Transcription Elongation.pdf

Pol IISer5-PSer7-PThr4-PTyr1-PSer2-PY1S2T4S5S7Y1S2T4S5S7Y1S2T4S5S7Pol II pause,release,elongation rate,and processivity factorsK4K79K4K14K9S10Dot1K9S10K16K36Paused Pol IIPol IIPol IIPol IICdc73Ski8Rtf1Ctr9Paf1Leo1Cdc73Ski8Rtf1Ctr9Paf1Leo1Rad6Bre114-3-3MOFBRD4PIM1SET2HATHDACCOMPASSSuper Elongation Complex(SEC)Little Elongation Complex(LEC)Polymerase-associated factor 1 complexReleased Pol IINucleosome disassemblyand reassembly Pol II CTD phosphorylationHistone chaperones and chromatin remodelersNucleosome spacingHistone modifications involved in elongationH2B K123 monoubiquitylation cascadeH3 S10 phosphorylation cascadeH3 K36 methylationAF9/ENLAFF1/4P-TEFbELLEAFICE2EAFICE1ELLPol IIPol IIPol IIPol IIY1S2T4S5S7Pol IIP-TEFbDSIFP-TEFbNELFY1S2T4S5S7ADP-RPol IIRecruited by:SECBRD4DSIFNELFElongationP-TEFbPARP-1PPPPPPPPUbUbUbPPPPMeMeMeMeAcAcAcAcAc H2A H2B H3 H4 H2A H2B H3 H4 H2A H2B H3 H4 H2A H2B H3 H4 H2A H2B H3 H4 H2A H2B H3 H4 H2A H2B H3 H4UbUbUbp81058 Cell 166,August 11,2016 2016 Elsevier Inc.DOI http:/dx.doi.org/10.1016/j.cell.2016.07.039See online version for legend and references.SnapShot:Transcription ElongationChristine E.Cucinotta and Karen M.ArndtDepartment of Biological Sciences,University of Pittsburgh,Pittsburgh,PA 15260,USAProteinFunctionP-TEF-b/Cdk9/CycT1/(S.c.:Bur1/Bur2)Cyclin-dependent kinase,releases Pol II from pausing and phosphorylates Pol II,NELF,and DSIFDSIF(S.c.:Spt4-Spt5)Stabilizes Pol II pausing,recruits elongation factors,stimulates elongationNELFNegative elongation factorPARP-1Polyadenosine diphosphate(ADP-ribose)polymerase,transfers ADP-ribose to NELF to inhibit NELFBRD4Recruits and activates P-TEFbTFIISResumes Pol II elongation from backtracked-arrestTFIIFPrevents transient pausing of Pol IIElonginIncreases transcription elongation rateSuper elongation complexRecruits P-TEFb,increases Pol II elongation rateLittle elongation complexRequired for snRNA expression in metazoansPaf1CAssociated with Pol II and Spt4-Spt5,recruits chromatin remodelers,histone chaperones,and modifiersGDOWN1Tightly associated with Pol II,stabilizes pausing RNA processing factorsCCR4-NOT,THO/TREX,Xrn2:mRNA processing and export factors that also regulate elongationKinasePhosphataseCdk9(S.c:Bur1)Cdk12(S.c:Ctk1)Fcp1Cdk7(S.c:Kin28)Rtr1,Ssu72Cdk7(S.c:Kin28)Cdk9(S.c:Bur1)Ssu72Plk3,Cdk9?Rtr1(S.c.)ProteinFunctionRole in elongationFACTHistone chaperone complex of H.s.:hSPT16,Ssrp1,S.c.:Spt16,Nhp6,Pob3Displaces H2A-H2B dimer in the wake of transcribing Pol II,evicts nucleosome;reassembles nucleosomes,regulates H2BK123ub,prevents cryptic transcriptionSpt6Histone chaperonePrevents cryptic transcription,required for proper histone occupancy during elongationAsf1Histone chaperoneControls H3 exchange during transcriptionNap1Histone chaperoneBinds H2A-H2B and forms hexasome structures through RSC,promotes nucleosome assemblyRtt106Histone chaperoneBinds H3-H4 and promotes transcription-coupled H3 deposition,prevents cryptic transcriptionChd1Chromatin remodelerControls nucleosome spacing and histone exchange,promotes Pol II promoter escape(mammals)ISW1Chromatin remodelerControls nucleosome spacing and histone exchangeRSCChromatin remodelerHelps Pol II passage through nucleosomes and maintains proper nucleosome occupancy1058.e1 Cell 166,August 11,2016 2016 Elsevier Inc.DOI http:/dx.doi.org/10.1016/j.cell.2016.07.039SnapShot:Transcription ElongationChristine E.Cucinotta and Karen M.ArndtDepartment of Biological Sciences,University of Pittsburgh,Pittsburgh,PA 15260,USATranscription elongation is a key regulatory step in gene expression.Elongation is controlled by many proteins and mechanisms,ranging from RNA