14 - Gene Regulation in Eukaryotes

BIO 375: Genetics and Molecular Biology 1

14 - Gene Regulation inEukaryotes

Comparing Gene Regulation in Prokaryotes andEukaryotes

The lac operon provided an excellent example of how bacteriaperform gene regulation in response to an environment that lackedglucose yet contained lactose. In the case of the lac operon, welearned that gene regulation involves an activator protein (CAP) and arepressor protein (lac repressor). Effector molecules (cAMP andallolactose) regulate CAP and the lac repressor binding to DNAsequences near the lac operon structural genes. Ultimately thebinding of the CAP and the lac repressor proteins determined if sigma(σ) factor protein and the RNA polymerase core enzyme could activatetranscription.

Even though gene regulation in prokaryotes and eukaryotes is similar(both involve activator proteins, repressor proteins, and effectormolecules), eukaryotic gene regulation is more complex. Thiscomplexity is needed to produce multicellular eukaryotic organismswith cells in each tissue having unique phenotypes. For example, awhite blood cell (leukocyte) and a muscle cell have the samecollection of structural genes; however, gene regulation ensures thata leukocyte expresses leukocyte-specific proteins, while a muscle cellexpresses muscle-specific proteins. Further, many eukaryoticorganisms progress from a fertilized egg through complexdevelopmental stages to produce the mature adult organism. Gene


regulation ensures that embryonic genes are expressed only duringembryonic development, while other genes are expressed only in anadult.

Regulation of a typical eukaryotic gene involves combinatorialcontrol. For example, a single eukaryotic gene can be regulated by acombination of:

Activator proteins binding to enhancer DNA sequences.Repressor proteins binding to silencer DNA sequences.Regulation of the activities of the activator and repressorproteins. This regulation involves effector molecules, covalentmodification, and protein-protein interactions.Modifying the structure of chromatin to activate orrepress transcription. Modifying chromatin involves alteringthe structure and the arrangement of nucleosomes (see Part 2)near the core promoter of a gene.DNA methylation to silence transcription. The methylationof cytosine bases near the core promoter region of a geneinhibits transcription.

Key Questions

What is meant by combinatorial control?What factors can influence the transcription of a eukaryoticgene?

Core Promoter vs. Regulatory Promoter

We learned earlier this semester that transcription in eukaryotesinvolves several types of DNA sequences. The core promoter, forexample, determines where RNA polymerase II will bind to the DNAand begin transcription. The core promoter includes the TATA box(-25 sequence), which serves as the binding site for the generaltranscription factor protein TFIID and the +1 site, the first base in


the template DNA strand that is transcribed by RNA polymerase II. For transcription to occur, the TATA box and the +1 site must bepresent. If these two sequences are the only sequences presentupstream of a gene, the gene will be transcribed at a low, yet constantrate (the basal level of transcription).

In addition to the core promoter, many eukaryotic genes also includea regulatory promoter (see figure 14.1). The components of theregulatory promoter are required for transcription levels higher thanthe basal level provided by the core promoter. A common regulatorypromoter component that is present in many eukaryotic genes is theCAAT box. The CAAT box is located at -80 and has the sequence 5’-GGCCAATCT-3’. Another common regulatory promoter component isa GC box (5’- GGGCGG – 3’) located at -100. The CAAT and GC boxesare the binding sites for certain activator proteins. Thus, the CAATand GC boxes can be considered enhancers adjacent to manyeukaryotic structural genes.

Figure 14.1 Core and Regulatory Promoter --- Image created by SL


Key Questions

What is meant by basal transcription?What is the function of the regulatory promoter?What are the names of two common DNA sequences found inthe regulatory promoters of eukaryotic genes?

General and Regulatory Transcription Factors

Transcription factors are proteins that influence the ability of RNApolymerase II to bind to a eukaryotic core promoter. There aretwo categories of transcription factor proteins:

General transcription factor proteins (GTFs). The generaltranscription factor proteins include TFIID, TFIIA, TFIIB,TFIIF, TFIIE, and TFIIH. These proteins function to recruitRNA polymerase II to the core promoter to begin transcription. The general transcription factors are required for alltranscription events. If these general transcription factors arethe only proteins involved, the gene is transcribed at the basallevel. The general transcription factors are also required fortranscription rates above this basal level.Regulatory transcription factor proteins. Regulatorytranscription factors function to regulate transcription by eitherincreasing transcription above the basal level or decreasingtranscription below the basal level. An activator proteinincreases the level of transcription above the basal level; arepressor protein decreases the level of transcription belowthe basal level. Many activator and repressor proteins are onlyexpressed in certain tissues or at certain times duringdevelopment, thus playing a critical role in tissue-specific ortime-specific gene expression.


