RNA Polymerase II Transcription (Homo sapiens)

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337, 593687766821683, 27, 58, 6513, 81633, 1921684163686173, 21, 29, 30, 47...215, 78683, 1957324, 27, 35, 794, 9, 25684, 9, 25281, 21635722, 727738, 55, 68, 823, 275710, 466821nucleoplasmNTPNCBP1 TCEB1 POLR2D POLDIP3 POLR2F CLP1 GTF2A1(1-274) template DNA:9 nucleotide transcript hybrid POLR2I upstreammRNAfragment:CPSF:PAP:PABPN1 complexTAF7 GTF2H1 GTF2H1 NELFB TBP ERCC3 PABPN1 POLR2L GTF2H4 GTF2F1 DNA containing RNA Polymerase II promoter MLLT1 NCBP1 MNAT1 GTF2H5 CLP1 NELFBATP GTF2H4 TAF3 ERCC3 TAF2 GTF2F2 ERCC2 TCEB3B GTF2A1(275-376) SNRPF POLR2K GTF2E1 CDK7 POLR2D GTF2H5 TBP TAF2 TAF1L POLR2E CCNT2 PPip-S2,S5-POLR2A GTF2E2 ADPPOLR2J GTF2H1 GTF2A1(1-274) POLR2C MAGOHB ERCC2 CASC3 TAF3 TCEB3 POLR2G GTF2F2 POLR2L TAF2 GTF2H5 GTP MNAT1 SSRP1 CDK7 TAF3 GTF2H1 POLR2L IWS1 ERCC2 ERCC3 POLR2J RTF1 CDC73 TFIIATAF2 TAF4B ERCC2 CDK7 RTF1 CSTF2 NELFE ERCC2 TAF7L TCEB3CL TCEB1 POLR2J POLR2E TAF13 WDR61 NELFE GTF2H5 GTF2F2 template DNA:4-9 nucleotide transcript hybrid ERCC2 POLR2E POLR2A CCNH TAF11 TAF9 POLR2B POLR2L GTF2H3 SUPT6H pol II transcriptioncomplex containing11 nucleotide longtranscriptTFIIHPOLR2I TAF13 POLR2H SplicedmRNA:CBC:EJC:TREXpol IIpromoter:TFIIDcomplexATP NUDT21 POLR2H POLR2A CF I - 72 kDa subunit POLR2B POLR2K MNAT1 POLR2K POLR2C GTF2F1 GTF2A2 GTF2A1(275-376) POLR2C TAF13 PABPN1 POLR2B GTF2A1(275-376) p-S5-POLR2A ERCC2 POLR2E GTF2H2 POLR2D TAF4B CPSF1 POLR2H PAF1 CTDP1 capped pre-mRNA CASC3 NELFCD TAF7 Aborted elongationcomplex afterarrestGTF2F1 POLR2F POLR2D TAF5 TCEB2 U7 snRNA ERCC2 NCBP1 ERCC3 Elongating transcript prior to cleavage LEO1 POLR2H MNAT1 TAF7L POLR2K NELFB CSTF3 SRSF4 GTF2F1 POLR2E CTDP1 CTP PABPN1 GTF2F1 TAF1L PAF1CPOLR2F GTF2F1 POLR2G WDR61 ATP GTF2A1(275-376) TAF5 UTP NELFESRRM1 GTF2E1 NCBP2 SUPT6H SNRPD3 MNAT1 POLR2F POLR2G GTF2E2 NCBP2 Aborted earlyelongation complexPOLR2L SRSF2 CTP POLR2K POLR2K UTP TCEA1 CTP TAF7 TAF1 TAF9 NELFE TCEB1 POLR2D POLR2E SNRPF capped pre-mRNA SUPT16H GTF2F2 FIP1L1 GTF2F1 POLR2G TCEA1 POLR2D TAF2 GTF2H5 GTF2F2 TAF4 MLLT1 CDK7 GTF2A1(275-376) GTF2F1 TAF4B TCEB3C NCBP1 POLR2I GTF2H1 GTF2A2 TAF4 mRNA 3'-end cleavagefactorPOLR2H POLR2D CDC73 TAF10 POLR2D TAF10 CCNH TAF7L POLR2D NCBP2 TAF7L TAF2 UTP GTF2A2 RNMT POLR2I POLR2H GTF2H3 NELFE GTF2F2 TAF1L CCNT1 TAF1L CTR9 SNRPG pol II transcriptioncomplex containing4 nucleotide longtranscriptPOLR2F TAF2 TAF13 GTF2A1(1-274) TCEB1 GTF2H3 CTP ERCC3 CDC73 SRSF7 WDR61 POLR2H TAF11 POLR2D TAF1 POLR2J MLLT3 GTF2F2 GTF2H2 GTF2F1 TCEB3C POLR2C POLR2J POLR2I CSTF3 POLR2J GTF2H1 EAF2 EAF1 downstreamintronless mRNAfragmentElongating transcript prior to separation TAF6 GTF2E1 ZC3H11A POLR2E CCNH POLR2F GTF2H2 GTF2H5 RNGTT AFF4TFIIELUZP4 TAF7L GTF2H2 CPSF2 TAF3 CDK7 TAF5 CF I - 68 kDa subunit CTR9 WDR61 POLR2H CCNT2 CDC73 TAF10 GTF2H2 CTDP1 TAF6 TAF4 POLR2H Cap Binding Complex(CBC)MLLT1 EAF2 TAF9B POLR2A GTF2H2 POLR2E GTP POLR2I SUPT6H p-S5-POLR2A CDK7 POLR2H CTDP1 CTDP1 POLR2J POLR2K GTF2H4 ATP CSTF2T TAF7 NCBP1 Elongin B:C complexRNPS1 POLR2B GTP TAF1 CTDP1 POLR2F POLR2H CDK7 POLR2G GTF2H3 TAF7L TBP GTF2H2 TAF1 CPSF7 POLR2D GTF2H4 TCEB3 CF I - 68 kDa subunit Paused processiveelongation complexFIP1L1 NELFA GTF2H2 GenericTranscriptionPathwayTAF12 TCEB3B POLR2J ERCC3 GTF2E2 NTPp-SUPT5H TAF1L DNA containing RNA Polymerase II promoter POLR2J GTF2F2 TAF10 WDR33 CCNH p-S5-POLR2A MNAT1 ELL POLR2D TAF6 CCNT1 ERCC2 TCEB3CL ERCC3 POLR2D NELFCD SNRPF Elongation complexprior to separationIWS1TCEB3CL RTF1 THOC7 SRSF2 TCEB3B AFF4 POLR2L RNGTT PPiGTF2F2 POLR2J POLR2G p-S2,S5-POLR2A GTF2F1 TAF13 TAF12 POLR2G CCNT2 TAF7L GTF2H1 CCNT1 GTF2H3 TAF4 CPSF4 SUPT6H ATP Elongating transcript in processive Pol II mediated elongation CCNK Mature Intronless transcript derived Histone mRNA POLR2A SNRPE CF I - 72 kDa subunit POLR2E POLR2J CDK7 POLR2K TCEB3CL2 SNRPG CCNK GTF2A1(275-376) POLR2L TAF11 PAF1 GTF2H4 LSM10 CDC73 TAF12 CCNH GTF2H2 POLR2F EAF1 NELFA POLR2K TAF7 GTF2F2 TAF4 CCNK CPSF7 TAF5 POLR2B POLR2L GTF2A2 EAF2 TAF5 GTF2A1(275-376) CTP TCEB1 POLR2F RNGTTLUZP4 POLR2G POLR2B POLR2H GTF2F2 MNAT1 TAF1L POLR2L TCEB3B TCEA1 LEO1 PAF1 CDK9EAF1 GTF2H4 MLLT1 TAF7 p-SUPT5H POLR2C SSRP1 GTF2A1(275-376) TAF10 NELFAGTF2A2 POLR2F POLR2D POLR2C SSRP1 TAF5 TAF1 POLR2C NELFE TAF4B CCNT2 POLR2D POLR2E DDX39B CF IIPOLR2H CTP TAF10 GTF2H1 GTF2H4 POLR2F POLR2G TCEB1 POLR2F AFF4 POLR2G NELFE TAF11 TAF1 GTP POLR2B POLR2L GTF2E2 NCBP1 ERCC3 SUPT16H SYMPK CCNK TAF1 p-SUPT5H TAF9 TCEB3 p-SUPT5H CTDP1 NELFCDTAF13 GTF2H2 POLR2I SLBP SRSF5 UTP TAF13 GTF2H2 GTF2F1 POLR2F TAF9 NELFE POLR2D NCBP1 TAF5 MNAT1 TAF4B Capped IntronlessHistonepre-mRNA:CBC:ZFP100ComplexTCEB2 LEO1 cappedpre-mRNA:CBC:RNAPol II(phosphorylated)complexPOLR2A CTR9 NTPGTF2H1 Intronless Histone pre-mRNA CDK7 MLLT3 THOC3 POLR2A TAF9B ERCC3 UTP TAF6 GTF2A1(275-376) TAF4 TCEB3 DHX38 POLR2G ATP P-TEFb complexTAF9 LEO1 TAF5 POLR2K POLR2L LEO1 CTDP1 CPSF3 template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end TCEB2 ERCC2 GTF2F1 CTDP1 GTF2F2 POLR2I NTPTFIIHGTF2H2 TAF4 ERCC3 SUPT4H1 p-S2,S5-POLR2A POLR2J GTP EAF1 POLR2C p-S2,S5-POLR2A p-S2,S5-POLR2A POLR2H POLR2C CCNT1,CCNT2,CCNKGTF2H5 ATP POLR2G TAF3 GTF2F2 ATP ELL NELFCD