Module IV: Control of Gene Expression PDF

Module IV: Control of Gene Expression Lecture Outline Part I: Intranuclear Gene Regulation 1. Transcriptional Control - A. Histone and DNA Modifications - B. Transcription Factors 2. RNA Processing (alternative splicing) Part II: Cytoplasmic Gene Regulation (part II) TRANSCRIPTIONAL CONTROL H...

Module IV: Control of Gene Expression Lecture Outline Part I: Intranuclear Gene Regulation 1. Transcriptional Control - A. Histone and DNA Modifications - B. Transcription Factors 2. RNA Processing (alternative splicing) Part II: Cytoplasmic Gene Regulation (part II) TRANSCRIPTIONAL CONTROL HISTONE + DNA MODIFICATIONS 1A Histone and DNA Modification Chromatin structure can influence genome expression • if a gene is accessible, then its transcription is influenced by the precise nature and positioning of the nucleosomes A gene can be activated or silenced 1A Histone and DNA Modification A. ACTIVATING THE GENOME: Histone acetylation and Nucleosome remodelling 1A Histone modification determine Chromatin Structure The octamer comprises a central tetramer of two histone H3 (blue) and two histone H4 (bright green) subunits plus a pair of H2A (yellow)–H2B (red) dimers Histone acetylation – the attachment of acetyl groups to lysine amino acids in the Nterminal regions of each of the core molecules by Histone Acetyl Transferase (HATs) 1A Histone Acetylation • Acetylation reduces the affinity of the histones for DNA • Possibly also reduces the interaction between individual nucleosomes Generally… Euchromatin: histones are acetylated Heterochromatin: histones are deacetylated 1A Histone Acetylation Acetylation and deacetylation of the lysine residue. 1A Nucleosome Remodeling Nucleosome remodeling influences the expression of individual genes • modification or repositioning of nucleosomes within a short region of the genome • Three types of change can occur: – Remodeling – Sliding/ cis -displacement – Transfer/ trans – displacement • Involves Swi/Snf chromatin-remodeling complex 1A Nucleosome Remodeling Different ways nucleosomes be remodeled 1A Nucleosome Remodeling How? Mechanisms that allow DNA accessibility. a | A stable nucleosome. b | A remodelled nucleosome. c | An evicted nucleosome 1A Histone and DNA Modification SILENCING THE GENOME: Histone deacetylation DNA methylation (Histone Methylation) 1A Histone Deacetylation Histone deacetylation represses gene expression • removing acetyl groups from histone tails • This is the role of the histone deacetylases (HDACs). • Increases the affinity of the DNA for nucleosome Prevents the access of the general transcription factors to the promoter, so transcription is repressed. 1A DNA Methylation Genome silencing by DNA methylation • In eukaryotes, cytosine bases in chromosomal DNA molecules are sometimes changed to 5methylcytosine by the addition of methyl groups by enzymes called DNA methyltransferases. 1A DNA Methylation Two types of Methylation: Maintenance methylation (DNMT – DNA Methyl Transferase protein) De novo methylation 1A • Active genes are located in unmethylated regions. • In humans, 40–50% of all genes are located close to CpG islands • Housekeeping genes have unmethylated CpG islands. • methyl-CpG-binding proteins(MeCPs) are components of both the Sin3 and NuRD histone deacetylase complexes – promote chromatin packing 1A DNA Methylation Prevents Transcription Mechanisms of transcriptional repression by DNA methylation. A stretch of nucleosomal DNA is shown with all CpGs methylated 1) Many transcription factors are repelled by methylation. 