

1-261

1-333

1-396

56-414

∆ 170-200

YY1(1-414)

200 400 600 800 1000

histone deacetylase activity (cpm)

∆ 261-333

261-333

333-414

261-414

1200 1400

170-414

histone deacetylase activity domain261 333

HDAC-binding domains170 200 261 333

FlagFlag-YY1 (1-414)

competitor

Flag-YY1 (261-333)

1000

2000

TSA

+ -+

+

+ ++ + +

+- - - --

- ---

-

- -

- ----- +

+ ++

-- -

-

-

--

-

his

ton

e d

eace

tyla

se

acti

vity

(cp

m)

B C

FIG. 14B, C. Identification of amino acid 261-333 as the histone deacetylase

activity domain of YY1. Flag-tagged YY1 deletion constructs were transfected

into HeLa cells, immunoprecipitated with anti-Flag antibody, and assayed for

deacetylase activity against the H4 peptide. "+ TSA" indicates addition of TSA

to 400 nM prior to addition of the peptide substrate. "+ competitor" indicates

addition of excess Flag peptides prior to addition of the peptide substrate.

54

was highly specific, because the activity was sensitive to TSA (Fig. 14B) and

competed by excess Flag peptide (Fig. 14B). A representative western blot shows

that different F-YY1 deletion mutants expressed equally well (Fig. 14D). These

results strongly suggest that stable interaction between HDACs and YY1 contributes

to YY1’s histone deacetylase activity. Immunofluorescence analysis confirmed that

F-YY1 deletion proteins that did not exhibit histone deacetylase activity localized to

either the nucleus or both the nucleus and cytoplasm, ruling out the possibility that the

lack of histone deacetylase activity was due to abnormal localization of the mutants

(Fig 14E).

Acetylation of YY1 at the C-terminal zinc finger domain decreases the

DNA-binding activity of YY1 . Because the C-terminal acetylation domain (residues

261-333) of YY1 overlaps with the zinc finger DNA-binding domain (residues 261-

414) of YY1, we tested whether acetylation of YY1 at the zinc finger domain would

affect the DNA binding activity of YY1 . Indeed, when in vitro acetylated by PCAF,

GST-YY1 bound less avidly than did unacetylated GST-YY1 to the Inr element of the

68

43

29

MW(kD) 1-

122

1-17

01-

200

1-26

1

1-33

3Flag 1-

396

FIG. 14D. Expression of F-YY1 deletion

mutants. Overexpressed F-YY1 deletion

constructs and Flag alone from the

parental vector were immunoprecipitated

from HeLa cells using anti-Flag

antibody, separated by SDS-PAGE, and

analyzed by western blotting using anti-

Flag antibody. Arrows indicate the

positions of F-YY1 deletion proteins.

55

AAV P5 promoter, which contains a consensus YY1 binding site (Fig. 15A, compare

lane 7 to lane 8). Similar results were obtained when a GST-YY1 deletion construct

that contained only the zinc finger domain of YY1 was tested for its DNA binding

properties (Fig. 15A, compare lane 5 to lane 6). In contrast, and consistent with

earlier reports, acetylated GST-p53 bound to its recognition sequence better than

unacetylated GST-p53 (Fig. 15A, compare lane 3 to lane 2). Thus, the decrease in

DNA binding activity caused by acetylation is specific to YY1. To rule out the

(1-414)

(1-261)

(1-200)

(1-170)

DAPIFITC merge

(1-122)

F-YY1

FIG. 14E. Sub-cellular

localization of F-YY1 deletion

constructs. Various F-YY1

deletion constructs were

transiently transfected into

HeLa cells. Transfected HeLa

cells were then fixed and

probed with anti-Flag FITC

conjugate antibody. The nuclei

were stained with DAPI.

Images were obtained from a

fluorescence microscope.

Merged images from FITC and

DAPI stains indicate sub-

cellular localization of F-YY1

deletion constructs.

56

possibility that this decrease in DNA binding activity was associated with the GST

fusion constructs, we tested non-tagged YY1 purified from E. coli, as well as Flag-

tagged YY1 purified from HeLa cells. Both forms of YY1 exhibited decreased DNA

binding activity upon acetylation (Fig. 15B), proving that the DNA-binding activity of

YY1 decreases when the zinc finger domain of YY1 is acetylated.