POLR2E POLR2I POLR2E U2AF1 p-S5-POLR2A TCEB2 NELFB POLR2B POLR2B TCEA1 POLR2K CCNH POLR2G CSTF3 POLR2B CstFEAF1 MNAT1 TAF10 POLR2G POLR2L GTF2F1 NELFA POLR2H POLR2C TCEB3CL2 TBP TAF11 CCNT1 CDC73 POLR2L GTF2F2 GTF2H1 POLR2L DNA containing Pol II promoter with transcript with 2 or 3 nucleotides CDK9 TAF3 TAF9 CDK7 EAF2 TAF9 RNA Pol II withphosphorylated CTD:CE complex withactivated GTTAF1L GTF2A1(275-376) POLR2F TAF13 p-S5-POLR2A PABPN1 SNRPB p-S5-POLR2A NTPGTF2A2 TAF5 TAF10 template DNA:30 nt transcript hybrid CTP CCNT1 CCNT1 TAF1 GTF2F2 DNA containing RNA Polymerase II promoter TAF10 TAF10 TAF13 MLLT1 NCBP1 NCBP1 SUPT4H1 TAF7L TBP CDK9 GTF2H1 CCNK TBP TCEA1 POLR2G POLR2L GTF2F1 3'-end cleaved mRNA with spliced exons TCEB2 RTF1 CDK7 POLR2J TAF4B GTF2H4 POLR2K SUPT16H MAGOHB TCEB3B EAF2TCEB3 POLR2A TAF3 GTF2H3 GTF2H5 POLR2A POLR2F template DNA:4 nucleotide transcript hybrid POLR2E pol II openpre-initiationcomplexTAF3 SRSF7 POLR2F GTF2A2 POLR2D WDR33 ERCC3 TCEB3B GTF2A1(275-376) TBP NTPTFIIHATP SUPT4H1 SUPT6H ERCC2 NELFE GTF2H4 hTra2 Elongin ComplexTAF1L POLR2L CTDP1POLR2K ERCC2 CDC73 NELFCD POLR2F GTF2E2 TAF9B TAF12 TFIIHCDK9 POLR2I GTF2H5 EAF2 THOC3 CCNH CTR9 Pol II initiationcomplexp-S2,S5-POLR2A Intronless Histone pre-mRNA CDK7 POLR2L CTP TAF2 NCBP2 POLR2E POLR2F MLLT3 GTF2F2 p-SUPT5H CDK9 MNAT1 TAF1 MLLT3 NCBP1 TAF2 TAF13 GTF2H1 TCEB2 DDX39A template DNA:30 nt transcript hybrid CTP TCEB3CL POLR2B POLR2G TAF12 GTF2H4 POLR2J POLR2F CSTF1 THOC2 EAF1 NELFB CSTF2T POLR2I POLR2L POLR2H TAF1 NELFE TAF4 NELFA POLR2L CF IGTF2A2 NCBP2 GTF2F2 TAF3 CCNK damaged DNAsubstrate:nascentmRNA hybridGTF2E1 POLR2E POLR2C POLR2L SRSF6 RTF1 U2AF1L4 ERCC3 TAF12 GTF2H4 SSRP1ATP TCEB1 GTP TCEB3C POLR2G CDK7 TAF9 POLR2E CPSF2 GTP GTF2H2 POLR2J POLR2G POLR2J GTF2F2 POLR2E POLR2G GTF2H3 p-SUPT5H NCBP1 Capped intronless pre-mRNA ERCC3 ZC3H11A POLR2H TBP NTPCTP POLR2B PPiERCC2 TAF5 GTF2B GTF2A1(1-274) upstream intronless mRNA fragment NELFB EAF1GTF2H4 CF I - 72 kDa subunit GTF2E1 GTF2H3 CCNH POLR2F THOC5 TAF4 SUPT16H POLR2I SUPT4H1 THOC6 GTF2H4 Elongation complexPOLR2J NELFA TAF4 GTF2E2 GTF2H5 GTP POLR2L GTF2H3 ERCC2 POLR2L RNAPolymeraseIIholoenzymecomplex(hyperphosphorylated)TBP NELFA GTP SRSF3 MLLT1 POLR2G NUDT21 GTF2F2 TAF13 template DNA withfirst transcriptdinucleotide,opened to +8positionPOLR2E POLR2F GTF2F1 GTF2H1 TBP CTP IWS1 POLR2H TAF7 TAF6 POLR2J GTF2F1 POLR2E TAF9 POLR2G UTP POLR2H POLR2C GTF2F2 CSTF2 POLR2A LSM10 POLR2L TAF12 TCEB3CL2 PCF11 TCEB2 GTF2A2 TAF1 POLR2H POLR2H PCF11 POLR2F CPSF2 SSRP1 TCEB3C GTF2A1(1-274) DNA containing PolII promoter withtranscript with 2or 3 nucleotidesTAF9 Elongation complexwith separated anduncleavedtranscriptCCNK GTF2H5 GTF2F1 POLR2K GTF2H4 POLR2B NELFA POLR2I GTF2H5 MNAT1 THOC1 POLR2B ATP POLR2A POLR2B CPSF3 GTP U2AF1L4 POLR2I MNAT1 TAF9B template:capped transcript hybrid GTF2A1(275-376) UPF3B MLLT1 GTF2E1 CCNH pol II transcriptioncomplex containing9 nucleotide longtranscriptGTF2A1(1-274) TAF10 GTF2A1(275-376) Pol II Initiationcomplex withphosphodiester-PPiintermediateATP GTF2H2 GTF2F2 polIIpromoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF complexCDK7 GTF2H3 NELFA POLR2J TAF12 CDC40 TAF11 POLR2G TAF1L TAF6 POLR2L TBP POLR2B PAF1 p-S5-POLR2A UTP ELL AFF4 POLR2C GTF2B POLR2L CF I - 68 kDa subunit ELL CTP Early elongationcomplex withhyperphosphorylatedPol II CTDMNAT1 GTF2B UTP CDK7 NCBP2 ZNF473 POLR2C POLR2G CCNH CDK9 CDK7 ZNF473 PAF1 ATP FYTTD1 TAF1L POLR2E POLR2H CCNT1 GTF2H5 SUPT4H1 p-S2,S5-POLR2A POLR2I POLR2C GTF2F1 GTF2H5 TAF9B SUPT16H GTF2H3 MatureIntronlesstranscriptderivedHistonemRNA:SLBP:CBP80:CBP20CCNH POLR2D GTF2F2 POLR2C EIF4A3 POLR2D POLR2F RNGTT GTF2E2 TAF10 NELFA POLR2G FACT complexGTF2H4 CTR9 POLR2K SRSF3 POLR2B GTF2B POLR2H Processiveelongation complexPOLR2J ERCC3 SRSF9 TAF9B TCEB3CL TAF10 CTDP1 p-SUPT5H CTP capped pre-mRNA POLR2H MLLT3 POLR2D GTF2F2 POLR2C POLR2B GTF2H3 ELL TAF9B TCEB3CL POLR2G POLR2H ATP POLR2K CSTF1 MNAT1 TAF11 TCEB2POLR2K TAF10 DDX39A CCNH CCNH TCEB3 POLR2L CSTF2 p-SUPT5H TAF12 template DNA:3 nucleotide transcript hybrid GTF2F1 mRNA with spliced exons GTF2H4 TAF6 TCEB3CL2 CDK7 GTF2H1 POLR2G TFIIDTAF7 GTF2H3 NELFCD MLLT3 NELFCD CCNK POLR2L TAF13 MNAT1 MNAT1 ERCC3 TAF11 POLR2J GTF2A1(1-274) p-S2,S5-POLR2A CE:Pol II CTD:Spt5complexCTP MAGOH GTF2H3 TAF9 GTF2A1(1-274) TAF9 GTF2H3 GTF2A2 THOC2 polIIpromoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF:TFIIE complexCCNT1 TCEB3CL2 NELFE TCEB3CL2 AFF4 POLR2C UTP GTF2F2 TCEB3CL2 CCNH template DNA with first transcript dinucleotide, opened to +8 position NUDT21 ATP POLR2J POLR2I U7 snRNA p-SUPT5H GTP CTR9 TCEB3B NCBP2 MNAT1 GTF2A1(1-274) Pol II transcriptioncomplex with (ser5)phosphorylated CTDcontaining extrudedtranscript to +30POLR2J ERCC2 POLR2B MNAT1 SUPT6H SARNP GTF2F1 MLLT1 TAF9B TAF9B LEO1 POLR2I CPSF1 PPiTCEB3 TCEB3C NCBP2 NCBP1 GTF2E1 POLR2G POLR2A SNRPD3 polIIpromoter:TFIID:TFIIA:TFIIB complexPOLR2D POLR2D CPSF4 GTF2E2 POLR2K GTF2B LSM11 GTP TCEA1 CPSF1 TAF1L EIF4A3 SSRP1 SUPT4H1 NTPU2AF1 GTF2H5 TAF7L POLR2L WDR33 POLR2G POLR2E TAF4B POLR2L GTF2H5 TAF5 UTP POLR2C template DNA:4-9nucleotidetranscript hybridCF I - 68 kDa subunit CCNH LSM11 p-SUPT5H p-SUPT5HPOLR2J TCEA1 POLR2C POLR2K TAF9 GTF2F1 GTF2H3 