Transcription factors proteins are trans-acting factors (i.e., canregulate genes found throughout the genome) and bind to DNAsequences called cis-acting elements (i.e., the DNA binding sites forthese transcription factors tend to be near the genes they control)(see figure 14.2). However, these cis-acting elements do not need tobe immediately adjacent to the core and regulatory promoters. Sometranscription factor binding sites can be within the gene that theycontrol or can be thousands of base pairs away.

Recall that the mediator protein complex communicates the signalsfrom activator and repressor proteins to RNA polymerase II. Mediatorthus serves as a link between transcription factors that bind toenhancer and silencer DNA sequences and RNA polymerase II,thereby determining the overall rate of transcription.

Figure 14.2 Trans-acting factors binding to cis-acting elements. In this case, mediator interprets threeactivation signals and two silencing signals. Overall, transcription is increased above the basal level. --- Image

created by SL.


Key Questions

Review the functions of TFIID, TFIIH, and mediator.Which transcription components are considered trans-actingfactors?Which transcription components are considered cis-actingelements?

Enhancers and Silencers

Other regulatory DNA sequences assist the core promoter andregulatory promoter to regulate transcription by serving as thebinding sites for transcription factor proteins. The binding ofregulatory transcription factors to these DNA sequences may:

Increase the rate of transcription. Transcription canincrease 10 to 1000-fold when activator proteins bind toenhancer DNA sequences (up-regulation). Activator proteinsand enhancer DNA sequences are generally responsible fortissue-specific expression of a gene.Decrease the rate of transcription. Transcription candecrease below the basal level when repressor proteins bind tosilencer DNA sequences (down-regulation). Repressorproteins and silencer DNA sequences are generally responsiblefor tissue-specific repression of a gene.

A particular gene can be regulated by many transcription factorsbound to different combinations of enhancers and silencers (seefigure 14.2). The combination of the transcription factor proteinsand regulatory DNA sequences involved determines the transcriptionpattern of the gene.


Key Questions

Review the functions of activator proteins, repressor proteins,enhancer sequences, and silencer sequences.

Structural Features of Transcription Factors

Transcription factor proteins have been identified in many organisms,including bacteria, fungi, plants, and animals. Nearly all transcriptionfactor proteins contain conserved structural features that areimportant in either binding to regulatory DNA sequences, effectormolecules, or other transcription factor proteins. These structuralfeatures are called structural motifs.

The structural motifs found in transcription factors contain α-helices,a type of protein secondary structure. An α-helix is produced whencertain amino acids in the polypeptide sequence interact throughhydrogen bonding to produce a helical structure. An α-helix is theproper width to bind to the major groove in DNA. Thus, the α-helix isoften used by transcription factors proteins to recognize specificnucleotide sequences in the major groove of DNA.

The four common structural motifs that are found in transcriptionfactor proteins include (see figure 14.3):

Helix-turn-helix (HTH) motif. The helix-turn-helix motif isfound in both prokaryotic and eukaryotic transcription factorproteins. The HTH motif includes two α-helices separated by a“turn” of 3-4 amino acids. One α-helix is called therecognition helix, and functions to bind to the nitrogenousbases in the major groove of the DNA. The recognition helixalso includes many basic (positively charged) amino acids thatbind to the DNA backbone (negatively charged). Examples oftranscription factor proteins that contain the HTH motif includesigma (σ) factor, the lac repressor protein, and the