.

A

acet

ylate

d p53

mock

acet

ylate

d p53

acet

ylate

d YY1 (

1-41

4)

acet

ylate

d YY1 (

261-

414)

free probe1 2 3 4 5 6 7 8

mock

acet

ylate

d YY1 (

1-41

4)

mock

acet

ylate

d YY1 (

261-

414)

p53 p

robe a

lone

YY1 pro

be alo

ne+ -+ -acetylated

E. coliYY1

HeLaFlag-YY1

free probe1 2 3 4

B

FIG. 15A, B. The effect of acetylation on YY1’s sequence-specific DNA-

binding activity. Representative EMSAs of GST-tagged YY1, bacterially

expressed non-tagged YY1 and HeLa cell-expressed Flag-tagged YY1..

Purified proteins were in vitro acetylated or mock acetylated with PCAF

and mixed with 32P-labeled probes containing either a YY1 or p53 binding

sequence. Protein-DNA complexes were resolved on non-denaturing

polyacrylamide gels. Black arrows indicate the positions of full-length

YY1- and p53-DNA complexes. The empty arrow indicates the position of

the complex between DNA and the zinc finger domain of YY1.

57

YY1 exists in a high molecular weight protein complex. To determine if

YY1 exists in a protein complex in the cell, gel filtration chromatography was

employed. Nuclear extract from HeLa cells was applied to a Superdex 200 column.

Proteins were fractionated and differentially eluted according to their molecular

weights, and the presence of YY1 was demonstrated by western blot analysis. Figure

16 shows that YY1, which normally runs at about 68 kD on SDS-polyacrylamide

gels, eluted at about 150 kD, suggesting that YY1 associated with other proteins in

HeLa nuclear extract. YY1 could also be detected in earlier fractions (Fig. 16,

fractions 1 and 3); however, because those fractions were outside the fractionation

range of this column, the precise molecular weight of the higher molecular weight

YY1 complex could not be determined.

Purification of native YY1 complexes. To purify a YY1 complex active in

transcription from HeLa nuclear extract, anion exchange chromatography was chosen

M97

68

43

kD 1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33Input

200kD 150kD 66kD 29kD 12.4kD

fractions

YY1

FIG. 16. Gel filtration analysis of YY1 in HeLa cells. HeLa nuclear extract

was fractionated on a Superdex 200 column. Eluted fractions were analyzed

for the presence of YY1 by western blot analysis. Calibrated molecular

weights are indicated above the fraction numbers.

58

as the initial purification step. The DNA-binding activity of the YY1 complex was

monitored using EMSA, and the histone deacetylase activity associated with YY1 was

determined using histone deacetylation assay against a labeled H4 peptide. Figures

17A and 17B show that YY1 was eluted from a Q Sepharose column at 200 mM to

.

M W 11 12 13 14 17 18 19 20 21 23Inp

ut

9768

43

kD200

29

18

fractions

A

.

M W 11 12 13 14 17 18 19 20 21 23 25 27

YY1

Inp

ut

97

68

43

kD200

fractions

B

FIG. 17. Purification of a native YY1 complex from

HeLa cells using anion exchange chromatography and

IMAC. (A) A Coomassie-stained SDS-polyacrylamide

gel of the Q Sepharose fractions. (B) Western blot

analysis of the Q Sepharose fractions. An arrow

indicates the position of YY1.

59

500 mM of salt concentrations. Fractions containing YY1 also exhibited strong DNA

binding activity (Fig. 17C) and histone deacetylase activity (Fig. 17D). Q Sepharose

Input 11 12 13 14 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 330

500

1000

1500

his

ton

e d

eace

tyal

se a

ctiv

ity

(cp

m)

fractions

D

11 12 13 14 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33Input

free probe

fractions

C

FIG. 17. Purification of a native YY1 complex from HeLa cells using

anion exchange chromatography and IMAC. (C) EMSA of the Q

Sepharose fractions using the AAV P5+1 YY1 binding sequence as a

probe. (D) Histone deacetylation assay of the Q Sepharose fractions.

Fractions from the Q Sepharose column were assayed for histone

deacetylase activity against the H4 peptide.

