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Chapter 4 Transcription in Eukaryotes: Mechanism and
Regulation4.1 Eukaryotic RNA
polymerases
4.2 Eukaryotic Promoters
4.3 General Transcription
Factors and Initiation
4.4 Specific Transcription Factors
and Transcriptional Regulation
4.5 Structures of specific
transcription factors
4.6 Experiments
4.1 真核生物 RNA 聚合酶
4.2 真核生物启动子4.3 通用转录因子与 转录起始4.4 特异转录因子与 转录调控4.5 特异转录因子的结构
4.6 实验研究
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Transcription in Eukaryotes: Mechanism and Regulation
真核生物转录:机理与调控
Prokaryote Eukaryote
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Transcription in prokaryotes
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Transcription in eukaryotes
Eukaryotic RNA polymerase II and transcription factors
Specific transcription
factor
General transcription
factorsGeneral
transcription factors
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4.1 Eukaryotic RNA polymerases真核生物 RNA 聚合酶
Table 5.1 Eukaryotic RNA polymerases and their roles
表 5.1 真核生物 RNA 聚合酶 和它们的作用
Polymerase Location Products
Polymerase I Nucleolus A large rRNA precursor for 5.8S, 18S, and 28S rRNAs
Polymerase II Nucleoplasm hnRNAs (precursors for mRNAs) and most of the snRNAs
Polymerase III Nucleoplasm Precursors for 5S rRNA and 4.5S tRNAs, and U6 snRNA, etc.
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Locations of RNA polymerases
Nucleolus ( RNA polymerase I )
Nucleoplasm ( RNA polymerase II and III )
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RNA polymerase I
RNA polymerase IrRNAprecursor
Processing
5.8SrRNA
18SrRNA
28SrRNA
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RNA polymerase III
RNA polymerase IIIRNAprecursor
Processing
5SrRNA4.5S
tRNA
U6snRNA
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RNA polymerase II
RNA polymerase II RNAprecursor
Processing
snRNAs
Translation
Protein
mRNA
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RNA polymerase II
Holoenzyme: Core enzyme (β’, β & α) + Subunit σ
RNA pol II: Core subunits (1, 2 & 3) + Subunits 4-12
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RNA polymerase II
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4.2 Eukaryotic Promoters真核生物启动子
Prokaryoticpromoter
Eukaryotic promoter
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Eukaryotic Promoters真核生物启动子
“I would like to have TATA box and Initiator as
my promoter. What would you like?”
“Well, I prefer BRE and DPE.”
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TATA box
TATAAA-10 boxTATAAT
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Specialized genes have TATA boxes
TATA box
Specialized genes +
Housekeeping genes –
Genes of development –
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DPE: Downstream Promoter Element
G CGAT
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Initiator / 起始子
PyPyAN PyPyTA
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BRE: TFIIB Recognition Element
CGCCGGGCCA
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4.3 General Transcription Factors and Initiation (通用转录因子与转录起始)
Prokaryotic RNApolymerase
pre-initiation complex
IIA
IIFIIBIIE
IIH
RNA pol IITATAbox
IID
Eukaryotic RNApolymerase II:“I need help fromother proteins.”
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4.3.1 TFIID
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TBP: TATA-Binding Protein
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Show 3D structure of TBP
File: TBP-TATA box complex 1.val
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TAFIIs: TBP-Associated Factors II
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TAFIIs: 1) Binding to DPE or Inr
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TAFIIs: 2) Binding to Activator
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4.3.2 Other TFIIs
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Now showing
Initiation of Transcription
File: biophoto7 \ Life \ Initiation of transcription (5’)
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4.3.3 General Transcription factors for RNA Polymerase I and III
RNA 聚合酶 I 和 III 的通用转录因子
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1. General TFs of RNA polymerase I
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2. General TFs of RNA polymerase III
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General TFs of RNA polymerase III
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4.4 Specific Transcription Factors and Transcriptional Regulation
特异转录因子与转录调控
RNA pol II
TATAbox
Specific transcription factor
IIA
IIFIIBIIE
IIHIID
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Specific Transcription Factors and Transcriptional Regulation
特异转录因子与转录调控
4.4.1 Activators / 激活蛋白
4.4.2 Repressors / 阻遏蛋白
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4.4.1 Activators / 激活蛋白
Specific transcription factors that enhance the rate of transcription are called activators.
能提高转录速率的特异转录因子称为激活蛋白。
1. Help recruit the pre-initiation complex.
2. Help organize the subunits of the pre-initiation complex, and maintain cohesion of the complex.
3. Attract enzymes to loosen DNA from proteins, freeing important regions like the promoter.
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1. Help recruit the pre-initiation complex
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2. Help organize the subunits of the pre-initiation complex
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3. Attract enzymes to loosen DNA
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4.4.2 Repressors / 阻遏蛋白Specific transcription factors that prevent the transcription of a gene are called repressors.
能阻碍基因转录的特异转录因子称为阻遏蛋白。
1. Blocking the activity of activators.
2. Blocking access of the pre-initiation complex to the promoter.
3. Recruiting enzymes that tighten DNA around proteins.
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1. Blocking the activity of activators
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2. Blocking access of the pre-initiation complex to the promoter.