catabolite activator protein (CAP).Basic helix-loop-helix (bHLH) motif. The bHLH motif issimilar to the helix-turn-helix motif and contains a recognitionhelix. Instead of a turn, this type of transcription factor uses alonger loop of amino acids to connect two α-helices. bHLHtranscription factors play an important role in thedifferentiation of cells. For example, the MyoD protein,important in the differentiation of muscle cells, is a bHLHtranscription factor.Zinc finger motif. The zinc finger motif is composed of afinger-like structure composed of an α-helix (recognitionhelix) and two β-strands (another type of protein secondarystructure). Electrostatic interactions between zinc ions (Zn2+)and negatively charged amino acid side chains within thetranscription factor protein stabilize the zinc finger motif. Steroid hormone receptors, including the glucocorticoidreceptor transcription factor protein (see below), contain zincfinger motifs.Leucine zipper motif. The leucine zipper motif contains manyhydrophobic leucine amino acids in a row. When the leucine-rich regions on two transcription factors interact, they form acoiled-coil to exclude water. The coiled-coli resembles azipper. The DNA binding site is recognized by α-helices(recognition helices) that extend from the coiled-coil region ofthese two transcription factor proteins. The CREB protein (seebelow) contains a leucine zipper motif.

It is important to note that all transcription factor motif structuresallow transcription factors to bind to each other. Two identicaltranscription factors can interact to form a transcription factorhomodimer, or two different transcription factor proteins caninteract to form a heterodimer. Higher order interactions (trimers,tetramers) are also possible when transcription factor proteins bind toeach other.


Caption


Figure 14.3 Transcription Factor Structural Motifs a) Helix-turn-helix motif b) Basic helix-loop-helix motif c) Zincfinger motif d) Leucine zipper motif --- Images created by SL

Key Questions

What are three examples of transcription factor proteins thatcontain the helix-turn-helix (HTH) motif?What is an example of a transcription factor protein thatcontains the basic helix-loop-helix (bHLH) motif?What is an example of a transcription factor protein thatcontains the zinc finger motif?What is an example of a transcription factor protein thatcontains the leucine zipper motif?What protein secondary structure is found in all transcriptionfactor structural motifs?What is meant by a transcription factor homodimer orheterodimer?


Mechanisms to Regulate Transcription FactorProteins

If an activator protein is present in a cell, it does not always bind to anenhancer DNA sequence and up-regulate transcription. Similarly, arepressor protein does not always bind to a silencer DNA sequenceand repress transcription. The DNA-binding activities of activator andrepressor proteins is regulated in three general ways:

Effector binding. Small effector molecules can bind toactivator/repressor proteins, change the conformation of theactivator/repressor, and influence the ability of theactivator/repressor to bind to enhancer or silencer DNAsequences. In animals, steroid hormones such asglucocorticoid, testosterone, and estrogen are effectors thatregulate the functions of transcription factor proteins.Transcription factor dimerization. The formation oftranscription factor homodimers or heterodimers influences theability of the activator/repressor protein to bind toenhancer/silencer DNA sequences and influence transcription.Covalent modification. Phosphorylation can stimulateactivator/repressor proteins to bind to enhancer/silencer DNAsequences.

Note that for a particular gene, one or more of the above mechanismsmay be involved in regulating gene expression.

Key Questions

Describe the three ways that activator and repressor proteinscan be regulated?What is an example of a eukaryotic effector molecule?


Control of Transcription (TFIID)

We have seen that regulatory transcription factor proteins (activatorand repressor proteins) influence the ability of RNA polymerase II totranscribe a gene. However, these regulatory transcription factorproteins do not typically bind to RNA polymerase II directly. Instead,transcription factor proteins communicate DNA binding indirectly toRNA polymerase II through other protein complexes. Eukaryotictranscription factors influence RNA polymerase II activity throughTFIID, mediator, the enzymes involved in chromatin remodeling,and the enzymes involved in DNA methylation.

We will consider regulation of RNA polymerase II activity throughTFIID first. TFIID is a general transcription factor that binds to theTATA box (the -25 sequence) within the core promoter. TFIID recruitsthe other five general transcription factors (GTFs) that bring RNApolymerase II to the +1 site to initiate transcription.

Suppose an activator protein binds to an enhancer DNA sequence (seefigure 14.4). This activator protein then encourages TFIID to bind tothe TATA box, and TFIID then recruits the other general GTFs andRNA polymerase II to the +1 site. As a result, transcription is upregulated.

Suppose instead that a repressor protein binds to a silencer DNAsequence. The repressor protein then prevents TFIID from binding tothe TATA box. The absence of TFIID on the core promoter preventsthe other GTFs and RNA polymerase II from binding to the corepromoter. As a result, transcription is down regulated.