60

1 2 3 4 5 6 7 8 9

300mM

10

free probe

fractions

F

M input 1 2 3 1 2 1 2 3 4 5 6 7 8 9 10

FT Wash 300mM

YY168

43

kD fractions

E

FIG. 17. Purification of a native YY1 complex from HeLa cells using

anion exchange chromatography and IMAC. (E) Western blot analysis

of the Ni2+ column fractions. An arrow indicates the position of YY1.

FT, flowthrough fractions; Wash, wash fractions; 300 mM, 300 mM

imidazole-eluted fractions. (F) EMSA of the 300 mM imidazole-eluted

fractions using the AAV P5+1 YY1 binding sequence as a probe.

61

fractions 13 to 17 were pooled and further fractionated using a Ni2+ column. YY1

contains a stretch of histidines at the N-terminus, which potentially serve as binding

moieties to the Ni2+ column. Bound YY1 and the YY1-associated proteins were

eluted with 300 mM imidazole. Figure 17E and 17F show that the eluted fractions

containing YY1 were still active in sequence-specific DNA-binding; however, they

did not contain significant histone deacetylase activity (data not shown). Several

kD

200

97

68

43

29

18

M 300 mM

*

*

**

YY1

G

FIG. 17. Purification of a native YY1

complex from HeLa cells using anion

exchange chromatography and IMAC.

(G) Silver-staining analysis of the

second fraction from the 300 mM

imidazole-eluted fractions. A black

arrow indicates the YY1 protein band.

Empty arrows with stars indicate the

positions of protein bands that are

present in YY1 complexes purified by

other methods presented in this

dissertation.

62

protein bands from fraction 2 of the 300 mM imidazole fractions were stained with

silver, suggesting that those proteins associate with YY1 after both anion exchange

and immobilized metal affinity chromatography steps.

Because the final fractions from the Ni2+ column lost their histone deacetylase

activity, a different purification scheme was employed to purify a YY1 complex

97

68

43

kD

200

29

18

M Inp

ut

2 4 6 8 10 1214 16 1820 22 24 2826 30 fractions

A

M W 2 4 6 8 10 12 14 16 18 20 22 24

YY1

Inp

ut

97

68

43

kD200

26 fractions

B

FIG. 18. Purification of a native YY1 complex from HeLa cells using

anion exchange chromatography and antibody-affinity chromatography. (A)

A Coomassie-stained SDS-polyacrylamide gel of the Q Sepharose fractions.

(B) Western blot analysis of the Q Sepharose fractions. An arrow indicates

the position of YY1.

63

2 4 6 8 10 12 14 16 18 20 22 24 26 28 30Input

free probe

fractions

C

FIG. 18. Purification of a native YY1 complex from HeLa cells

using anion exchange chromatography and antibody-affinity

chromatography. (C) EMSA of the Q Sepharose fractions using

the AAV P5+1 YY1 binding sequence as a probe. (D) Histone

deacetylation assay of the Q Sepharose fractions. Fractions from

the Q Sepharose column were assayed for histone deacetylase

activity against the H4 peptide.

Input 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 fractions0

1000

2000

3000

his

ton

e d

eace

tyla

se a

ctiv

ity

(cp

m)

D

64

retaining histone deacetylase activity. HeLa nuclear extract was first fractionated on

the Q Sepharose column as described above, and fractions containing YY1 (Fig. 18A

and 18B, fractions 8 to 18) were pooled. These fractions still possessed sequence-

specific DNA-binding activity and histone deacetylase activity (Fig. 18C and 18D).

Pooled Q Sepharose fractions were passed through a protein G column and the

flowthrough fraction re-loaded on an antibody affinity column containing protein G

resin coupled to the H-10 mAb against YY1. Bound protein complexes were eluted

200

68

97

43

29

kD

YY1

1 2

protein G

H-10

*

**

*

18

E FIG. 18. Purification of a native YY1

complex from HeLa cells using anion

exchange chromatography and antibody-

affinity chromatography. (E) Silver-staining

analysis of fractions from the anti-YY1 H-

10 column (lane 2) and the protein G control

column (lane 1). A black arrow indicates

the position of the YY1 protein band.

Empty arrows show the presence of multiple

protein bands that exist in the fractions from

the H-10 column but not in those from the

protein G column. Stars indicate the

positions of protein bands that are present in

YY1 complexes purified by other methods

presented in this dissertation.