2) protein complexes can be attracted by methylation Mec - methyl-CpG binding protein 2 MBD – Methyl-CpG binding domains 1A DNA Methylation can promote Histone Deacetylation A model for the link between DNA methylation and genome expression 1A Epigenetic inheritance • Covers any difference in phenotype of an organisms that does not result from changes in nucleotide sequence. – The ability of daughter cells to retain the memory for gene expression pattern observed in the parent cell is an example. In reality, It’s actually more complicated… 1A TRANSCRIPTIONAL CONTROL TRANSCRIPTION FACTORS 1B Transcription Factors DNA-Binding proteins that can activate, enhance, and repress transcription. Common Structures of DNA Binding Proteins: 1. HTH (Helix Turn Helix) 2. Homeodomain 3. HLH (Helix Loop Helix) 4. Zinc Fingers 5. Leucine Zipper 1B Transcription Factors 1B Transcription Factors 1B Transcription Factors 1B Transcription Factors 1B Transcription Factors 1B Transcription Factors 1B General Transcription 1B Transcription (More details) PROKARYOTIC (Module III) EUKARYOTIC 1. Promoter Region 2. RNA Polymerase Holoenzyme 1. Promoter Region 2. Transcription Factors 3. RNA Polymerase (I, II, III) STEPS: 1. Initiation 2. Elongation 3. Termination E coli RNA Polymerase: 1B Initiation of Transcription Promoter Region B. Specific Transcription Factor: Other DNA Consensus Sequence: - TFIIB Recognition Elements (BRE) - Enhancers – Stimulates/ Enhances transcription - Repressors – Represses/ Attenuate Transcription A. General Transcription Factors (GTF): TFIID - TATA Binding Protein + TAF (TBPAssociated factors) TFIIH, TFIIE, TFIIF, TFIIA, TFIIB Yap et al. 2018 1B Initiation of Transcription STEPS – General Transcirption 1. TFIID (TBP + TAF) binds to promoter region 2. Recruits TFIIB (2nd GTF) 3. TBP-TFIIB binds RNA Pol II along with TFIIF 4. TFIIE and TFIIH binds to form the Pre-initiation complex (PIC) 5. TFIIH acts as helicase to open DNA and kinase to phosphorylate CTD of RNAPolII 6. Phosphorylation of CTD (5th Ser), releases RNA Pol from the PIC and initiate transcription. 7. p-CTD acts as binding site for elongation factors and Chromatin remodeling factors to facilitate Transcription 1B Elongation (Review) Free RNA Nucleotides RNA polymerase A T C C A A T U T C A U C C A G T A G G T Direction of transcription A T A G U G T C A C C Template strand of DNA Newly made RNA Synthesis of mRNA from 5’ -> 3’ direction 1B Termination (Review) 2 Types A. Rho-Indepedent - Inverted Repeat - GC-rich Hairpin loop, followed by 7A’s B. Rho- Dependent Steps: 1. Rho Sequence binds to the mRNA 2. Moves along mRNA 5’ -> 3’ 3. Rho acts as a helicase and separates RNA from DNA Kaplan et al. 2003 Current Biology 1B TRANSCRIPTIONAL CONTROL BRINGING EVERYTHING TOGETHER Regulation of Transcription Initiation TRANSCRIPTIONAL CONTROL BY DIRECT INFLUENCE OF ACTIVATORS AND REPRESSORS: - Activators stimulate the assembly of transcription initiation complex - Repressors interfere with transcription initiation complex 1 Regulation of Transcription Initiation 1 Regulation of Transcription Initiation Activation of Transcription. 1. Activation Protein binds to DNA 2. Recruits Histone modification Enzymes 3. Histone PTM 4. Recruits Chromatin Remodeling Complex 5. Recruits Transcription Factors 6. Transcription machinery assembles 7. Initiate Transcription 1 Regulation of Transcription Initiation Repressors Interfere Directly with Transcription Initiation • repressor is any protein that interferes with transcription initiation when it is bound to a specific site on DNA Repression of Transcription: 1. Competitive DNA Binding 2. Masking of Activation Surface 3. Direct Interaction with TF 4. Recruitment of Histone Modifying Enzymes 5. Recruitment of Chromatin Remodeling Complex 1 Regulation of Transcription Initiation 1 Regulation of Transcription Initiation 1 Regulation of Transcription Initiation 1 Regulation of Transcription Initiation 1 Regulation of Transcription Initiation 1 Regulation of Transcription Initiation 1