GTF2H4 EAF1 pol II transcriptioncomplex containing3 Nucleotide longtranscriptCCNH EAF2 GTP POLR2B AFF4 CTR9 SYMPK TAF6 TFIIECDK9 GTF2H4 POLR2E TCEB3 IWS1 SYMPK TAF4B POLR2F POLR2E NCBP2 GTF2A1(1-274) TAF2 GTF2H5 POLR2F TCEB3CL2 GTF2H4 GTF2H1 CPSF7 TAF1L ELL GTF2E2 Elongating transcript in processive Pol II mediated elongation TAF7L POLR2I TAF9B NELFCD SUPT6HCDC40 CDK7 UTP SRSF11 TFIIHGTF2F2 GTF2BPAPOLA THOC1 UTP POLR2C PPiTAF7L GTF2F2 GTF2H4 GTF2H2 GTF2F1 ERCC2 POLR2K EAF2 GTF2F2 ERCC3 DDX39B POLR2E MLLT3 MAGOH POLR2G TAF9B TAF12 CDK7 TCEB3B POLR2K TAF2 TAF5 TAF7 WDR61 GTF2B TCEB1PPiTAF9B POLR2K WDR61 GTF2A1(1-274) GTF2H3 TAF4 GTF2H3 SUPT4H1 SRSF6 AFF4 PAPOLA POLR2I POLR2D GTF2A2 POLR2C TAF12 POLR2B POLR2A GTF2F2 GTF2F1 hSLU7 POLR2B template DNA:30 nt transcript hybrid pol II closedpre-initiationcomplexCCNH POLR2C GTF2F1 CTDP1 POLR2C POLR2K POLR2D POLR2J TAF4 POLR2E template DNA:30 nt transcript hybrid POLR2E PCF11 NELFA TCEB3CL GTF2H2 GTF2F2 SUPT16HPOLR2D SRSF9 GTF2E2 template DNA:30 nt transcript hybrid GTF2H5 CCNK CPSF1 SSRP1 POLR2C POLR2H capped pre-mRNA SUPT16H Template DNA hybrid with phosphodiester-PPi intermediate NCBP2 TAF7L ALYREF NELFB POLR2B TCEB3CL TFIIFPOLR2I GTF2F2 TAF9 POLR2J CPSF4 NELFB POLR2I POLR2H SRSF1 TAF12 RNA polymerase IItranscribes snRNAgenesDNA containing RNAPolymerase IIpromoterGTF2B GTF2H1 MNAT1 NTPPOLR2G POLR2K RNAPolymeraseII(unphosphorylated):TFIIF complexSNRPD3 CLP1 TBP THOC5 TCEB2 TAF7L CDC73 POLR2E TAF3 DSIF complexPOLR2K TAF5 TAF1L TCEB3 RNAPolII(hypophosphorylated):capped pre-mRNA complexPOLR2B TAF4 POLR2K PAPOLA GTF2H1 TCEB1 U7 snRNA FIP1L1 IWS1 POLR2G GTF2H1 NTPELLGTF2H5 GTP GTF2H5 POLR2I CCNT2 POLR2E IWS1 POLR2I POLR2F TAF4B CSTF1 UTP POLR2B POLR2I Elongin Ap-SUPT5H POLR2J POLR2E TAF13 POLR2I Pol II transcriptioncomplex containingextruded transcriptto +30POLR2I GTF2F2 pol II transcriptioncomplex containing4-9 nucleotide longtranscriptTHOC7 POLR2J TAF6 PAF1 TAF1 POLR2F p-S2,S5-POLR2A CPSF3 TAF1 GTF2A1(1-274) POLR2B GTF2F1 NCBP1 TAF3 TAF12 ATP TAF3 CCNT1 GTF2F1 ERCC2 EAF2 POLR2K GTF2H3 CDK7 GTF2F1 TCEB3C TCEA1MLLT3 POLR2I TAF11 NCBP2 NELFCD NCBP2 GTF2H2 LEO1 TAF11 POLR2L NCBP1 POLR2J SRRM1 CCNT2 TAF4B SUPT4H1 CHTOP POLR2K TAF7 GTF2H2 CLP1 POLR2K NELFE POLR2H POLR2I ERCC3 UTP NELFB LSM11 CCNT2 POLR2C template DNA:30 nt transcript hybrid GTF2H3 CPSF7 UTP TCEB3C GTF2E1 POLR2I ERCC2 TAF4B Mature Intronless transcript derived Histone mRNA CTP TAF9B SUPT4H1 CPSF4 TCEB3B GTF2F1 POLR2D SSRP1 RTF1 GTF2H2 FIP1L1 POLR2J pol II transcriptioncomplexSUPT4H1SUPT16H GTF2E1 POLR2L POLR2F POLR2B TCEB2 AFF4 Elongating transcript in processive Pol II mediated elongation EAF1 POLR2F LSM10 U7 snRNP:ZNF473POLR2C TCEB3C POLR2A POLR2G p-S5-POLR2A POLR2I POLR2B POLR2F GTF2H4 GTF2H1 POLR2H SRSF1 TBP POLR2B SYMPK SRSF4 POLR2L GTF2F1 p-SUPT5H POLR2E POLR2K CPSF2 p-S5-POLR2A RNAPolII(hypophosphorylated) complex bound to DSIF proteinSRSF5 POLR2J hSLU7 TAF6 GTF2H2 ERCC2 TAF6 DSIF:NELF:earlyelongation complexArrested processiveelongation complexTAF11 POLR2B NELFB GTF2A2 ZNF473 PiGTF2F2 TCEB3CL2 SUPT16H SNRPG Mature intronlesstranscript derivedHistonepre-mRNA:CBCcomplexTAF7 POLDIP3 POLR2D POLR2I GTF2F2 template:capped transcript hybrid GTF2H5 CCNH POLR2C POLR2C POLR2B TAF7 CTP GTP GTF2B ATPERCC3 SNRPB SUPT4H1 NUDT21 MLLT3TAF9B ERCC3 POLR2I CSTF2T PAPOLA POLR2H POLR2C POLR2A TCEB3CL SARNP POLR2H SUPT4H1 ATP GTF2E2 NELFCD POLR2D ALYREF GTF2F1 TAF6 GTF2B POLR2C PCF11 MNAT1 TAF11 GTF2H3 ERCC3 Pol II transcriptioncomplex containingtranscript to +30CDK7 TAF4B GTF2H5 POLR2C DNA containing RNA Polymerase II promoter POLR2F SNRPE Open DNA -10 to +2 containing RNA Polymerase II promoter SNRPE GTF2H4 NELFCD SUPT4H1 RTF1 NELFB TAF1L TAF2 ERCC2 TCEB3C GTF2H2 MLLT1POLR2I POLR2F ERCC3 TAF5 TAF3 GTF2H1 SRSF11 CF I - 72 kDa subunit NTPU2AF2 GTF2H3 UTP TAF1 POLR2F POLR2C ERCC2 GTF2H1 GTF2F2 POLR2D ERCC2 WDR33 POLR2B GTF2H4 GTF2BRNPS1 POLR2H TAF4B NCBP2 Elongating transcript in processive Pol II mediated elongation SSRP1 NELFA CPSF3 CCNH CCNH CCNH GTP CCNT2 GTP POLR2K ERCC2 POLR2E CCNK TAF2 POLR2I CCNT1 POLR2J UPF3B POLR2A POLR2L GTF2F1 GTF2F1 POLR2G ERCC3 POLR2H PAF1 IWS1 MNAT1 ELL MNAT1 DHX38 GTF2E2 RNA Pol II withphosphorylated CTD:CE complexPOLR2K GTF2H2 POLR2D SLBP POLR2D POLR2G POLR2K ATP POLR2E GTF2A1(1-274) TAF4 CDK9 TFIIACTR9 RBM8A TAF12 GTF2H1 TCEB1 POLR2K GTF2E1 POLR2D TAF11 CDK9 MNAT1 GTF2H5 GTF2H3 DNA containing RNA Polymerase II promoter CappedIntronlessHistonepre-mRNA:CBP80:CBP20:SLBP:ZFP100 ComplexTHOC6 CDK9 CCNT2 intronless pre-mRNAcleavage complexGTF2H2 POLR2D TAF7 TAF2 NELFCD NELFB WDR61 AFF4 NELF complexPOLR2B SUPT6H POLR2B LEO1 CDK7 TAF3 WDR61 ERCC3 RBM8A POLR2A TAF11 CTP Pol II PromoterEscape ComplexTFIIDCCNH POLR2H CCNH UTP CHTOP FYTTD1 3' end cleaved,ligated exoncontaining complexCDK7 IWS1 SNRPB TAF6 POLR2E PAF1 capped pre-mRNA RTF1 TAF7L GTF2E1 TAF4B POLR2L GTF2F1 template DNA:11 nucleotide transcript hybrid RNMTELL TAF13 U2AF2 GTF2B POLR2F TAF7 POLR2J GTF2F1 POLR2J GTF2E1 p-SUPT5H POLR2D POLR2C NTPCTDP1 TAF6 CCNT2 ATP NCBP2 GTF2H1 TBP GTF2A2 POLR2E 60776048, 52, 6260606048, 52, 6215, 31, 43, 6426, 53168248, 52, 6260607748, 52, 627612, 20, 32, 33, 40...412, 6, 8, 11, 14...602841, 82603623, 4248, 52, 6215, 31, 43, 64