65

from both columns with acidic glycine. The protein components of the eluted YY1

complex were compared to those from the protein G column (Fig. 18E). The YY1

complex from the H-10 column still retained histone deacetylase activity (Fig. 18F).

Purification of a Flag-tagged YY1 complex. To purify a YY1 complex

using a different method, Flag-tagged YY1 (F-YY1) was over-expressed in HeLa

FIG. 18. Purification of a native YY1 complex from HeLa cells using anion

exchange chromatography and antibody-affinity chromatography. (F)

Histone deacetylation assay from the protein G control column (protein G)

and the anti-YY1 H-10 column (H-10) against the H4 peptide.

Protein G H-10

1000

2000

3000

4000

5000

6000

his

ton

e d

eace

tyal

se a

ctiv

ity

(cp

m)

F

66

cells, and the proteins associated with F-YY1 were purified from whole cell lysates on

an antibody column against the Flag epitope. As a control, empty Flag vector was

transiently transfected into HeLa cells and the whole cell lysate purified on an anti-

Flag column. The protein components of the F-YY1 complex and the proteins eluted

from the Flag alone control were compared on silver-stained SDS-polyacrylamide

gels (Fig. 19A). Protein bands that are present in the F-YY1 lane but not in the Flag

lane represent proteins specifically associate with YY1, including the over-expressed

F-YY1 as well as a degradation product of F-YY1, F-YY1’. Fractions from the F-

200

68

97

43

29

kD Flag F-YY1

*

F-YY1

F-YY1'

1 2

*

*

*

FIG. 19A. Silver-staining analysis of the

second fractions from the Flag-alone (lane

1) column and the F-YY1 column (lane 2).

Black arrows indicate the positions of the

full-length F-YY1 (F-YY1) and a

degradation product of F-YY1 (F-YY1’).

Empty arrows show the presence of

multiple protein bands that exist in the

fractions from the F-YY1 column but not

in those from the Flag alone column. Stars

indicate the positions of protein bands that

are present in YY1 complexes purified by

other methods presented in this

dissertation.

67

YY1 column contained significant histone deacetylase activity after concentration

through ultrafiltration (Fig. 19B).

Proteins specifically associate with F-YY1 were also visualized by

radioimmunoprecipitation analysis (RIPA) (Fig. 20A). HeLa cells were transiently

transfected with F-YY1 or Flag alone and the proteins within the cells metabolically

labeled with 35S-containing amino acids. Proteins were subsequently

immunoprecipitated from cell lysates with anti-Flag beads. Several protein bands

specific to F-YY1 were visible upon comparison to the Flag control. RIPA was also

used as a tool to analyze patterns of protein association specific to different regions of

YY1. Amino acid residues 261-333 were shown to be involved in YY1-associated

histone deacetylase activity. Therefore, F-YY1 (261-333) and F-YY1 (∆261-333)

were transiently transfected into HeLa cells and subjected to RIPA. However, despite

numerous attempts, comparisons among immunoprecipitated proteins from Flag, F-

.

Flag F-YY1

100

200

300

400

500

his

ton

e d

eace

tyal

se a

ctiv

ity

(cp

m)

FIG. 19B. Histone deacetylation

analysis of the second fractions

from the Flag alone column and the

F-YY1 column against the H4

peptide.

68

YY1, F-YY1 (261-333), and F-YY1 (∆261-333) failed to suggest proteins that were

specifically associated with constructs that had been shown to contain associated

histone deacetylase activity [F-YY1 and F-YY1 (261-333)] (Fig. 20B).

kD

200

97

68

43

29

F-YY1

Flag F-YY1

F-YY1'

1 2

*

*

*

*

Fig. 20A. A representative autoradiograph

showing proteins bound to Flag alone or F-

YY1. Black arrows indicate the positions of

the full-length F-YY1 (F-YY1) and a

degradation product of F-YY1 (F-YY1’).

Empty arrows show the presence of multiple

protein bands that were present in the F-

YY1 immunoprecipitate (lane 2) but not in

the Flag alone immunoprecipitate (lane 1).

Stars indicate the positions of protein bands

that are present in YY1 complexes purified

by other methods presented in this

dissertation.