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3. Recruiting enzymes that tighten DNA around proteins
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4.4.3 Enhancers and Silencers增强子和沉默子
Specific transcription factors rely on DNA sequences to tell them how each gene should be regulated. These sequences are called enhancers or silencers, depending whether they bind activators or repressors, respectively.
特异转录因子依靠DNA 序列来告诉它们应该怎样调控每一种基因。这些序列称为增强子或沉默子,分别依赖于它们结合的是激活蛋白还是阻遏蛋白。
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Enhancers and Silencers
Transcriptionis activated
Enhancer
Transcriptionis repressed
Silencer
Repressor
Activator
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DNA looping / DNA 成环
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Sea Urchin Endo 16 gene
A red sea urchin红海胆
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4.5 Structures of Specific Transcription Factors
4.5 特异转录因子的结构
?
?
Prokaryotic
Eukaryotic
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Major Groove vs. Minor Groove
Major grooveA ≠ TG≠ C
Minor grooveA ≈ TG ≈ C
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4.5.1 DNA-Binding Motifs in Prokaryotes原核生物 DNA 结合基序
Recognitionhelix
The helix-turn-helix(HTH) motif
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Negative Regulation – the lac Repressor负调控── lac 阻遏蛋白
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Show 3D structure of the lac repressor
File: lac repressor with DNA.val
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The trp repressor
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The trp repressor
Trp
Trp repressor
DNA
E. coli
Operator
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Show 3D structure of the trp repressor
File: trp repressor.val
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4.5.2 DNA-Binding Motifs in eukaryote真核生物 DNA 结合基序
1. The homeodomain
同源异型域2. Zinc finger motif
锌指基序3. Leucine zipper
亮氨酸拉链4. HLH motif
螺旋 - 环 - 螺旋基序 ?
Eukaryotic
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1. The homeodomain / 同源异型域
Similar to HTHof prokaryotes
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Mutation of homeotic genes
Homeotic genes
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Show 3D structure of homeodomain
File: Homeodomain.val
Baird-Titus JM, et al. The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site J. Mol. Biol. v356, p.1137-1151
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2. Zinc finger motif / 锌指基序
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Show 3D structure of zinc fingers
Finger 1
Finger 2
Finger 3
File: Zinc finger.val
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3. Leucine zipper / 亮氨酸拉链
Leucines
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Heterodimerization / 异源二聚化作用
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Show 3D structure of leucine zipper
Wu SW, et al. Design and characterization of a multimeric DNA binding protein using Sac7d and GCN4 as templates Proteins v60, p.617-628
File: Leucine zipper.val
Yeast cells www.zeiss.de/C12567BE0045ACF1/ContentsWWWInte
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4. Helix-loop-helix motif / 螺旋 - 环 - 螺旋基序
The helix-loop-helix(HLH) motif
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HLH versus HTH
The helix-loop-helix(HLH) motif
The helix-turn-helix(HTH) motif
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Show 3D structure of HLH
Ferre-D'Amare AR, et al. Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain Nature v363, p.38-45
File: HLH.val
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4.6 Experiments / 实验研究
5.5.1 RNA polymerase targets RNA 聚合酶的目标
5.5.2 Modularity of Specific Transcription Factors 特异转录因子的模块化
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4.6.1 RNA polymerase targetsRNA 聚合酶的目标
Table 5.1 Eukaryotic RNA polymerases and their roles
表 5.1 真核生物 RNA 聚合酶 和它们的作用
Polymerase Location Products
Polymerase I Nucleolus A large rRNA precursor for 5.8S, 18S, and 28S rRNAs
Polymerase II Nucleoplasm hnRNAs (precursors for mRNAs) and most of the snRNAs
Polymerase III Nucleoplasm Precursors for 5S rRNA and 4.5S tRNAs, and U6 snRNA, etc.
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α- amanitin / α 鹅膏蕈碱
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Why is α- amanitin poisonous?
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Functions of RNA polymerases
RNA polymerase IRNA polymerase IIRNA polymerase III
rRNA precursor
High concentrationof α-amanitin
RNA polymerase Iproduces rRNAprecursors.
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Functions of RNA polymerases
RNA polymerase IRNA polymerase IIRNA polymerase III
rRNA precursortRNA, 5S rRNA …
Low concentrationof α-amanitin
RNA polymerase IIIproduces tRNA, 5S rRNA and other snRNAs.
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4.6.2 Modularity of Specific Transcription Factors
特异转录因子的模块化
Moduleexchange
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The reporter genes / 报告基因physicalsciences.ucsd.edu/outreach/image_gall...
www.bio-itworld.com/archive/091103/russell.html
Brain cancer models Human U-87-RFP glioma growing in brain of nude mouse.脑瘤模型:生长在裸鼠脑中的人神经胶质瘤 www.metamouse.com/brain.html
RFP
GFP
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The modularity of Gal4
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The modularity of Gal4
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The modularity of Gal4