MCB 252 Topic 12 Chromosome Organization and Gene Regulation IV Protein Domains and Epigenetics Prof David Rivier MCB 252 Spring 2015 Reading Lodish 256 262 Lodish 7 7 Outline Evolution Protein domains and gene structure Epigenetics and X chromosome inactivation Gene silencing in yeast Regulation of transcription polycomb trithorax in development TFIIIA Transcription Factor TFIIIA contains 9 Zinc Finger Domains Each Zinc Finger Recognizes 3 bp 9 Fingers Specifically Bind 27 nts Antibodies made up of several Ig domains Ig repeats Homeodomain Transcription Factors What process facilitates the assembly of coding regions containing domains What process facilitates the modular construction of open reading frames Gene 1 Gene 2 Exon shuffling New gene Transcription and splicing mRNA for protein with new domain architecture Copyright McGraw Hill Education Permission required for reproduction or display Fig 9 17 Positioning of Nand C termini of some many domains Structure of Regulatory Regions E1 E2 RP CP CR E Enhancer RP Regulatory Promoter CP Core promoter CR Coding Region Genes can have many enhancers Each enhancer can turn the gene on in response to a different signal or condition Eve Expression in Drosophila Development Eve transcription in different segments is activated by different enhancers Txn in 7 segments directed by 7 enhancers What process facilitates the modular assembly of regulatory regions What process allows for multiple enhancers Protein Domains Readers Chromodomain Bromodomain binds methylated lysines binds acetylated lysines Writers SET domain RING domain lysine methylase monoubiquitinylation Outline Evolution Protein domains and gene structure Epigenetics X chromosome Inactivation Gene silencing in yeast Regulation of transcription polycomb trithorax and development Epigenetics Classic definition An epigenetic trait is a stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence Conrad Waddington 1950s heritability through mitosis or meiosis but most examples are heritability through mitosis X Chromosome Inactivation in Mammals Gene Silencing in Yeast Hox Gene Activation and Repression X inactivation an epigenetic mechanism of dosage compensation Establishment Mitotic Inheritance Cellular Memory Saccharomyces cerevisiae Budding yeast Brewing and Baking Single celled organism Can grow as a haploid or diploid Saccharomyces cerevisiae life cycle 3 copies of the mating type genes Copy at MAT locus is transcribed Copies at HML and HMR are repressed silenced Silencing Genes Proteins SIR1 SIR2 SIR3 SIR4 Rap1 ORC Acts in complex at the silencer A histone deacetylase writer an HDAC A reader of the histone code A reader of the histone code Repressor Activator Protein binds silencer Origin Recognition Complex binds silencer Silencing is heritable through mitosis sir1D strain HML repressed silenced in 20 of cells transcribed in 80 of cells Silencing is heritable through mitosis ADE2 ade2D white red ADE2 transcribed white ADE2 silenced red ADE2 in a silent region plus a mutation in silencing that behaves like sir1D Sir2 Sir4 Sir3 R A P 1 Sir1 O R C Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir4 Sir3 Sir3 Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir4 Sir3 Sir3 Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir4 Sir3 Sir2 Sir3 Sir4 Sir3 Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir4 Sir3 Sir2 Sir3 Sir4 Sir3 Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir4 Sir3 Sir2 Sir3 Sir2 Sir4 Sir3 Sir4 Sir3 Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir4 Sir3 Sir2 Sir3 Sir2 Sir4 Sir3 Sir4 Sir3 Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir4 Sir3 Sir2 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir4 Sir3 Sir3 Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir4 Sir3 Sir3 Barrier Boundary Element Silencing Establishment Maintenance Inheritance Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir4 Sir3 Sir2 Sir3 DNA Replication Sir4 Sir3 Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir4 Sir4 Sir3 Sir2 Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir3 Sir2 Sir4 Sir3 Sir4 Sir3 Sir2 Sir2 Sir3 Sir3 Sir2 Sir4 Sir3 Sir4 Sir4 Sir4 Sir2 Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir3 Sir2 Sir4 Sir3 Sir4 Sir3 Sir2 Sir2 Sir3 Sir3 Sir2 Sir4 Sir3 Sir4 Sir4 Sir4 Sir2 Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir3 Sir2 Sir4 Sir3 Sir4 Sir3 Sir2 Sir2 Sir4 Sir3 Sir4 Sir3 Sir2 Sir3 Sir4 Sir3 Sir3 Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir4 Sir3 Sir2 Sir4 Sir2 Sir2 Sir4 Sir3 Sir3 Sir4 Sir3 Sir2 Sir4 Sir4 Sir3 Sir3 Sir2 Sir2 Sir4 Sir4 Sir3 Sir2 Sir2 Sir2 Sir4 Sir3 Sir4 Sir3 Sir2 Sir2 Sir4 Sir3 Sir4 Sir3 Sir2 Sir3 Sir4 Sir3 Sir3 Sir2 Sir2 Sir4 Sir3 Sir2 Sir4 Sir4 Sir3 Sir2 Sir4 Sir2 Sir2 Sir4 Sir3 Sir3 Sir4 Sir3 Sir2 Sir4 Sir4 Sir3 Sir3 Sir2 Sir2 Sir4 Sir4 Sir3 Sir2 Sir2 Sir2 Sir4 Sir3 Sir4 Sir3 Sir2 Sir2 Sir4 Sir3 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir4 Sir3 Sir2 Sir2 Sir4 Sir3 Sir4 Sir3 Outline Evolution Protein domains and gene structure Epigenetics and gene silencing in yeast Regulation of transcription polycomb trithorax and development Segment Identity is Set up in Larva and Results in Development of Adult Structures Some genes that are turned on in larva stay on through development and in adult others that are shut off in the larva remain shut off through development and into the adult Homeotic Genes Homeotic Genes Mutation in Ultrabithorax Ubx Hox genes regulate development Conserved from flies to humans 1 Hox cluster in flies 4 Hox clusters in humans Hox genes encode transcription factors that regulate transcription of sets of genes that specify cell fate Hox Homeobox Transcription of HOX genes Tissue 1 Tissue 2 Hox gene A ON Hox gene B OFF Hox gene A OFF Hox gene B ON Fate A Fate B Transcription of HOX genes Active Hox gene Repressed Hox gene Early in development Early in development Transcription factors HATs Chromatin remodelers Co activators Gene transcribed Transcription repressors HDACs Chromatin remodelers Co repressors incl PRC2 Gene repressed Trithorax genes Polycomb genes Late in development Gene transcribed Late in development Gene repressed AbdB is a Hox gene PRC2 complex E z subunit SET domain H3K27 Me3 PRC1 complex PC subunit chromodomain H3K27 Me3 binding PRC1 condenses chromatin PRC1 recruits PRC2 reader recruits writer