69

..

kD

200

97

68

43

29

F-YY1

Flag F-YY1

F-YY1'

F-YY1 (∆ 261-333)

F-YY1 (∆ 261-333)

F-YY1 (261-333)

FIG. 20B. A representative autoradiograph showing

proteins bound to different F-YY1 deletion mutants.

Black arrows indicate the positions of the full-length F-

YY1 (F-YY1), a degradation product of F-YY1 (F-

YY1’), and one of the F-YY1 deletion mutants [F-YY1

(∆261-333)].

70

DISCUSSION

In this dissertation, the isolation and characterization of a genomic clone of

human YY1 is presented. Deletional analysis reveal that the human YY1 promoter

possesses many characteristics typical of housekeeping genes. For example, the YY1

gene does not contain a TATA box, and the elements critical for basal transcription

reside within a small region around the transcriptional start site. One unusual

observation is that plasmid p+54Luc, which contains sequences downstream of the

transcriptional initiation site, still possesses significant activity compared to the wild-

type YY1 promoter. Only one transcriptional start site of the human YY1 gene has

been detected by primer extension, and no other start sites were found around or

downstream of position +54. It is possible that minor transcription initiation sites

exist downstream of the mapped +1 site, but they are too weak to be detected by

primer extension analysis. It is also possible that the YY1 gene contains alternative

start sites that are utilized only when the natural start site is not present.

A notable feature of the human YY1 promoter is its similarity to the mouse

YY1 promoter (135). The proximal promoter region between positions -741 and

+476 in the human gene and that between positions -751 and +434 in the mouse gene

share a remarkable 70% identity. The human YY1 promoter is quite active with a

small sequence of position -277 to position +475. Similarly, the mouse YY1

promoter only requires a region as short as from position -58 to position +32 for

activity. Moreover, many transcription factor binding sites that are present in the

71

human YY1 promoter are also present in the mouse promoter. An Sp1 binding site

plays an important role in the expression of the mouse YY1 gene (135), and three Sp1

sites are found within the region critical for the activity of the human YY1 promoter.

These observations suggest that the human and the mouse YY1 promoter are

controlled by a similar regulatory mechanism.

The adenovirus E1A protein can convert YY1 from a repressor to an activator.

Many studies have been devoted to the mechanistic details of this interesting

phenomenon. It was elegantly demonstrated that physical interactions among E1A,

YY1, and p300 are critical in this conversion from repression to activation (95). Our

study shows here that E1A down-regulates the YY1 promoter and that a minimal

YY1 promoter is sufficient for E1A-mediated repression. These findings suggest an

alternate, albeit non-mutually exclusive, model of how the transcriptional activity of

YY1 is affected by E1A. Under physiological concentrations of YY1, YY1 represses

transcription in certain cell types. However, the presence of the E1A protein

decreases the expression level of YY1, which results in activation of genes normally

repressed by YY1. In this model, the activity of YY1 is similar to that of the

Drosophila Krüpple transcription factor, which activates or represses target genes

depending on its cellular concentrations (138). It will be interesting to study if the

expression of YY1 could be regulated by other viral and cellular transcription factors.

At the polypeptide level, the activity of the multifunctional transcription factor

YY1 is shown to be regulated by acetylation and deacetylation. Acetylation and

deacetylation of YY1 represents a novel and complex means of regulating the activity

of a DNA-binding transcription factor (Fig. 21). YY1 is acetylated in two regions:

72

one at the previously identified HDAC-interacting domain of residues 170-200, and

the other at the C-terminal DNA-binding zinc finger domain. Residues 170-200 of

YY1 are acetylated by p300 and PCAF, while the C-terminal zinc finger domain is

acetylated only by PCAF (Fig. 21). Acetylation of these two regions results in

54 80 154 414200 295170

transcriptionalactivationdomain

transcriptionalrepression

domain

transcriptionalrepression

domain

DNA-binding domain

Zn FingersSpacerAcidic GKGAHisAcidic

HDAC?

histones

HDAC

in vivo acetylated domains

p300 acetylated domain

PCAF acetylated domains

in vivo HDAC-binding domains

histone deacetylase activity domain

170 200

170 200 261 398

170 200 261

261 333

170 200 414261

333

in vitro HDAC-binding domain170 200

deacetylated domain170 200

FIG. 21. Summary of regulation of YY1 by acetylation and deacetylation.