Figure 14.4 Regulating TFIID - Image created by SL

Key Questions

How do activator and repressor proteins influence TFIID?

Control of Transcription (mediator)

Mediator is a protein complex that mediates the interaction betweenthe regulatory transcription factors (i.e., activator and repressorproteins) and RNA polymerase II. If mediator activates RNApolymerase II, transcription begins.


Suppose an activator protein binds to an enhancer DNA sequence (seefigure 14.5). The activator protein in turn activates mediator, andmediator then activates the general transcription factor TFIIH. Next,TFIIH acts as a helicase to separate the template and coding DNAstrands. TFIIH also acts as a kinase, phosphorylating RNApolymerase II to begin transcription.

Suppose a repressor protein binds to a silencer DNA sequence. Therepressor protein inhibits the activity of mediator. Mediator fails toactivate TFIIH, and TFIIH fails to separate the template and codingDNA strands. TFIIH also fails to phosphorylate RNA polymerase II,preventing the initiation of transcription.

Note that the DNA between the enhancer/silencer DNA sequencesand the core promoter can form a loop to permit the proteinsdescribed above to bind to each other.


Figure 14.5 Regulating Mediator --- Image created by SL

Key Questions

How do activator and repressor proteins influence the activityof mediator?

An Example of Transcription Activation(glucocorticoid receptor)

Steroid hormones produced by endocrine glands can activate thetranscription of many genes. One example is a group of steroidhormones called glucocorticoid hormones (GCs) produced by the


adrenal glands. Glucocorticoid hormones are produced in response tofasting as well as physical activity, leading to an increase in glucosesynthesis, an increase in protein metabolism, an increase in fatmetabolism, and a decrease in inflammation. Other steroid hormones,such as estrogen and testosterone, influence the development ofgonad tissue.

Glucocorticoid hormones can increase the transcription of a geneabove the basal level as follows (see figure 14.6):

GCs are steroid hormones, which are nonpolar in structure. As1.a result, these nonpolar steroid hormones cross the cytoplasmicmembrane and enter the cytoplasm of a target cell.GCs act as effector molecules by binding to an inactive2.activator protein called glucocorticoid receptor (GR) that isfound in many cell types. Prior to GC binding, GR is bound toHSP90 proteins. HSP90 helps maintain the proper three-dimensional shape of GR, so that GR can bind to GC when GCsare produced by the adrenal glands.GC binds to GR and HSP90 is released.3.GC binding changes the conformation of GR, exposing a4.nuclear localization signal (NLS). The NLS is a polypeptidesequence that helps to target the GR (with bound GC) to thenucleus of the cell.Two GRs (with bound GC hormones) from a homodimer in the5.cytoplasm of the cell.The GR homodimer travels to the nucleus of the cell.6.The GR homodimer binds to an enhancer DNA sequence called7.a glucocorticoid response element (GRE). GREs arecommon enhancers found adjacent to many genes involved inmetabolism.GR bound to GRE activates transcription.8.


Figure 14.6 Transcription Regulation by Glucocorticoid --- Image created by SL

Key Questions

What is GC, GR, and GRE?How does the production of GC by the adrenal gland lead totranscriptional activation of a target gene?

An Example of Transcription Activation (CREB)

Many signaling molecules in the body, such as peptide hormones,


growth factor proteins, and cytokine proteins, are not able to diffusethrough the cytoplasmic membrane into the cytoplasm of the targetcell. Instead, these signaling proteins bind to cell receptors on thesurface of a target cell, and binding of the signaling protein to thereceptor is transmitted to the nucleus to activate transcription.

Consider how transcription is activated by an activator protein calledcAMP response element-binding protein (CREB). CREB activatestranscription when (see figure 14.7):

A receptor embedded in the cytoplasmic membrane binds to a1.peptide hormone, growth factor, or cytokine protein.The binding of the signaling protein to the receptor activates a2.G protein.The G protein activates adenylyl cyclase inside the cell, which3.converts ATP into cAMP.cAMP binds to and activates protein kinase A (PKA).4.PKA moves into the nucleus and phosphorylates the inactive5.CREB protein homodimer.The phosphorylated CREB protein homodimer binds to6.enhancer sequences called cAMP response elements(CREs).CREB bound to CRE activates transcription.7.