Description

View original pathway at:Reactome.

Comments

Reactome-Converter 
Pathway is converted from Reactome ID: 73857
Reactome-version 
Reactome version: 62

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Bibliography

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  8. Gnatt AL, Cramer P, Fu J, Bushnell DA, Kornberg RD.; ''Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution.''; PubMed Europe PMC Scholia
  9. Yu M, Yang W, Ni T, Tang Z, Nakadai T, Zhu J, Roeder RG.; ''RNA polymerase II-associated factor 1 regulates the release and phosphorylation of paused RNA polymerase II.''; PubMed Europe PMC Scholia
  10. Yao C, Choi EA, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, Shi Y.; ''Overlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3' processing.''; PubMed Europe PMC Scholia
  11. Hernandez N.; ''Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription.''; PubMed Europe PMC Scholia
  12. Bray SJ.; ''Notch signalling: a simple pathway becomes complex.''; PubMed Europe PMC Scholia
  13. Yamazaki K, Guo L, Sugahara K, Zhang C, Enzan H, Nakabeppu Y, Kitajima S, Aso T.; ''Identification and biochemical characterization of a novel transcription elongation factor, Elongin A3.''; PubMed Europe PMC Scholia
  14. Justice NJ, Jan YN.; ''Variations on the Notch pathway in neural development.''; PubMed Europe PMC Scholia
  15. Sims RJ, Belotserkovskaya R, Reinberg D.; ''Elongation by RNA polymerase II: the short and long of it.''; PubMed Europe PMC Scholia
  16. Pal M, McKean D, Luse DS.; ''Promoter clearance by RNA polymerase II is an extended, multistep process strongly affected by sequence.''; PubMed Europe PMC Scholia
  17. Holstege FC, Fiedler U, Timmers HT.; ''Three transitions in the RNA polymerase II transcription complex during initiation.''; PubMed Europe PMC Scholia
  18. Kadonaga JT.; ''Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors.''; PubMed Europe PMC Scholia
  19. Dvir A, Tan S, Conaway JW, Conaway RC.; ''Promoter escape by RNA polymerase II. Formation of an escape-competent transcriptional intermediate is a prerequisite for exit of polymerase from the promoter.''; PubMed Europe PMC Scholia
  20. Jawdekar GW, Henry RW.; ''Transcriptional regulation of human small nuclear RNA genes.''; PubMed Europe PMC Scholia
  21. Tirode F, Busso D, Coin F, Egly JM.; ''Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7.''; PubMed Europe PMC Scholia
  22. Yoh SM, Cho H, Pickle L, Evans RM, Jones KA.; ''The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export.''; PubMed Europe PMC Scholia
  23. Wahle E, Rüegsegger U.; ''3'-End processing of pre-mRNA in eukaryotes.''; PubMed Europe PMC Scholia
  24. Van Arsdell SW, Weiner AM.; ''Human genes for U2 small nuclear RNA are tandemly repeated.''; PubMed Europe PMC Scholia
  25. Bertolotti A, Melot T, Acker J, Vigneron M, Delattre O, Tora L.; ''EWS, but not EWS-FLI-1, is associated with both TFIID and RNA polymerase II: interactions between two members of the TET family, EWS and hTAFII68, and subunits of TFIID and RNA polymerase II complexes.''; PubMed Europe PMC Scholia
  26. Duan DR, Pause A, Burgess WH, Aso T, Chen DY, Garrett KP, Conaway RC, Conaway JW, Linehan WM, Klausner RD.; ''Inhibition of transcription elongation by the VHL tumor suppressor protein.''; PubMed Europe PMC Scholia
  27. Maston GA, Evans SK, Green MR.; ''Transcriptional regulatory elements in the human genome.''; PubMed Europe PMC Scholia
  28. Gangloff YG, Pointud JC, Thuault S, Carré L, Romier C, Muratoglu S, Brand M, Tora L, Couderc JL, Davidson I.; ''The TFIID components human TAF(II)140 and Drosophila BIP2 (TAF(II)155) are novel metazoan homologues of yeast TAF(II)47 containing a histone fold and a PHD finger.''; PubMed Europe PMC Scholia
  29. Jacob GA, Luse SW, Luse DS.; ''Abortive initiation is increased only for the weakest members of a set of down mutants of the adenovirus 2 major late promoter.''; PubMed Europe PMC Scholia
  30. Kamakaka RT, Bulger M, Kadonaga JT.; ''Potentiation of RNA polymerase II transcription by Gal4-VP16 during but not after DNA replication and chromatin assembly.''; PubMed Europe PMC Scholia
  31. Frontini M, Soutoglou E, Argentini M, Bole-Feysot C, Jost B, Scheer E, Tora L.; ''TAF9b (formerly TAF9L) is a bona fide TAF that has unique and overlapping roles with TAF9.''; PubMed Europe PMC Scholia
  32. Yamaguchi Y, Takagi T, Wada T, Yano K, Furuya A, Sugimoto S, Hasegawa J, Handa H.; ''NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation.''; PubMed Europe PMC Scholia
  33. Chen J, Wagner EJ.; ''snRNA 3' end formation: the dawn of the Integrator complex.''; PubMed Europe PMC Scholia
  34. O'Reilly D, Kuznetsova OV, Laitem C, Zaborowska J, Dienstbier M, Murphy S.; ''Human snRNA genes use polyadenylation factors to promote efficient transcription termination.''; PubMed Europe PMC Scholia
  35. Takagaki Y, Manley JL.; ''Complex protein interactions within the human polyadenylation machinery identify a novel component.''; PubMed Europe PMC Scholia
  36. Zhao J, Hyman L, Moore C.; ''Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis.''; PubMed Europe PMC Scholia
  37. Schultz P, Fribourg S, Poterszman A, Mallouh V, Moras D, Egly JM.; ''Molecular structure of human TFIIH.''; PubMed Europe PMC Scholia
  38. Zhou Z, Licklider LJ, Gygi SP, Reed R.; ''Comprehensive proteomic analysis of the human spliceosome.''; PubMed Europe PMC Scholia
  39. Egloff S, Dienstbier M, Murphy S.; ''Updating the RNA polymerase CTD code: adding gene-specific layers.''; PubMed Europe PMC Scholia
  40. Orphanides G, Lagrange T, Reinberg D.; ''The general transcription factors of RNA polymerase II.''; PubMed Europe PMC Scholia
  41. Hu D, Smith ER, Garruss AS, Mohaghegh N, Varberg JM, Lin C, Jackson J, Gao X, Saraf A, Florens L, Washburn MP, Eissenberg JC, Shilatifard A.; ''The little elongation complex functions at initiation and elongation phases of snRNA gene transcription.''; PubMed Europe PMC Scholia
  42. Barolo S, Posakony JW.; ''Three habits of highly effective signaling pathways: principles of transcriptional control by developmental cell signaling.''; PubMed Europe PMC Scholia
  43. Giglia-Mari G, Giglia-Mari G, Coin F, Ranish JA, Hoogstraten D, Theil A, Wijgers N, Jaspers NG, Raams A, Argentini M, van der Spek PJ, Botta E, Stefanini M, Egly JM, Aebersold R, Hoeijmakers JH, Vermeulen W.; ''A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A.''; PubMed Europe PMC Scholia
  44. Morris DP, Michelotti GA, Schwinn DA.; ''Evidence that phosphorylation of the RNA polymerase II carboxyl-terminal repeats is similar in yeast and humans.''; PubMed Europe PMC Scholia
  45. Bourbon HM, Aguilera A, Ansari AZ, Asturias FJ, Berk AJ, Bjorklund S, Blackwell TK, Borggrefe T, Carey M, Carlson M, Conaway JW, Conaway RC, Emmons SW, Fondell JD, Freedman LP, Fukasawa T, Gustafsson CM, Han M, He X, Herman PK, Hinnebusch AG, Holmberg S, Holstege FC, Jaehning JA, Kim YJ, Kuras L, Leutz A, Lis JT, Meisterernest M, Naar AM, Nasmyth K, Parvin JD, Ptashne M, Reinberg D, Ronne H, Sadowski I, Sakurai H, Sipiczki M, Sternberg PW, Stillman DJ, Strich R, Struhl K, Svejstrup JQ, Tuck S, Winston F, Roeder RG, Kornberg RD.; ''A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II.''; PubMed Europe PMC Scholia
  46. Egloff S, Murphy S.; ''Role of the C-terminal domain of RNA polymerase II in expression of small nuclear RNA genes.''; PubMed Europe PMC Scholia
  47. Aso T, Lane WS, Conaway JW, Conaway RC.; ''Elongin (SIII): a multisubunit regulator of elongation by RNA polymerase II.''; PubMed Europe PMC Scholia
  48. Cramer P.; ''Structure and function of RNA polymerase II.''; PubMed Europe PMC Scholia
  49. Baillat D, Wagner EJ.; ''Integrator: surprisingly diverse functions in gene expression.''; PubMed Europe PMC Scholia
  50. Woudstra EC, Gilbert C, Fellows J, Jansen L, Brouwer J, Erdjument-Bromage H, Tempst P, Svejstrup JQ.; ''A Rad26-Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage.''; PubMed Europe PMC Scholia
  51. Rachez C, Lemon BD, Suldan Z, Bromleigh V, Gamble M, Näär AM, Erdjument-Bromage H, Tempst P, Freedman LP.; ''Ligand-dependent transcription activation by nuclear receptors requires the DRIP complex.''; PubMed Europe PMC Scholia
  52. Louvi A, Artavanis-Tsakonas S.; ''Notch signalling in vertebrate neural development.''; PubMed Europe PMC Scholia
  53. Wada T, Takagi T, Yamaguchi Y, Ferdous A, Imai T, Hirose S, Sugimoto S, Yano K, Hartzog GA, Winston F, Buratowski S, Handa H.; ''DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs.''; PubMed Europe PMC Scholia
  54. Goodrich JA, Tjian R.; ''Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II.''; PubMed Europe PMC Scholia
  55. Conaway JW, Florens L, Sato S, Tomomori-Sato C, Parmely TJ, Yao T, Swanson SK, Banks CA, Washburn MP, Conaway RC.; ''The mammalian Mediator complex.''; PubMed Europe PMC Scholia
  56. Shilatifard A, Conaway RC, Conaway JW.; ''The RNA polymerase II elongation complex.''; PubMed Europe PMC Scholia
  57. Fiedler U, Marc Timmers HT.; ''Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II.''; PubMed Europe PMC Scholia
  58. Bunick D, Zandomeni R, Ackerman S, Weinmann R.; ''Mechanism of RNA polymerase II--specific initiation of transcription in vitro: ATP requirement and uncapped runoff transcripts.''; PubMed Europe PMC Scholia
  59. Chen Y, Yamaguchi Y, Tsugeno Y, Yamamoto J, Yamada T, Nakamura M, Hisatake K, Handa H.; ''DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation.''; PubMed Europe PMC Scholia
  60. Lin X, Taube R, Fujinaga K, Peterlin BM.; ''P-TEFb containing cyclin K and Cdk9 can activate transcription via RNA.''; PubMed Europe PMC Scholia
  61. Conaway RC, Conaway JW.; ''ATP activates transcription initiation from promoters by RNA polymerase II in a reversible step prior to RNA synthesis.''; PubMed Europe PMC Scholia
  62. Blazek E, Mittler G, Meisterernst M.; ''The mediator of RNA polymerase II.''; PubMed Europe PMC Scholia
  63. Wang W, Carey M, Gralla JD.; ''Polymerase II promoter activation: closed complex formation and ATP-driven start site opening.''; PubMed Europe PMC Scholia
  64. Hoffmann A, Roeder RG.; ''Cloning and characterization of human TAF20/15. Multiple interactions suggest a central role in TFIID complex formation.''; PubMed Europe PMC Scholia
  65. Gonatopoulos-Pournatzis T, Cowling VH.; ''Cap-binding complex (CBC).''; PubMed Europe PMC Scholia
  66. Rossignol M, Kolb-Cheynel I, Egly JM.; ''Substrate specificity of the cdk-activating kinase (CAK) is altered upon association with TFIIH.''; PubMed Europe PMC Scholia
  67. Orphanides G, LeRoy G, Chang CH, Luse DS, Reinberg D.; ''FACT, a factor that facilitates transcript elongation through nucleosomes.''; PubMed Europe PMC Scholia
  68. Egloff S, O'Reilly D, Murphy S.; ''Expression of human snRNA genes from beginning to end.''; PubMed Europe PMC Scholia
  69. Pavelitz T, Bailey AD, Elco CP, Weiner AM.; ''Human U2 snRNA genes exhibit a persistently open transcriptional state and promoter disassembly at metaphase.''; PubMed Europe PMC Scholia
  70. Malik S, Roeder RG.; ''Dynamic regulation of pol II transcription by the mammalian Mediator complex.''; PubMed Europe PMC Scholia
  71. Dominski Z, Erkmann JA, Yang X, Sànchez R, Marzluff WF.; ''A novel zinc finger protein is associated with U7 snRNP and interacts with the stem-loop binding protein in the histone pre-mRNP to stimulate 3'-end processing.''; PubMed Europe PMC Scholia
  72. Archambault J, Pan G, Dahmus GK, Cartier M, Marshall N, Zhang S, Dahmus ME, Greenblatt J.; ''FCP1, the RAP74-interacting subunit of a human protein phosphatase that dephosphorylates the carboxyl-terminal domain of RNA polymerase IIO.''; PubMed Europe PMC Scholia
  73. Buratowski S.; ''Progression through the RNA polymerase II CTD cycle.''; PubMed Europe PMC Scholia
  74. Schweisguth F.; ''Regulation of notch signaling activity.''; PubMed Europe PMC Scholia
  75. Aso T, Yamazaki K, Amimoto K, Kuroiwa A, Higashi H, Matsuda Y, Kitajima S, Hatakeyama M.; ''Identification and characterization of Elongin A2, a new member of the Elongin family of transcription elongation factors, specifically expressed in the testis.''; PubMed Europe PMC Scholia
  76. Pal M, Luse DS.; ''Strong natural pausing by RNA polymerase II within 10 bases of transcription start may result in repeated slippage and reextension of the nascent RNA.''; PubMed Europe PMC Scholia
  77. Parvin JD, Sharp PA.; ''DNA topology and a minimal set of basal factors for transcription by RNA polymerase II.''; PubMed Europe PMC Scholia
  78. Fiedler U, Timmers HT.; ''Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation.''; PubMed Europe PMC Scholia
  79. Lin C, Smith ER, Takahashi H, Lai KC, Martin-Brown S, Florens L, Washburn MP, Conaway JW, Conaway RC, Shilatifard A.; ''AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia.''; PubMed Europe PMC Scholia
  80. Bernstein LB, Manser T, Weiner AM.; ''Human U1 small nuclear RNA genes: extensive conservation of flanking sequences suggests cycles of gene amplification and transposition.''; PubMed Europe PMC Scholia
  81. Kugel JF, Goodrich JA.; ''Translocation after synthesis of a four-nucleotide RNA commits RNA polymerase II to promoter escape.''; PubMed Europe PMC Scholia
  82. Hernandez N.; ''TBP, a universal eukaryotic transcription factor?''; PubMed Europe PMC Scholia
  83. Näär AM, Lemon BD, Tjian R.; ''Transcriptional coactivator complexes.''; PubMed Europe PMC Scholia
  84. Zawel L, Kumar KP, Reinberg D.; ''Recycling of the general transcription factors during RNA polymerase II transcription.''; PubMed Europe PMC Scholia
  85. Cramer P, Bushnell DA, Kornberg RD.; ''Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution.''; PubMed Europe PMC Scholia
  86. Schaeffer L, Roy R, Humbert S, Moncollin V, Vermeulen W, Hoeijmakers JH, Chambon P, Egly JM.; ''DNA repair helicase: a component of BTF2 (TFIIH) basic transcription factor.''; PubMed Europe PMC Scholia