YY1 is acetylated in two regions: residues 170-200 and the C-terminal

DNA-binding domain. Acetylation of residues 170-200 targets YY1 for

deacetylation. Acetylation of the C-terminus of YY1 results in stable

association of histone deacetylase activity with YY1 as well as decreased

DNA-binding activity. The in vivo association between YY1 and HDACs

at the C-terminal region is probably mediated through an unidentified

protein (depicted as a question mark in an oblong circle).

73

dramatically different outcomes: First, when residues 170-200 of YY1 are acetylated,

YY1 becomes a more effective transcriptional repressor and binds HDACs more

efficiently. However, upon binding to acetylated YY1 residues 170-200, HDACs also

actively deacetylate this region, possibly resulting in a negative feedback loop.

Second, YY1 possesses histone deacetylase activity toward histone H4 by associating

with HDACs using the C-terminal zinc finger region. This is most likely a result of

active targeting of acetylated YY1 zinc finger domains by HDACs. However, our

data do not indicate that association of the YY1 C-terminus with HDACs brings about

deacetylation of YY1 in this region. In contrast, the interaction between YY1 and

HDACs at residue 170-200 is likely to be a dynamic and highly regulated process and

does not result in associated histone deacetylase activity stable enough to be detected

in our experimental system. Finally, acetylation of YY1 zinc fingers decreases YY1’s

DNA-binding activity, which will have further impact on YY1’s activity as a

transcription factor.

This differential regulation of YY1 by acetylation and deacetylation suggests a

complex regulatory system unlike that of any other transcription factors known to

date. In cells where YY1 functions primarily as a transcriptional repressor,

acetylation of YY1 at the central HDAC-binding region and the C-terminal DNA-

binding region most likely will result in an intricate network of negative-feedback

regulation: Acetylation of YY1 at residues 170-200 augments YY1’s repressor

activity, but acetylation of this region also targets YY1 for deacetylation. In the mean

time, acetylation of the C-terminal DNA-binding region of YY1 most likely stabilizes

interaction between YY1 and HDACs, but acetylation of this region in turn decreases

74

YY1’s DNA binding activity. To date, we have not been able to determine the

relative levels of acetylation between the central region and the C-terminus of YY1

under physiological conditions; therefore, the relative contribution of acetylating these

two regions is unknown. Interestingly, we also found that TSA had little effect on the

acetylation status of YY1 (data not shown), suggesting that regulation of YY1 by

acetylation is more prominent than by deacetylation. This finding is also in

agreement with our discovery that deacetylation of YY1 only occurs at residues 170-

200, while acetylation of YY1 can happen at the C-terminal DNA-binding domain as

well.

In many experimental systems, YY1 can also activate transcription, and it is

still uncertain how this is accomplished. Different models, including bending of

DNA, the relative distance between the YY1 binding site and the transcriptional

initiation site, as well as protein-protein interactions have been proposed (reviewed in

references 143, 154). Increasingly more evidence shows that interactions with other

proteins are probably the most important factors in YY1-mediated transcriptional

activation. It has been suggested that interactions of YY1 with other cellular proteins

or viral proteins can either disrupt the quenching activity of YY1 on other

transcriptional activators or stimulate transcription with associated enzymatic

activities such as HATs (95, 144, 154). Our findings here provide an additional

speculation that on promoters activated by YY1, YY1-associated p300 and PCAF can

activate transcription by both acetylating core histones and acetylating YY1 at the C-

terminal zinc finger domain (PCAF only), which in turn decreases the overall histone

deacetylation activity at the promoter.