Figure 14.7 Transcriptional Regulation by CREB --- Image created by SL

Key Questions

What is CREB and CRE?How does the binding of a peptide hormone to a receptor leadto transcriptional activation of a target gene via the CREBpathway?


Chromosome Compaction and Transcription

The arrangement of nucleosomes (see Part 2) can also influence thetranscription of a eukaryotic gene. For a gene to be transcribed, RNApolymerase II must be able to bind to the core promoter. If the corepromoter region of a gene is in a chromosomal region with tightlypacked nucleosomes (heterochromatin), RNA polymerase IIstruggles to bind to the core promoter. As a result, theheterochromatin form of DNA is said to be in a closed conformationand transcription is limited. Regions of the chromosome with looselypacked or absent nucleosomes are called euchromatin (openconformation). RNA polymerase II can access a core promoterlocated in euchromatin, and as a result, transcription occurs.

Chromatin is a dynamic structure with a specific region of DNAalternating between the closed and open conformations depending onthe needs of the cell. When an activator protein binds to an enhancerDNA sequence, chromatin is converted to the open conformation. When a repressor protein binds to a silencer DNA sequence,chromatin is converted to the closed conformation.

Key Questions

Review the structure of a nucleosome and the termsheterochromatin and euchromatin (see Part 2).What is the difference between the open conformation and theclosed conformation?

Arrangement of Chromatin at the β-globin Gene

As an example of how chromatin structure can influence thetranscription of a gene, consider the human β-globin gene (see figure14.8). The β-globin gene, which encodes the β-globin proteincomponents of hemoglobin, is not normally expressed in many cell

https://equitypress.org/genetics_and_molecul/13___chromosome_comp


types, including fibroblast cells. When the DNA region thatencompasses the β-globin gene from fibroblasts was analyzed withrespect to nucleosomes, scientists discovered that nucleosomes arefound in regular intervals from -3000 to +1500. Thus, the β-globingene in fibroblasts is in the closed conformation (heterochromatin)and is not accessible to the general transcription factors (GTFs) andRNA polymerase II. As a result, the β-globin gene is transcriptionallysilent in fibroblasts.

The β-globin gene is expressed in erythroblasts (precursor red bloodcell). When the nucleosome arrangement surrounding the β-globingene was examined in erythroblasts, a different result was observed. Nucleosomes are displaced from the -500 to +200 region of the gene. This open conformation (euchromatin) area includes the regulatoryand core promoters. Thus, the GTFs and RNA polymerase II canaccess the promoter region, leading to the transcription of the β-globin gene in erythroblasts.

Figure 14.8 Nucleosome arrangement on the B-globin gene --- Image created by SL


Key Questions

In terms of the core promoter for the β-globin gene, describethe difference between chromatin structure in fibroblasts anderythroblasts.

Histone Acetylation

The results from fibroblasts and erythroblasts discussed abovesuggest that nucleosomes can be altered to influence transcription. Alterations in chromatin structure to promote transcription includethe covalent modification of histone proteins and therearrangement of nucleosomes by ATP-dependent chromatinremodeling (see figure 14.9).

Covalent modification involves the acetylation, methylation, andphosphorylation of histone proteins within nucleosomes. Acetylation will serve as an example of the covalent modification ofhistones. Enzymes called histone acetyltransferases (HATs) addacetyl groups to the tails of histone proteins. Specifically, acetylationneutralizes the positive charge on lysine amino acids within thehistone tail, disrupting the interaction between the histone tail andthe negatively charged DNA backbone. Neutralization of the positivecharges on the histone tails cause the histones to release from theDNA; the DNA is now accessible for transcription.

When transcription needs to be turned off, the histones can bemodified using histone deacetylase (HDAC) proteins. HDACsremove the acetyl groups from histones, restoring the positive chargeon the histone tail. As a result, the histone tails once again bind to thenegatively charged DNA backbone, and the chromatin is converted tothe closed conformation (heterochromatin), decreasing transcriptionof the gene.


Note that when an activator protein binds to an enhancer DNAsequence, the activator recruits HATs to the promoter, activatingtranscription. Alternatively, when repressor proteins bind to silencerDNA sequences, HDACs are recruited to the promoter, silencingtranscription.

