PowerPoint PresentationSlide 2Slide 3Slide 4Slide 5Response to Phosphate (Pho system)Slide 7PHO5 Promoter Has 4 Positioned NucleosomeSlide 9Slide 10DNase I Sensitivity Changes with Phosphate LevelsNucleosome Remodeling is LocalizedChromatin Remodeling Requires Pho4/2 & ATPSlide 14Histone Acetylation is a Dynamic MarkerHistone Acetyl Transferase (HAT) ProteinsDeletion of GCN5 Delays Response to Phosphate StarvationDelay Occurs at Level of TranscriptionSlide 19Pho5 Activation Requires Multiple HAT ActivitiesSAGA Required for TBP RecruitmentOrdered RecruitmentSwi/Snf-the First Chromatin Remodeling ComplexPho8 is Swi/Snf-Dependent but Pho5 is NotSlide 25How are HATs and Remodelers working?In vitro Chromatin TemplateChromatin Templates Required to Mimic in vivo Promoter RegulationHAT (p300) Influences Transcription from a Chromatin TemplateHAT and Chromatin Remodelers Are Required for Transcription in vivoSlide 31Bromodomains Increase Binding to Acetylated PartnersBromodomains Can Display Binding SelectivitySlide 34Acetyl/Bromodomain Interaction Increases Remodeling EfficiencySelect Acetylation Marks and Bromodomains can Drive PathwaysHistone Remodeling ComplexesChromatin Remodeling ComplexesCommon Types of RemodelingTemplate for Monitoring Nucleosome PositionsNURF Induces Nucleosome SlidingSWI Doesn’t Induce SlidingRSC Transfers OctamersSliding and TransferSlide 45Different RolesSelectivity of Chromatin Remodeling ComplexesMultiple Chromatin Remodeling Complexes in a Single CellActivators Can Drive SelectionChromatin Remodeling Complexes Only Work in Proper ContextPost Remodeling Events During ActivationHistone Modifications are Lost After Prolonged Promoter ActivationHistones Are Gone Following HyperacetylationSlide 54Slide 55Slide 56Slide 57Inverse Correlation between Global Histone Occupancy and Transcription RatesSlide 59Slide 60Slide 61Slide 621Next Readings ReviewNuclear receptor coregulators: judges, juries, and executioners of cellular regulation.Lonard DM, O'malley BW.Mol Cell. 2007 Sep 7;27(5):691-700.Journal Club PaperDistinct properties of cell-type-specific and shared transcription factor binding sites.Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, Cooper GM, Reddy TE, Crawford GE, Myers RM.Mol Cell. 2013 Oct 10;52(1):25-36.2Points for the lecture:Chromatin Remodeling Complexes Move OctamersHAT Complexes Mark Histones for Movement Remodeling Mechanism Can VaryPromoters Use Distinct Order of Recruitment3General Transcription Events4Chromatin Events5Complexity of Chromatin Events6Response to Phosphate (Pho system)7Phosphate Signaling8PHO5 Promoter Has 4 Positioned NucleosomeClaITATA/2/29Chromatin Immunoprecipitation (ChIP)10Histone and Basal Factor Occupancy are Mutually Exclusive11DNase I Sensitivity Changes with Phosphate LevelsTime after phosphate removal12Nucleosome Remodeling is Localized13Chromatin Remodeling Requires Pho4/2 & ATP14Marking Histones for Movement15Histone Acetylation is a Dynamic Marker16Histone Acetyl Transferase (HAT) Proteins17Deletion of GCN5 Delays Response to Phosphate StarvationPhosphataseEnzymeActivity18Delay Occurs at Level of Transcription19Deletion of GCN5 Impairs Chromatin RemodelingWT WT WTgcn5 gcn5gcn520Pho5 Activation Requires Multiple HAT ActivitiesDifferential use of SAGA complexesSpt-Ada-Gcn5 (SAGA) Acetyltransferase21SAGA Required for TBP RecruitmentChromatin RemodelingTBP Recruitment by ChIP22Ordered Recruitment23Swi/Snf-the First Chromatin Remodeling Complex1. Genetic screen for regulators of mating type switching in yeast(regulators of HO endonuclease gene)Swi1, Swi2 and Swi3Snf1, Snf2, Snf3, Snf4, Snf5, Snf62. Genetic screen for regulators of sucrose non-fermentors(regulators of regulators of SUC2)Swi2/Snf2 Motor ProteinATPasebromodomain24Pho8 is Swi/Snf-Dependent but Pho5 is Not25Ordered RecruitmentGcn5NuA4SAGAINO8026How are HATs and Remodelers working?27In vitro Chromatin Template28Chromatin Templates Required to Mimic in vivo Promoter Regulation29HAT (p300) Influences Transcription from a Chromatin Template30HAT and Chromatin Remodelers Are Required for Transcription in vivo31What is the specific role of the Histone Code?32Bromodomains Increase Binding to Acetylated Partners33Bromodomains Can Display Binding SelectivityGeneral StabilizerMedium SpecificityHigh Specificity34Increasing Modularity and Stability35Acetyl/Bromodomain Interaction Increases Remodeling Efficiency36Select Acetylation Marks and Bromodomains can Drive Pathways37Histone Remodeling Complexes38Chromatin Remodeling Complexes39Common Types of Remodeling(c)Transfer40Template for Monitoring Nucleosome Positions41NURF Induces Nucleosome Sliding42SWI Doesn’t Induce Sliding43RSC Transfers Octamers44Sliding and TransferAdapted: Rippe et al., 200746Different Roles47Selectivity of Chromatin Remodeling Complexes48Multiple Chromatin Remodeling Complexes in a Single Cell49Activators Can Drive Selection50Chromatin Remodeling Complexes Only Work in Proper Context51Post Remodeling Events During Activation52Histone Modifications are Lost After Prolonged Promoter Activation53Histones Are Gone Following Hyperacetylation54Asf1 Histone Chaperone is Required for RemovalPho ResponseTxn ResponseChromatin AccessHistone Occupancy55PHO5 Promoter Remodeling56Histones Reoccupy After Phosphate Addition57Stepwise versus Equilibrium Models58Inverse Correlation between Global Histone Occupancy and Transcription Rates59DNA Curvature Contributes to Nucleosome SpacingNDRMapping Global DNase I Hypersensitive Sites (Open Chromatin)Hesselberth et al. (2009)Transcription Factors Serve Multiple FunctionsHistoneHistoneRemodelingRemodelingHistoneHistoneRemodelingRemodelingHAT/PTM HAT/PTM Complexes Complexes HAT/PTM HAT/PTM Complexes Complexes Binding of Binding of Accessible Accessible DNA ElementDNA ElementBinding of Binding of Accessible Accessible DNA ElementDNA ElementHistoneHistoneRemovalRemovalHistoneHistoneRemovalRemovalNucleosomeNucleosomeDepleted SiteDepleted SiteNucleosomeNucleosomeDepleted SiteDepleted Site62Chromatin Structure of a Typical “Activatable” Gene5’ NDR 3’
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