75

In addition to histones and several non-histone chromatin proteins, many

transcription factors have been shown to be regulated by acetylation. These

transcription factors include p53 (54), HIV Tat (84), E1A (176), GATA-1 (15, 73),

EKLF (177), MyoD ((131, 137), E2F (110), TFIIE, TFIIF (75), CIITA (149), TCF

(167), HNF-4 (147), UBF (128), TAL1/SCL (71), and nuclear receptor co-activators

ACTR, SRC-1, and TIF2 (29). Many of these factors are acetylated by both

p300/CBP and PCAF; therefore, it is not surprising that YY1 is also acetylated by

both p300 and PCAF. The p300-interaction domain of YY1 has been mapped to the

C-terminal 17 residues (95, 97), which were not acetylated by p300 in our study. This

finding is reminiscent of acetylation of p53 by p300/CBP, where the N-terminus of

p53 interacts with CBP (55, 102) while the region acetylated by p300 is at the C-

terminus of p53 (54). Moreover, the arrangement of the 6 lysines within the p300-

acetylation domain of YY1 closely resembles the sequence of the p300-acetylated

region of histone H2B (150), indicating that YY1 contains an authentic p300-

acetylation domain. Interestingly, the PCAF-interacting domain of p300 overlaps

with its YY1-interacting domain (5, 173), which suggests that acetylation of YY1 by

PCAF versus by p300 might be either cooperative or mutually exclusive in vivo,

depending on whether or not YY1 binding to p300 can be competed by PCAF.

Furthermore, in our in vitro acetylation studies, full-length GST-YY1 was acetylated

by PCAF and not by p300, which further suggests that the conformation of YY1,

perhaps affected by selective interaction with p300 and PCAF, is important to YY1

acetylation. We also found that in HeLa cells, overexpression of PCAF, but not p300,

partially alleviated the transcriptional repressor activity of a Gal4 DNA-binding

76

domain-YY1 fusion protein. However, in NIH3T3 cells, overexpression of p300, but

not PCAF, relieved repression from Gal4-YY1 (data not shown). In this regard, it

will be important to identify the in vivo triggers directing PCAF versus p300

acetylation. p53 is particularly interesting among acetylated transcription factors

because it has been elegantly demonstrated that DNA damage (UV and ionizing

radiation) causes p53 acetylation at two distinct lysines, one by p300 and the other by

PCAF (103). To date, this is the only report linking specific environmental cues to

acetylation of transcription factors by HATs, and yet it is still uncertain why

acetylation would require two HATs. It is interesting to note that while an increase in

DNA-binding activity has been observed for most acetylated DNA-binding

transcription factors, HMG I(Y) binds DNA less when it is acetylated (117). The

most striking observation is that only when HMG I(Y) is acetylated by CBP, not by

PCAF, is there a decrease in its DNA-binding activity (117). This phenomenon is

reminiscent of YY1 acetylation in its zinc finger domain by PCAF but not by p300,

and the consequent reduction in the DNA-binding activity of YY1.

We were also interested in finding out if acetylation of YY1 also contributes

to cellular events other than transcriptional control. So far, we have no evidence to

suggest that acetylation changes the sub-cellular localization of YY1 (data not

shown). YY1 has been shown to be a rather stable protein expressed at comparable

levels in both growing and differentiating cells (5). Interestingly, acetylation affects

the conformation of HNF-4 (147), the half-live of E2F (110), and promotes protein-

protein interactions between Rch1 and importin-β (9). Therefore, it will be

informative to test whether acetylation of YY1 may have similar consequences.

77

Recently it was demonstrated that YY1 null mutations resulted in peri-

implantation lethality in mice (38). In Drosophila, lack of a maternally derived YY1

homolog results in severe defects in pattern formation (16, 45). This Drosophila

homolog of YY1 was identified as PHO, which is encoded by pleiohomeotic, a

member of the Polycomb group (PcG) genes (18). PcG genes encode proteins

necessary for maintaining the repression state of homeotic genes in Drosophila, which

is absolutely essential for patterning (127, 146, 152). It has been proposed that the

Drosophila YY1 homolog, PHO, binds to PcG response elements and interacts with

other proteins to form a repressor complex (18). A Drosophila protein, dMi-2, has

been found to participate in PcG-mediated repression (82). dMi-2 shares high

sequence homology to the human autoantigen Mi-2. Xenopus Mi-2 homolog was

recently shown to be a subunit of a histone deacetylase complex with nucleosome

remodeling activity (164, 165). Incidentally, repression mediated by PcG proteins

resembles that of mating-type silencing in yeast and position-effect variegation in

Drosophila, both of which contain transcriptionally silent chromatin structures (112).