History

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CompareRevisionActionTimeUserComment
115030view16:57, 25 January 2021ReactomeTeamReactome version 75
113475view11:55, 2 November 2020ReactomeTeamReactome version 74
112674view16:06, 9 October 2020ReactomeTeamReactome version 73
101591view11:46, 1 November 2018ReactomeTeamreactome version 66
101127view21:31, 31 October 2018ReactomeTeamreactome version 65
100655view20:04, 31 October 2018ReactomeTeamreactome version 64
100205view16:49, 31 October 2018ReactomeTeamreactome version 63
99756view15:15, 31 October 2018ReactomeTeamreactome version 62 (2nd attempt)
99318view12:47, 31 October 2018ReactomeTeamreactome version 62
93793view13:36, 16 August 2017ReactomeTeamreactome version 61
93329view11:20, 9 August 2017ReactomeTeamreactome version 61
86414view09:17, 11 July 2016ReactomeTeamreactome version 56
83471view13:23, 18 November 2015ReactomeTeamVersion54
81416view12:56, 21 August 2015ReactomeTeamVersion53
76887view08:16, 17 July 2014ReactomeTeamFixed remaining interactions
76592view11:57, 16 July 2014ReactomeTeamFixed remaining interactions
75625view10:49, 10 June 2014ReactomeTeamReactome 48 Update
74980view13:50, 8 May 2014AnweshaFixing comment source for displaying WikiPathways description
74624view08:40, 30 April 2014ReactomeTeamReactome46
45042view18:59, 6 October 2011ThomasOntology Term : 'RNA Polymerase II transcription pathway' added !
42122view21:58, 4 March 2011MaintBotAutomatic update
39932view05:57, 21 January 2011MaintBotNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
3' end cleaved,

ligated exon

containing complex
ComplexR-HSA-72177 (Reactome)
3'-end cleaved mRNA with spliced exons R-ALL-71998 (Reactome)
ADPMetaboliteCHEBI:16761 (ChEBI)
AFF4 ProteinQ9UHB7 (Uniprot-TrEMBL)
AFF4ProteinQ9UHB7 (Uniprot-TrEMBL)
ALYREF ProteinQ86V81 (Uniprot-TrEMBL)
ATP MetaboliteCHEBI:15422 (ChEBI)
ATPMetaboliteCHEBI:15422 (ChEBI)
Aborted early elongation complexComplexR-HSA-113410 (Reactome)
Aborted elongation

complex after

arrest
ComplexR-HSA-113722 (Reactome)
Arrested processive elongation complexComplexR-HSA-113721 (Reactome)
CASC3 ProteinO15234 (Uniprot-TrEMBL)
CCNH ProteinP51946 (Uniprot-TrEMBL)
CCNK ProteinO75909 (Uniprot-TrEMBL)
CCNT1 ProteinO60563 (Uniprot-TrEMBL)
CCNT1,CCNT2,CCNKComplexR-HSA-6807466 (Reactome)
CCNT2 ProteinO60583 (Uniprot-TrEMBL)
CDC40 ProteinO60508 (Uniprot-TrEMBL)
CDC73 ProteinQ6P1J9 (Uniprot-TrEMBL)
CDK7 ProteinP50613 (Uniprot-TrEMBL)
CDK9 ProteinP50750 (Uniprot-TrEMBL)
CDK9ProteinP50750 (Uniprot-TrEMBL)
CE:Pol II CTD:Spt5 complexComplexR-HSA-77061 (Reactome) Spt5 reacts with Guanyl Transferase (GT) of the capping enzyme (CE).
CF I - 68 kDa subunit R-HSA-72013 (Reactome)
CF I - 72 kDa subunit R-HSA-72014 (Reactome)
CF IIComplexR-HSA-72020 (Reactome)
CF IComplexR-HSA-72015 (Reactome)
CHTOP ProteinQ9Y3Y2 (Uniprot-TrEMBL)
CLP1 ProteinQ92989 (Uniprot-TrEMBL)
CPSF1 ProteinQ10570 (Uniprot-TrEMBL)
CPSF2 ProteinQ9P2I0 (Uniprot-TrEMBL)
CPSF3 ProteinQ9UKF6 (Uniprot-TrEMBL)
CPSF4 ProteinO95639 (Uniprot-TrEMBL)
CPSF7 ProteinQ8N684 (Uniprot-TrEMBL)
CSTF1 ProteinQ05048 (Uniprot-TrEMBL)
CSTF2 ProteinP33240 (Uniprot-TrEMBL)
CSTF2T ProteinQ9H0L4 (Uniprot-TrEMBL)
CSTF3 ProteinQ12996 (Uniprot-TrEMBL)
CTDP1 ProteinQ9Y5B0 (Uniprot-TrEMBL)
CTDP1ProteinQ9Y5B0 (Uniprot-TrEMBL)
CTP MetaboliteCHEBI:17677 (ChEBI)
CTR9 ProteinQ6PD62 (Uniprot-TrEMBL)
Cap Binding Complex (CBC)ComplexR-HSA-77088 (Reactome)
Capped