Polymerase II pausing to cotranscriptional histone modifications.Here,we provide an overview of major factors involved in transcription elongation.Not discussed here are many transcription termination and RNA processing factors that also influence elongation.Pol II Pausing,Pause Release,Elongation Rate,and ProcessivityPausing of Pol II at a promoter-proximal position(2060 nt downstream of the initiation site)is a prominent regulatory event in transcription elongation in higher eukaryotes.Promoter-proximal pausing requires DSIF and NELF.DSIF,comprising Spt4/Spt5,is conserved throughout all kingdoms and in metazoans stabilizes paused Pol II in the pres-ence of the negative elongation factor NELF(Kwak and Lis,2013).To release Pol II and activate productive elongation,P-TEFb,a cyclin-dependent kinase consisting of Cdk9/CycT1(Bur1/Bur2 in S.cerevisiae),phosphorylates DSIF,NELF,and Pol II.BRD4 and the super elongation complex(SEC)recruit P-TEFb to chromatin,allowing it to phosphory-late DSIF and NELF,and enable pause release and elongation(Lu et al.,2016;Luo et al.,2012).Additionally,PARP-1 ADP-ribosylates NELF near its phosphorylation site to inhibit pausing(Gibson et al.,2016).TFIIF increases the elongation rate by preventing transient pausing;however,its association to Pol II may be blocked by the negative elongation factor GDOWN1 during initiation.Pol II can additionally stall via backtrack arrest.TFIIS releases Pol II at arrest sites by inducing cleavage of the nascent transcript,which has become misaligned in the Pol II active site.The speed of Pol II elongation is impacted by elongation factors that can attenuate transient pausing.Factors that enhance Pol II elongation rate include Elongin,the SEC,and the polymerase associated factor 1 complex(Paf1C),where Rtf1 is tightly associated in yeast(Luo et al.,2012;Tomson and Arndt,2013).The LEC and Integrator complex also have roles in promoting expression and transcription elongation of snRNA genes.Many termination,RNA processing,and export factors also regulate transcription elongation,including Xrn2,and the THO/TREX and CCR4-NOT complexes(Reese,2013).Pol II C-Terminal Domain PhosphorylationThe C-terminal domain(CTD)of Pol II is modified by multiple phosphorylation events across a repeated peptide sequence throughout the transcription cycle.The resulting“CTD code”dynamically controls the temporal recruitment of transcription,RNA processing,and histone modification machinery.The best understood modifications of the CTD consensus repeat sequence are Ser2 and Ser5 phosphorylation.Ser2-P is enriched at the 3-ends of many genes and promotes recruitment of several RNA processing and elongation factors,including Spt6 and Set2.Ser5-P is enriched at the 5-ends of genes and recruits elongation and RNA processing factors.Ser7-P is less understood;however,transcription of small nucleolar RNAs is facilitated by this modification.Thr4-P correlates with Ser2-P but is enriched further downstream into polyA sites.Alanine substitution of Thr4 in mammalian cells results in a transcription elongation defect.Tyr1-P is implicated in transcription elongation in yeast through recruitment of Spt6 and inhibition of termination factor binding(Jeronimo et al.,2013).Histone Modifications Involved in ElongationCells employ a vast repertoire of histone modifications to modulate transcription.A subset of modifications involved in transcription elongation include the H2B monoubiq-uitylation cascade(at K123 in S.cerevisiae;K120 in humans),the H3 S10 phosphorylation cascade(H3 S10ph),and H3 K36 methylation(H3 K36me).In both yeast and human cells,H2Bub correlates strongly with transcription elongation.The