Therefore, it is possible that dMi-2 also forms a complex containing histone

deacetylase activity and nucleosome remodeling activity, and the interaction between

dMi-2 and PcG proteins like PHO is important in proper expression of homeotic

genes. Our study showing stable interactions between HDACs and YY1 also suggests

that association with chromatin-modifying activities is central to the functions of

YY1. YY1, PHO, and the Xenopus YY1 homolog FIII are almost completely

identical in the zinc finger region in amino acid sequence, reinforcing the role of YY1

as a DNA-targeting factor in nucleating a repressor complex capable of modulating

78

chromatin structures. Our data demonstrating that YY1 interacts with HDACs at two

different regions open the possibility that these two HDAC-interacting regions might

have distinct effects on YY1's role in transcriptional control. Perhaps the stable

association of YY1 with HDACs at the C-terminal zinc finger region represents an

ancient mode of the functions of YY1, which is to form a repressor complex

associated with the promoter. However, regulation of the affinity of the central region

of YY1 for HDACs by acetylation might have evolved as a more sophisticated means

of control, which defines a novel functional consequence of non-histone factor

acetylation.

In this dissertation, four different methods of purifying the YY1 complex are

presented: anion exchange chromatography followed by IMAC, anion exchange

chromatography followed by antibody-affinity chromatography, antibody-affinity

chromatography directly against a Flag-epitope, and RIPA. Upon comparison of the

YY1 complexes purified with different methods, it became apparent that four protein

bands exist in YY1 complexes purified by all four methods. These proteins most

likely represent genuine YY1-associated proteins.

Among the four candidate YY1 complex constituents, only one appears to

have a molecular weight higher than 200 kD. Gel filtration analysis of HeLa nuclear

extract suggests that YY1 exists in potentially two protein complexes, one with a very

high molecular weight, and the other one with a molecular weight of 150 kD. This

high molecular weight YY1-associated protein very likely represents a component of

the higher molecular weight YY1 complex. Other YY1-associated proteins with

molecular weights lower than 97 kD may or may not exist exclusively in the 150 kD

79

YY1 complex. Because the apparent molecular weight of YY1 on SDS-

polyacrylamide gels is different from the predicted molecular weight of YY1 based on

amino acid composition, it is difficult to estimate the stoichiometric composition of

the YY1 complex(s).

IMAC using Ni2+ resin following anion exchange chromatography may not be

an ideal method to purify a YY1 complex. First, this method intrinsically lacks a

proper control. As a result, without comparison to the YY1 complexes purified by

other methods, it would have been extremely difficult, if not impossible, to identify

true YY1-associated protein. Second, the amounts of proteins bound to the Ni2+

column, except for YY1 itself, appear to be quite low. This might account for the

lack of histone deacetylase activity from the eluate of this column. However, it is not

to exclude the possible application of Ni2+ resin in purifying other protein complexes.

Because the Flag epitope of the F-YY1 construct provides a strong epitope for

the anti-Flag beads, and the YY1 part of the F-YY1 construct is free to interact with

other proteins, purification of the F-YY1 complex might be the best method to purify

a YY1 complex based on its ease and true representation of the protein-protein

interactions. This method can be easily scaled up to facilitate large quantity

purification and subsequent micro-sequencing using a recombinant adenovirus

expressing F-YY1. Similarly, a recombinant adenovirus expressing F-YY1 (261-333)

can be made to infect HeLa cells and to purify a protein complex specifically

associated with residue 261-333 of YY1. This will provide valuable information

about the critical protein components involved in the histone deacetylase activity

associated with YY1.

80

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ABOUT THE AUTHOR

Ya-Li Yao received a Bachelor's degree in Biological Sciences from University of

California, Davis in 1995. She enrolled in the Ph.D program of Molecular Medicine at

the University of Texas, Health Sciences Center at San Antonio in 1996. Subsequently,

she transferred to the Ph.D. program in the Department of Medical Microbiology and

Immunology at the University of South Florida. She was awarded a Master's degree in

Medical Sciences in 1999 and a Ph.D. degree in 2001.

While in the Ph.D. program at the University of South Florida, Ya-Li Yao

received a graduate student fellowship from the American Heart Association as well as a

travel award from the University. She co-authored several publications in peer-reviewed

journals and received the Time Warner Road Runner ETD (Electronic Thesis and

Dissertation) Award in 2001.