Intronless Histone

pre-mRNA:CBP80:CBP20:SLBP:ZFP100 Complex
ComplexR-HSA-110766 (Reactome)
Capped Intronless

Histone pre-mRNA:CBC:ZFP100

Complex
ComplexR-HSA-112045 (Reactome)
Capped intronless pre-mRNA R-ALL-112158 (Reactome)
CstFComplexR-HSA-72006 (Reactome)
DDX39A ProteinO00148 (Uniprot-TrEMBL)
DDX39B ProteinQ13838 (Uniprot-TrEMBL)
DHX38 ProteinQ92620 (Uniprot-TrEMBL)
DNA containing Pol

II promoter with transcript with 2

or 3 nucleotides
R-ALL-110068 (Reactome)
DNA containing Pol II promoter with transcript with 2 or 3 nucleotides R-ALL-110068 (Reactome)
DNA containing RNA

Polymerase II

promoter
R-ALL-109627 (Reactome)
DNA containing RNA Polymerase II promoter R-ALL-109627 (Reactome)
DSIF complexComplexR-HSA-112420 (Reactome)
DSIF:NELF:early elongation complexComplexR-HSA-113408 (Reactome)
EAF1 ProteinQ96JC9 (Uniprot-TrEMBL)
EAF1ProteinQ96JC9 (Uniprot-TrEMBL)
EAF2 ProteinQ96CJ1 (Uniprot-TrEMBL)
EAF2ProteinQ96CJ1 (Uniprot-TrEMBL)
EIF4A3 ProteinP38919 (Uniprot-TrEMBL)
ELL ProteinP55199 (Uniprot-TrEMBL)
ELLProteinP55199 (Uniprot-TrEMBL)
ERCC2 ProteinP18074 (Uniprot-TrEMBL)
ERCC3 ProteinP19447 (Uniprot-TrEMBL)
Early elongation

complex with hyperphosphorylated

Pol II CTD
ComplexR-HSA-113426 (Reactome)
Elongating transcript in processive Pol II mediated elongation R-ALL-113717 (Reactome)
Elongating transcript prior to cleavage R-ALL-113725 (Reactome)
Elongating transcript prior to separation R-ALL-113714 (Reactome)
Elongation complex prior to separationComplexR-HSA-113724 (Reactome)
Elongation complex

with separated and uncleaved

transcript
ComplexR-HSA-113726 (Reactome)
Elongation complexComplexR-HSA-112433 (Reactome)
Elongin AComplexR-HSA-8867795 (Reactome)
Elongin B:C complexComplexR-HSA-112424 (Reactome)
Elongin ComplexComplexR-HSA-112425 (Reactome)
FACT complexComplexR-HSA-112417 (Reactome)
FIP1L1 ProteinQ6UN15 (Uniprot-TrEMBL)
FYTTD1 ProteinQ96QD9 (Uniprot-TrEMBL)
GTF2A1(1-274) ProteinP52655 (Uniprot-TrEMBL)
GTF2A1(275-376) ProteinP52655 (Uniprot-TrEMBL)
GTF2A2 ProteinP52657 (Uniprot-TrEMBL)
GTF2B ProteinQ00403 (Uniprot-TrEMBL)
GTF2BProteinQ00403 (Uniprot-TrEMBL)
GTF2E1 ProteinP29083 (Uniprot-TrEMBL)
GTF2E2 ProteinP29084 (Uniprot-TrEMBL)
GTF2F1 ProteinP35269 (Uniprot-TrEMBL)
GTF2F2 ProteinP13984 (Uniprot-TrEMBL)
GTF2H1 ProteinP32780 (Uniprot-TrEMBL)
GTF2H2 ProteinQ13888 (Uniprot-TrEMBL)
GTF2H3 ProteinQ13889 (Uniprot-TrEMBL)
GTF2H4 ProteinQ92759 (Uniprot-TrEMBL)
GTF2H5 ProteinQ6ZYL4 (Uniprot-TrEMBL)
GTP MetaboliteCHEBI:15996 (ChEBI)
Generic

Transcription

Pathway
PathwayR-HSA-212436 (Reactome) OVERVIEW OF TRANSCRIPTION REGULATION:

Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or tissue-specific regulation of differential gene transcription is mediated (reviewed in Naar, 2001. Kadonaga, 2004, Maston, 2006, Barolo, 2002; Roeder, 2005, Rosenfeld, 2006). Of the three major classes of DNA polymerase involved in eukaryotic gene transcription, Polymerase II generally regulates protein-encoding genes. Figure 1 shows a diagram of the various components involved in cell-specific regulation of Pol-II gene transcription.

Core Promoter: Pol II-regulated genes typically have a Core Promoter where Pol II and a variety of general factors bind to specific DNA motifs:
i: the TATA box (TATA DNA sequence), which is bound by the "TATA-binding protein" (TBP).
ii: the Initiator motif (INR), where Pol II and certain other core factors bind, is present in many Pol II-regulated genes.
iii: the Downstream Promoter Element (DPE), which is present in a subset of Pol II genes, and where additional core factors bind.
The core promoter binding factors are generally ubiquitously expressed, although there are exceptions to this.

Proximal Promoter: immediately upstream (5') of the core promoter, Pol II target genes often have a Proximal Promoter region that spans up to 500 base pairs (b.p.), or even to 1000 b.p.. This region contains a number of functional DNA binding sites for a specific set of transcription activator (TA) and transcription repressor (TR) proteins. These TA and TR factors are generally cell- or tissue-specific in expression, rather than ubiquitous, so that the presence of their cognate binding sites in the proximal promoter region programs cell- or tissue-specific expression of the target gene, perhaps in conjunction with TA and TR complexes bound in distal enhancer regions.

Distal Enhancer(s): many or most Pol II regulated genes in higher eukaryotes have one or more distal Enhancer regions which are essential for proper regulation of the gene, often in a cell or tissue-specific pattern. Like the proximal promoter region, each of the distal enhancer regions typically contain a cluster of binding sites for specific TA and/or TR DNA-binding factors, rather than just a single site.

Enhancers generally have three defining characteristics:
i: They can be located very long distances from the promoter of the target gene they regulate, sometimes as far as 100 Kb, or more.
ii: They can be either upstream (5') or downstream (3') of the target gene, including within introns of that gene.
iii: They can function in either orientation in the DNA.

Combinatorial mechanisms of transcription regulation: The specific combination of TA and TR binding sites within the proximal promoter and/or distal enhancer(s) provides a "combinatorial transcription code" that mediates cell- or tissue-specific expression of the associated target gene. Each promoter or enhancer region mediates expression in a specific subset of the overall expression pattern. In at least some cases, each enhancer region functions completely independently of the others, so that the overall expression pattern is a linear combination of the expression patterns of each of the enhancer modules.

Co-Activator and Co-Repressor Complexes: DNA-bound TA and TR proteins typically recruit the assembly of specific Co-Activator (Co-A) and Co-Repressor (Co-R) Complexes, respectively, which are essential for regulating target gene transcription. Both Co-A's and Co-R's are multi-protein complexes that contain several specific protein components.

Co-Activator complexes generally contain at lease one component protein that has Histone Acetyl Transferase (HAT) enzymatic activity. This functions to acetylate Histones and/or other chromatin-associated factors, which typically increases that transcription activation of the target gene. By contrast, Co-Repressor complexes generally contain at lease one component protein that has Histone De-Acetylase (HDAC) enzymatic activity. This functions to de-acetylate Histones and/or other chromatin-associated factors. This typically increases the transcription repression of the target gene.

Adaptor (Mediator) complexes: In addition to the co-activator complexes that assemble on particular cell-specific TA factors, - there are at least two additional transcriptional co-activator complexes common to most cells. One of these is the Mediator complex, which functions as an "adaptor" complex that bridges between the tissue-specific co-activator complexes assembled in the proximal promoter (or distal enhancers). The human Mediator complex has been shown to contain at least 19 protein distinct components. Different combinations of these co-activator proteins are also found to be components of specific transcription Co-Activator complexes, such as the DRIP, TRAP and ARC complexes described below.

TBP/TAF complex: Another large Co-A complex is the "TBP-associated factors" (TAFs) that assemble on TBP (TATA-Binding Protein), which is bound to the TATA box present in many promoters. There are at least 23 human TAF proteins that have been identified. Many of these are ubiquitously expressed, but TAFs can also be expressed in a cell or tissue-specific pattern.


Specific Coactivator Complexes for DNA-binding Transcription Factors.

A number of specific co-activator complexes for DNA-binding transcription factors have been identified, including DRIP, TRAP, and ARC (reviewed in Bourbon, 2004, Blazek, 2005, Conaway, 2005, and Malik, 2005). The DRIP co-activator complex was originally identified and named as a specific complex associated with the Vitamin D Receptor member of the nuclear receptor family of transcription factors (Rachez, 1998). Similarly, the TRAP co-activator complex was originally identified as a complex that associates with the thyroid receptor (Yuan, 1998). It was later determined that all of the components of the DRIP complex are also present in the TRAP complex, and the ARC complex (discussed further below). For example, the DRIP205 and TRAP220 proteins were show to be identical, as were specific pairs of the other components of these complexes (Rachez, 1999).

In addition, these various transcription co-activator proteins identified in mammalian cells were found to be the orthologues or homologues of the Mediator ("adaptor") complex proteins (reviewed in Bourbon, 2004). The Mediator proteins were originally identified in yeast by Kornberg and colleagues, as complexes associated with DNA polymerase (Kelleher, 1990). In higher organisms, Adapter complexes bridge between the basal transcription factors (including Pol II) and tissue-specific transcription factors (TFs) bound to sites within upstream Proximal Promoter regions or distal Enhancer regions (Figure 1). However, many of the Mediator homologues can also be found in complexes associated with specific transcription factors in higher organisms. A unified nomenclature system for these adapter / co-activator proteins now labels them Mediator 1 through Mediator 31 (Bourbon, 2004). For example, the DRIP205 / TRAP220 proteins are now identified as Mediator 1 (Rachez, 1999), based on homology with yeast Mediator 1.