H2Bub pathway has been most completely described in budding yeast,where Rad6 and Bre1 catalyze the ubiquitylation of H2B K123(Fuchs et al.,2014;Smolle and Workman,2013).Deubiquitylation of H2B K123 by Ubp8 is thought to serve as a checkpoint for the recruitment of other proteins during transcription elongation.Ubp8 is part of the SAGA complex,which contains the histone acetyltransferase(HAT)Gcn5.H2B K123ub is a pre-requisite for additional histone modifications on gene bodies,namely H3 K4me2/3 and H3 K79me2/3.H3 K4me2/3,catalyzed by the Set1-containing COMPASS complex,recruit HATs such as NuA3 and Gcn5 and HDACs.The H3 S10 cascade,best characterized in metazoans,involves histone crosstalk that leads to recruitment of P-TEFb.PIM1 phosphorylates H3 S10 on nucleosomes acetylated at H3 K9.This phosphorylation mark recruits 14-3-3,which binds to the acetyltransferase MOF.MOF acetylates H4 K16,which in turn recruits BRD4.H3 K36me2 is required for recruitment of the histone deacetylase Rpd3S,which constrains histone acetylation levels and prevents cryptic initiation within genes.H3 K36me3 helps maintain nucleosomes during transcription by recruiting the chromatin remodeler ISW1.The H3 K36 methyltransferase Set2 interacts with the Ser2-P form of Pol II.This summary is not exhaustive,as all four core histones are posttranslationally modified in various ways to impact the entire transcription cycle.Histone Chaperones and Chromatin RemodelersDuring elongation,histones are dynamically exchanged and nucleosomes are shifted by histone chaperones and chromatin remodelers(Venkatesh and Workman,2015).Chromatin remodelers use DNA translocase activity to move or evict nucleosomes.Histone chaperones bind to histones to prevent aggregation and non-specific DNA binding and to evict and reassemble nucleosomes.The FACT histone chaperone complex associates with Pol II and removes and replaces H2A-H2B dimers in the wake of transcrip-tion.Spt6,another conserved histone chaperone,reorganizes nucleosomes after passage of Pol II by binding to H3-H4.Asf1 is a histone chaperone that removes histones by binding to H3-H4 dimers during transcription,while Rtt106 is important for H3 deposition and the prevention of cryptic transcription.Nap1 assembles nucleosomes during elongation and binds an H2A-H2B dimer to form RSC-dependent hexasomes,thereby allowing passage of transcribing Pol II through the nucleosome.The chromatin remod-eler RSC is recruited by Pol II CTD Ser2 kinases and histone acetyltransferases.Chd1 recruited by Paf1C and ISW1 recruited by H3K36me3 are chromatin remodelers that prevent trans-histone exchange during transcription,and control nucleosome spacing.ACKNOWLEDGMENTSWe thank Craig Kaplan and Stephen Buratowski for helpful comments.This was supported by an Andrew Mellon Fellowship to C.E.C.and NIH grant GM052593 to K.M.A.REFERENCESFuchs G.,Hollander,D.,Voichek,Y.,Ast,G.,and Oren,M.(2014).Genome Res.24,15721583.Gibson B.A.,Zhang,Y.,Jiang,H.,Hussey,K.M.,Shrimp,J.H.,Lin,H.,Schwede,F.,Yu,Y.,and Kraus,W.L.(2016).Science 353,4550.Jeronimo C.,Bataille,A.R.,and Robert,F.(2013).Chem.Rev.113,84918522.Kwak H.,and Lis,J.T.(2013).Annu.Rev.Genet.47,483508.Lu X.,Zhu,X.,Li,Y.,Liu,M.,Yu,B.,Wang,Y.,Rao,M.,Yang,H.,Zhou,K.,Wang,Y.,et al.(2016).Nucleic Acids Res.Published online June 28,2016.http:/dx.doi.org/10.1093/nar/gkw571 Luo Z.,Lin,C.,and Shilatifard,A.(2012).Nat.Rev.Mol.Cell Biol.13,543547.Reese J.C.(2013).Biochim.Biophys.Acta 1829,127133.Smolle M.,and Workman,J.L.(2013).Biochim.Biophys.Acta 1829,8497.Tomson B.N.,and Arndt,K.M.(2013).Biochim.Biophys.Acta 1829,116126.Venkatesh S.,and 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