ATP-dependent Chromatin Remodeling

The ATP-dependent chromatin remodeling process uses the energy inATP to alter nucleosomes (see figure 14.9). One example of anATP-dependent chromatin remodeling enzyme is a multi-subunitcomplex called SWI/SNF. SWI/SNF performs at least three types ofchromatin remodeling:

SWI/SNF can change the distribution of nucleosomes along theDNA, creating gaps between adjacent nucleosomes. This gapbetween nucleosomes includes the core promoter region of agene.SWI/SNF can release some of the core histones from thenucleosome, destabilizing the nucleosome. When thenucleosome is destabilized, the core promoter region isaccessible for transcription.SWI/SNF can replace the standard histone proteins (H2A, H2B,H3, and H4) with histone variant proteins. The presence ofthese histone variant proteins within the modified nucleosomeincreases transcription.


Figure 14.9 Histone Acetylation and ATP-Dependent Chromatin Remodeling --- Images created by SL.


Key Questions

When a HAT is active, what effect does this have ontranscription?When a HDAC is active, what effect does this have ontranscription?What is the function of the SWI/SNF complex?

Overview of DNA Methylation

Silencing of gene expression in many eukaryotes involves themethylation of DNA sequences near genes. The methyl group that isadded to the DNA double helix blocks the major groove of the DNA,preventing the binding of activator protein to the DNA. Cytosine baseswithin CG-rich sequences called CpG islands are typically targets formethylation. Not surprisingly, many CpG islands are located near thecore promoters of genes (see figure 14.10). Typical CpG islands are1,000 – 2,000 base pair (bp) long sequences that contain multiple CpGsites (i.e., many 5’-CG-3’ sequences in a row). Within CpG islands,adding methyl groups to the cytosine bases on both DNA strands iscalled full methylation. Full methylation inhibits transcription.

Figure 14.10 Overview of DNA Methylation. CpG islands are the targets for DNA methylation to silence a gene. ---Image created by SL

Housekeeping genes encode proteins that are required for cellviability. The promoters of these genes are unmethylated and as a


result, housekeeping genes are always transcribed. Tissue-specificgenes are only expressed in certain cell types. In cell types in whichthese genes are not expressed, the CpG island near the promoter isfully methylated. In cell types in which the gene is expressed, theCpG island near the promoter is unmethylated. As a final example,the inactive X chromosome (Barr body) in female mammals containsmethylated CpG islands adjacent to most structural genes.

Key Questions

How does methylation alter the structure of DNA?Where are many CpG islands located?In terms of DNA methylation, what is the difference between ahousekeeping gene and a tissue-specific gene?

Methylation Blocks Activator Proteins and RecruitsHDACs

DNA methylation is thought to silence the transcription of a nearbygene in two general ways. First, methylation at a CpG island near thepromoter of a gene can block an activator protein from binding to anenhancer DNA sequence (see figure 14.11). DNA methylationinhibits activator binding because the methyl group on cytosineprevents the activator protein from binding to the major groove in theenhancer region.

Second, methylated CpG islands near promoters serve as the bindingsites for a group of proteins called methyl-CpG-binding proteins. When a methyl-CpG-binding protein binds to a methylated CpG island,the methyl-CpG-binding proteins can recruit a histone deacetylase(HDAC). HDAC then removes the acetyl groups from the histone tails,converting the promoter region of the gene into heterochromatin. Transcription of the nearby gene is therefore inhibited.


Figure 14.11 Methylation Inhibits Transcription --- Image created by SL

Key Questions

Describe the two ways that DNA methylation can inhibittranscription.

DNA Methylation is Preserved During Cell Division

The DNA methylation pattern in the cell is established by a processcalled de novo methylation (see figure 14.12). De novomethylation converts unmethylated DNA to full methylation (bothDNA strands methylated). De novo methylation is a highly regulatedprocess that is thought to occur during embryonic and tissuedevelopment.


The DNA methylation pattern established during de novo methylationis preserved during cell division. For example, if a CpG island is fullymethylated in a cell prior to mitosis, the same CpG island is fullymethylated in the daughter cells after mitosis. Maintenancemethylation ensures that the daughter cells produced by mitosismaintain the same methylation pattern as the parental cell. As anexample, suppose that fully methylated DNA is replicated. Becausethe DNA replication machinery does not methylate bases duringreplication, the daughter DNA strands produced do not containmethylated cytosines. Thus, the daughter double-stranded DNAmolecules are initially hemimethylated, with a methylated parentalstrand and an unmethylated daughter DNA strand. Thishemimethylated DNA is recognized by DNA methyltransferase,which subsequently methylates the cytosine bases on the daughterDNA strands, thus preserving the DNA methylation patternestablished in the parental cell.

