MCB 252 Topic 9 Chromosome Organization and Gene Regulation I Prof David Rivier MCB 252 Spring 2015 Reading Lodish sections 6 1 6 6 6 7 II Chromosome Organization and Gene Regulation I Signal Reception Amplification Transmission Response Activation Repression of genes Distribution of the genetic information II Chromosome Organization and Gene Regulation I New questions How is the expression of a gene regulated at the transcriptional level How is the expression of a gene regulated at the posttranscriptional level How are mRNAs exported to the cytoplasm What regulates protein homeostasis II Chromosome Organization and Gene Regulation I Regulation of transcription A mammalian organism needs to regulate the expression of 20 000 25 000 protein coding and 1000s of non protein coding RNA genes In eukaryotes DNA is assembled into chromatin which regulates access of the transcriptional machinery to genes Genes Genes and and the the general general transcription transcription machinery machinery Transcription Transcription factors factors activators activators and and repressors repressors Chromatin organization and dynamics II Chromosome Organization and Gene Regulation I Model of a typical gene Locus Control Region LCR Boundary Element DNA Gene Boundary Element Enhancer 4k Matrix Attachment Region MAR Core Promoter 500 40 50 Coding region MAR Regulatory Promoter Core Promoter Regulatory Promoter RNA Enhancer Boundary Element MAR LCR II Chromosome Organization and Gene Regulation I Model of a typical gene Locus Control Region LCR Boundary Element DNA Gene Boundary Element Enhancer 4k Matrix Attachment Region MAR Core Promoter 500 40 50 Gene MAR Regulatory Promoter Core Promoter Regulatory Promoter RNA Enhancer Boundary Element MAR LCR II Chromosome Organization and Gene Regulation I 38 32 TFIIB RE 26 1 TATA box IID Initiator IID 30 DPE IID IIB IIB IIA TATA box Initiator IIE IIH PolII TFIIB Recognition Element Downstream Core Promoter Element TFIIA IIB IID IIE IIF IIH and RNA Polymerase II General Transcription Factors GTFs RNA pol II pre initiation complex In vitro II Chromosome Organization and Gene Regulation I PolII is a protein complex composed of 12 subunits Carboxyl Terminal Domain CTD II Chromosome Organization and Gene Regulation I Carboxyl Terminal Domain CTD Multiple repeats of the peptide YSPSTPS 26 in yeast 52 in mammals YSPTSPS Phosphorylation Sites CTD phosphorylation regulates transcription initiation and elongation and promotes interaction with other factors involved in transcription and splicing II Chromosome Organization and Gene Regulation I Model of a typical gene Locus Control Region LCR Boundary Element DNA Gene Boundary Element Enhancer 4k Matrix Attachment Region MAR Core Promoter 500 40 50 Gene MAR Regulatory Promoter Core Promoter Regulatory Promoter RNA Enhancer Boundary Element MAR LCR II Chromosome Organization and Gene Regulation I Transcription Factors are modular proteins Activation Domains ADs DNA Binding Domains DBDs DBD zinc fingers leucine zippers homeodomains basic helix loop helix bHLH etc DBDs define the specificity of TFs AD Many ADs contain an unusually high percentage of particular amino acids such as Glu Asp Pro and Gln AD are functionally autonomous II Chromosome Organization and Gene Regulation I Many if not all transcription factors contain multiple ADs P300 GTFs P65 The rational is twofold It increases the TFs potency Many TF may contact different targets Example The P65 subunit of NFkB contains two ADs II Chromosome Organization and Gene Regulation I Model of a typical gene Locus Control Region LCR Boundary Element DNA Gene Boundary Element Enhancer 4k Matrix Attachment Region MAR Core Promoter 500 40 50 Gene MAR Regulatory Promoter Core Promoter Regulatory Promoter RNA Enhancer Boundary Element MAR LCR II Chromosome Organization and Gene Regulation I Example of the beta interferon INF enhancer 70 bp of DNA GTFs Mediator Mediator of transcription complex Pol II Pre initiation Complex Gene control region in eukaryotics II Chromosome Organization and Gene Regulation I How is gene expression regulated by repressors General strategies a b c How is gene expression regulated by repressors General strategies 3 Role of repressors in altering the chromatin structure a b c