Methylation of DNA explains a phenomenon called genomicimprinting. In oogenesis (egg cell formation) or spermatogenesis(sperm cell formation), a specific gene is methylated by de novomethylation. Following fertilization, the methylation pattern ismaintained as the fertilized egg begins to divide. For example, if thematernal allele for a gene is fully methylated, that maternal alleleremains fully methylated in the cells of the offspring. We will discussgenomic imprinting more in Part 15.


Figure 14.12 Preserving DNA Methylation During Cell Division --- image created by SL

Key Questions

What is the difference between de novo and maintenancemethylation?What is the name of the enzyme responsible for maintenancemethylation?What is meant by genomic imprinting?

Insulators

In eukaryotes, the processes that regulate the expression of one gene


(activators/repressor proteins bound to enhancer/silencer DNAsequences, altering chromatin structure, and DNA methylation) do notnecessarily influence the regulation of an adjacent gene. DNAsequences called insulators function to define the boundariesbetween genes (see figure 14.13); an insulator sequence ensuresthat the gene regulation processes that affect one gene do not affectnearby genes.

Insulator DNA sequences can:

Serve as the binding sites for proteins that act as physicalbarriers for the HATs, HDACs and SWI/SNF complexes.For example, suppose a gene is flanked by two insulator DNAsequences, and HATs modify histone tails and activatetranscription of the gene. Because the proteins bound toinsulators serve as physical barriers to the HATs, genes beyondthe insulator sequences are not activated.Serve as the binding sites for proteins that limit theeffects of enhancer/silencer sequences. Suppose that GeneA has an adjacent enhancer DNA sequence. Gene B is also nearthe enhancer DNA sequence. A protein bound to the insulatorDNA sequence between Genes A and B ensures that theenhancer only activates Gene A; the transcription of Gene B isunaffected. Insulators can limit the effects of silencer DNAsequences in a similar manner.


Figure 14.13 Insulators --- Image created by SL

Key Questions

What is an insulator DNA sequence?How do insulators ensure that gene regulation is limited to asingle gene?

Part 14 Review

Fill in the blank:


The core promoter consists of two consensus DNA sequences1.located at position ______________ and ______________.The general transcription factor (GTF) proteins are2.________________________________________________________________.Some examples of regulatory transcription factor proteins are3.____________________, which increase transcription and_________________________, which decrease transcription belowbasal levels.Transcription factor proteins contain structural motifs. Two4.transcription factors with the _____________________ motifinteract and form a coiled coil. Two alpha-helices are part of a______________________ motif seen in proteins involved in musclecell differentiation.The interaction of two identical transcription factor proteins to5.produce one molecule is called a ________________________.One example of a steroid hormone is6.________________________________________.A glucocorticoid receptor is bound to _________________ until a7.glucocorticoid molecule comes along and binds to the receptorthus liberating it.CREB is a (protein OR DNA sequence; circle the correct8.answer), whereas CRE is a (protein OR DNA sequence; circlethe correct answer).Upon its activation in the CREB system, protein kinase A (PKA)9.enters the nucleus and phosphorylates CREB which then leadsto transcription being (turned ON or turned OFF; circle thecorrect answer).Histone acetyltransferases add acetyl groups to _______________10.amino acids on the histone tail.Acetyl groups are removed from histone tails by enzymes called11._____________________________________________.Methyl groups added to cytosine bases usually project into the12.(major OR minor; circle the correct answer) groove of the DNA.Housekeeping genes are usually (methylated OR unmethylated;13.circle the correct answer) while tissue-specific genes are


(methylated or unmethylated; circle the correct answer) in cellsthat do not express the gene._________________ methylation ensures that the methylation14.pattern continues in the daughter cells produced by mitosis.


Dewall, M. (n.d.). BIO 375: Genetics and MolecularBiology. BYU-I Books.https://books.byui.edu/genetics_and_molecul

https://books.byui.edu/genetics_and_molecul

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14 - Gene Regulation in Eukaryotes