Example Pathway: Specific Regulation of Target Genes During Notch Signaling:

One well-studied example of cell-specific regulation of gene transcription is selective regulation of target genes during Notch signaling. Notch signaling was first identified in Drosophila, where it has been studied in detail at the genetic, molecular, biochemical and cellular levels (reviewed in Justice, 2002; Bray, 2006; Schweisguth, 2004; Louvri, 2006). In Drosophila, Notch signaling to the nucleus is thought always to be mediated by one specific DNA binding transcription factor, Suppressor of Hairless. In mammals, the homologous genes are called CBF1 (or RBPJkappa), while in worms they are called Lag-1, so that the acronym "CSL" has been given to this conserved transcription factor family. There are at least two human CSL homologues, which are now named RBPJ and RBPJL.

In Drosophila, Su(H) is known to be bifunctional, in that it represses target gene transcription in the absence of Notch signaling, but activates target genes during Notch signaling. At least some of the mammalian CSL homologues are believed also to be bifunctional, and to mediate target gene repression in the absence of Notch signaling, and activation in the presence of Notch signaling.

Notch Co-Activator and Co-Repressor complexes: This repression is mediated by at least one specific co-repressor complexes (Co-R) bound to CSL in the absence of Notch signaling. In Drosophila, this co-repressor complex consists of at least three distinct co-repressor proteins: Hairless, Groucho, and dCtBP (Drosophila C-terminal Binding Protein). Hairless has been show to bind directly to Su(H), and Groucho and dCtBP have been shown to bind directly to Hairless (Barolo, 2002). All three of the co-repressor proteins have been shown to be necessary for proper gene regulation during Notch signaling in vivo (Nagel, 2005).

In mammals, the same general pathway and mechanisms are observed, where CSL proteins are bifunctional DNA binding transcription factors (TFs), that bind to Co-Repressor complexes to mediate repression in the absence of Notch signaling, and bind to Co-Activator complexes to mediate activation in the presence of Notch signaling. However, in mammals, there may be multiple co-repressor complexes, rather than the single Hairless co-repressor complex that has been observed in Drosophila.

During Notch signaling in all systems, the Notch transmembrane receptor is cleaved and the Notch intracellular domain (NICD) translocates to the nucleus, where it there functions as a specific transcription co-activator for CSL proteins. In the nucleus, NICD replaces the Co-R complex bound to CSL, thus resulting in de-repression of Notch target genes in the nucleus (Figure 2). Once bound to CSL, NICD and CSL proteins recruit an additional co-activator protein, Mastermind, to form a CSL-NICD-Mam ternary co-activator (Co-A) complex. This Co-R complex was initially thought to be sufficient to mediate activation of at least some Notch target genes. However, there now is evidence that still other co-activators and additional DNA-binding transcription factors are required in at least some contexts (reviewed in Barolo, 2002).

Thus, CSL is a good example of a bifunctional DNA-binding transcription factor that mediates repression of specific targets genes in one context, but activation of the same targets in another context. This bifunctionality is mediated by the association of specific Co-Repressor complexes vs. specific Co-Activator complexes in different contexts, namely in the absence or presence of Notch signaling.
IWS1 ProteinQ96ST2 (Uniprot-TrEMBL)
IWS1ProteinQ96ST2 (Uniprot-TrEMBL)
Intronless Histone pre-mRNA R-ALL-110756 (Reactome)
LEO1 ProteinQ8WVC0 (Uniprot-TrEMBL)
LSM10 ProteinQ969L4 (Uniprot-TrEMBL)
LSM11 ProteinP83369 (Uniprot-TrEMBL)
LUZP4 ProteinQ9P127 (Uniprot-TrEMBL)
MAGOH ProteinP61326 (Uniprot-TrEMBL)
MAGOHB ProteinQ96A72 (Uniprot-TrEMBL)
MLLT1 ProteinQ03111 (Uniprot-TrEMBL)
MLLT1ProteinQ03111 (Uniprot-TrEMBL)
MLLT3 ProteinP42568 (Uniprot-TrEMBL)
MLLT3ProteinP42568 (Uniprot-TrEMBL)
MNAT1 ProteinP51948 (Uniprot-TrEMBL)
Mature

Intronless transcript derived Histone

mRNA:SLBP:CBP80:CBP20
ComplexR-HSA-111682 (Reactome)
Mature Intronless transcript derived Histone mRNA R-ALL-111676 (Reactome)
Mature intronless

transcript derived Histone pre-mRNA:CBC

complex
ComplexR-HSA-156959 (Reactome)
NCBP1 ProteinQ09161 (Uniprot-TrEMBL)
NCBP2 ProteinP52298 (Uniprot-TrEMBL)
NELF complexComplexR-HSA-112432 (Reactome)
NELFA ProteinQ9H3P2 (Uniprot-TrEMBL)
NELFAProteinQ9H3P2 (Uniprot-TrEMBL)
NELFB ProteinQ8WX92 (Uniprot-TrEMBL)
NELFBProteinQ8WX92 (Uniprot-TrEMBL)
NELFCD ProteinQ8IXH7 (Uniprot-TrEMBL)
NELFCDProteinQ8IXH7 (Uniprot-TrEMBL)
NELFE ProteinP18615 (Uniprot-TrEMBL)
NELFEProteinP18615 (Uniprot-TrEMBL)
NTPComplexR-ALL-30595 (Reactome)
NUDT21 ProteinO43809 (Uniprot-TrEMBL)
Open DNA -10 to +2 containing RNA Polymerase II promoter R-ALL-109875 (Reactome)
P-TEFb complexComplexR-HSA-112431 (Reactome)
PABPN1 ProteinQ86U42 (Uniprot-TrEMBL)
PAF1 ProteinQ8N7H5 (Uniprot-TrEMBL)
PAF1CComplexR-HSA-8866690 (Reactome)
PAPOLA ProteinP51003 (Uniprot-TrEMBL)
PCF11 ProteinO94913 (Uniprot-TrEMBL)
POLDIP3 ProteinQ9BY77 (Uniprot-TrEMBL)
POLR2A ProteinP24928 (Uniprot-TrEMBL)
POLR2B ProteinP30876 (Uniprot-TrEMBL)
POLR2C ProteinP19387 (Uniprot-TrEMBL)
POLR2D ProteinO15514 (Uniprot-TrEMBL)
POLR2E ProteinP19388 (Uniprot-TrEMBL)
POLR2F ProteinP61218 (Uniprot-TrEMBL)
POLR2G ProteinP62487 (Uniprot-TrEMBL)
POLR2H ProteinP52434 (Uniprot-TrEMBL)
POLR2I ProteinP36954 (Uniprot-TrEMBL)
POLR2J ProteinP52435 (Uniprot-TrEMBL)
POLR2K ProteinP53803 (Uniprot-TrEMBL)
POLR2L ProteinP62875 (Uniprot-TrEMBL)
PPiMetaboliteCHEBI:29888 (ChEBI)
Paused processive elongation complexComplexR-HSA-113720 (Reactome)
PiMetaboliteCHEBI:18367 (ChEBI)
Pol II Initiation

complex with phosphodiester-PPi

intermediate
ComplexR-HSA-83601 (Reactome)
Pol II Promoter Escape ComplexComplexR-HSA-75859 (Reactome)
Pol II initiation complexComplexR-HSA-83551 (Reactome)
Pol II transcription

complex containing extruded transcript

to +30
ComplexR-HSA-157171 (Reactome)
Pol II transcription

complex containing

transcript to +30
ComplexR-HSA-111261 (Reactome)
Pol II transcription

complex with (ser5) phosphorylated CTD containing extruded

transcript to +30
ComplexR-HSA-157174 (Reactome)
Processive elongation complexComplexR-HSA-113719 (Reactome)
RBM8A ProteinQ9Y5S9 (Uniprot-TrEMBL)
RNA

Pol II

(hypophosphorylated) complex bound to DSIF protein
ComplexR-HSA-113406 (Reactome)
RNA

Pol II

(hypophosphorylated):capped pre-mRNA complex
ComplexR-HSA-113715 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
ComplexR-HSA-71307 (Reactome)
RNA

Polymerase II holoenzyme complex

(hyperphosphorylated)
ComplexR-HSA-109909 (Reactome)
RNA Pol II with

phosphorylated CTD: CE complex with

activated GT
ComplexR-HSA-77056 (Reactome)
RNA Pol II with

phosphorylated CTD:

CE complex
ComplexR-HSA-77053 (Reactome)
RNA polymerase II

transcribes snRNA

genes
PathwayR-HSA-6807505 (Reactome) Small nuclear RNAs (snRNAs) play key roles in splicing and some of them, specifically the U1 and U2 snRNAs, are encoded by multicopy snRNA gene clusters containing tandem arrays of genes, about 30 in the RNU1 cluster (Bernstein et al. 1985) and about 10-20 in the RNU2 cluster (Van Ardsell and Weiner 1984). Whereas U6 snRNA genes are transcribed by RNA polymerase III, U1,U2, U4, U4atac, U5, U11, and U12 genes are transcribed by RNA polymerase II. Transcription of the U1 and U2 genes has been most extensively studied and the other snRNA genes as well as other genes with similar promoter structures, for example the SNORD13 gene, are inferred to be transcribed by similar reactions. The snRNA genes transcribed by RNA polymerase II are distinguished from mRNA-encoding genes by the presence of a proximal sequence element (PSE) rather than a TATA box and the presence of the Integrator complex rather than the Mediator complex (reviewed in Egloff et al. 2008, Jawdeker and Henry 2008).
The snRNA genes are among the most rapidly transcribed genes in the genome. The 5' transcribed region of the U2 snRNA gene is largely single-stranded during interphase and metaphase (Pavelitz et al. 2008) and chromatin within the transcribed region is cleared of nucleosomes (O'Reilly et al. 2014). Transcriptional activation of the RNA polymerase II transcribed snRNA genes begins with binding of transcription factors to the distal sequence element (DSE) of the promoter (reviewed in Hernandez 2001, Egloff et al. 2008, Jawdeker and Henry 2008). The factors, which include POU2F1 (Oct-1), POU2F2 (Oct-2), ZNF143 (Staf) and Sp1, promote binding of the SNAPc complex (also known as PTF and PBP) to the PSE. SNAPc helps clear the gene of nucleosomes (O'Reilly et al. 2014) and recruits initiation factors (TFIIA, TFIIB, TFIIE, TFIIF, and snTAFc:TBP) which recruit RNA polymerase II. Phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (reviewed in Egloff and Murphy 2008) by CDK7 recruits RPAP2 and the Integrator complex, which is required for later processing of the 3' end of the pre-snRNA transcript (reviewed in Chen and Wagner 2010, Baillat and Wagner 2015). The Little Elongation Complex (LEC) also appears to bind around the time of transcription initiation (Hu et al. 2013). As transcription proceeds, RPAP2 dephosphorylates serine-5 and P-TEFb phosphorylates serine-2 of the CTD. As transcription reaches the end of the snRNA gene serine-7 of the CTD is phosphorylated. These marks serve to bind protein complexes and are required for 3' processing of the pre-snRNA (reviewed in Egloff and Murphy 2008). After transcription proceeds through the conserved 3' processing sequence of the pre-snRNA the Integrator complex cleaves the pre-snRNA. Transcription then terminates downstream in a less well characterized reaction that requires elements of the polyadenylation system.
RNGTT ProteinO60942 (Uniprot-TrEMBL)
RNGTTProteinO60942 (Uniprot-TrEMBL)
RNMT ProteinO43148 (Uniprot-TrEMBL)
RNMTProteinO43148 (Uniprot-TrEMBL)
RNPS1 ProteinQ15287 (Uniprot-TrEMBL)
RTF1 ProteinQ92541 (Uniprot-TrEMBL)
SARNP ProteinP82979 (Uniprot-TrEMBL)
SLBP ProteinQ14493 (Uniprot-TrEMBL)
SNRPB ProteinP14678 (Uniprot-TrEMBL)
SNRPD3 ProteinP62318 (Uniprot-TrEMBL)
SNRPE ProteinP62304 (Uniprot-TrEMBL)
SNRPF ProteinP62306 (Uniprot-TrEMBL)
SNRPG ProteinP62308 (Uniprot-TrEMBL)
SRRM1 ProteinQ8IYB3 (Uniprot-TrEMBL)
SRSF1 ProteinQ07955 (Uniprot-TrEMBL)
SRSF11 ProteinQ05519 (Uniprot-TrEMBL)
SRSF2 ProteinQ01130 (Uniprot-TrEMBL)
SRSF3 ProteinP84103 (Uniprot-TrEMBL)
SRSF4 ProteinQ08170 (Uniprot-TrEMBL)
SRSF5 ProteinQ13243 (Uniprot-TrEMBL)
SRSF6 ProteinQ13247 (Uniprot-TrEMBL)
SRSF7 ProteinQ16629 (Uniprot-TrEMBL)
SRSF9 ProteinQ13242 (Uniprot-TrEMBL)
SSRP1 ProteinQ08945 (Uniprot-TrEMBL)
SSRP1ProteinQ08945 (Uniprot-TrEMBL)
SUPT16H ProteinQ9Y5B9 (Uniprot-TrEMBL) DSIF is a heterodimer consisting of hSPT4 (human homolog of yeast Spt4- p14) and hSPT5 (human homolog of yeast Spt5-p160). DSIF association with Pol II may be enabled by Spt5 binding to Pol II creating a scaffold for NELF binding (Wada et al.,1998). Spt5 subunit of DSIF can be phosphorylated by P-TEFb.
SUPT16HProteinQ9Y5B9 (Uniprot-TrEMBL) DSIF is a heterodimer consisting of hSPT4 (human homolog of yeast Spt4- p14) and hSPT5 (human homolog of yeast Spt5-p160). DSIF association with Pol II may be enabled by Spt5 binding to Pol II creating a scaffold for NELF binding (Wada et al.,1998). Spt5 subunit of DSIF can be phosphorylated by P-TEFb.
SUPT4H1 ProteinP63272 (Uniprot-TrEMBL)
SUPT4H1ProteinP63272 (Uniprot-TrEMBL)
SUPT6H ProteinQ7KZ85 (Uniprot-TrEMBL)
SUPT6HProteinQ7KZ85 (Uniprot-TrEMBL)
SYMPK ProteinQ92797 (Uniprot-TrEMBL)
Spliced mRNA:CBC:EJC:TREXComplexR-HSA-8850671 (Reactome)
TAF1 ProteinP21675 (Uniprot-TrEMBL)
TAF10 ProteinQ12962 (Uniprot-TrEMBL)
TAF11 ProteinQ15544 (Uniprot-TrEMBL)
TAF12 ProteinQ16514 (Uniprot-TrEMBL)
TAF13 ProteinQ15543 (Uniprot-TrEMBL)
TAF1L ProteinQ8IZX4 (Uniprot-TrEMBL)
TAF2 ProteinQ6P1X5 (Uniprot-TrEMBL)
TAF3 ProteinQ5VWG9 (Uniprot-TrEMBL)
TAF4 ProteinO00268 (Uniprot-TrEMBL)
TAF4B ProteinQ92750 (Uniprot-TrEMBL)
TAF5 ProteinQ15542 (Uniprot-TrEMBL)
TAF6 ProteinP49848 (Uniprot-TrEMBL)
TAF7 ProteinQ15545 (Uniprot-TrEMBL)
TAF7L ProteinQ5H9L4 (Uniprot-TrEMBL)
TAF9 ProteinQ16594 (Uniprot-TrEMBL)
TAF9B ProteinQ9HBM6 (Uniprot-TrEMBL)
TBP ProteinP20226 (Uniprot-TrEMBL)
TCEA1 ProteinP23193 (Uniprot-TrEMBL)
TCEA1ProteinP23193 (Uniprot-TrEMBL)
TCEB1 ProteinQ15369 (Uniprot-TrEMBL)
TCEB1ProteinQ15369 (Uniprot-TrEMBL)
TCEB2 ProteinQ15370 (Uniprot-TrEMBL)
TCEB2ProteinQ15370 (Uniprot-TrEMBL)
TCEB3 ProteinQ14241 (Uniprot-TrEMBL)
TCEB3B ProteinQ8IYF1 (Uniprot-TrEMBL)
TCEB3C ProteinQ8NG57 (Uniprot-TrEMBL)
TCEB3CL ProteinQ3SY89 (Uniprot-TrEMBL)
TCEB3CL2 ProteinA6NLF2 (Uniprot-TrEMBL)
TFIIAComplexR-HSA-109629 (Reactome)
TFIIDComplexR-HSA-109626 (Reactome)
TFIIEComplexR-HSA-109633 (Reactome)
TFIIFComplexR-HSA-109631 (Reactome)
TFIIHComplexR-HSA-109634 (Reactome)
THOC1 ProteinQ96FV9 (Uniprot-TrEMBL)
THOC2 ProteinQ8NI27 (Uniprot-TrEMBL)
THOC3 ProteinQ96J01 (Uniprot-TrEMBL)
THOC5 ProteinQ13769 (Uniprot-TrEMBL)
THOC6 ProteinQ86W42 (Uniprot-TrEMBL)
THOC7 ProteinQ6I9Y2 (Uniprot-TrEMBL)
Template DNA hybrid with phosphodiester-PPi intermediate R-ALL-83602 (Reactome)
U2AF1 ProteinQ01081 (Uniprot-TrEMBL)
U2AF1L4 ProteinQ8WU68 (Uniprot-TrEMBL)
U2AF2 ProteinP26368 (Uniprot-TrEMBL)
U7 snRNA R-ALL-110761 (Reactome)
U7 snRNP:ZNF473ComplexR-HSA-110765 (Reactome)
UPF3B ProteinQ9BZI7 (Uniprot-TrEMBL)
UTP MetaboliteCHEBI:15713 (ChEBI)
WDR33 ProteinQ9C0J8 (Uniprot-TrEMBL)
WDR61 ProteinQ9GZS3 (Uniprot-TrEMBL)
ZC3H11A ProteinO75152 (Uniprot-TrEMBL)
ZNF473 ProteinQ8WTR7 (Uniprot-TrEMBL)
capped

pre-mRNA:CBC:RNA Pol II (phosphorylated)

complex
ComplexR-HSA-77089 (Reactome)
capped pre-mRNA R-ALL-72085 (Reactome)
damaged DNA

substrate:nascent

mRNA hybrid
R-ALL-110291 (Reactome)
downstream

intronless mRNA

fragment
R-ALL-112165 (Reactome)
hSLU7 ProteinO95391 (Uniprot-TrEMBL)
hTra2 R-HSA-72063 (Reactome)
intronless pre-mRNA cleavage complexComplexR-HSA-112162 (Reactome)
mRNA 3'-end cleavage factorComplexR-HSA-72075 (Reactome)
mRNA with spliced exons R-ALL-72156 (Reactome)
p-S2,S5-POLR2A ProteinP24928 (Uniprot-TrEMBL) The C-terminal domain (CTD) of POLR2A contains about 52 repeats of the consensus heptad YSPTSPS. Serines-2 and 5 of the heptads are phosphorylated in RNA polymerase II initiating transcription of protein coding genes. The exact repeats that are phosphorylated are not known.
p-S5-POLR2A ProteinP24928 (Uniprot-TrEMBL)
p-SUPT5H ProteinO00267 (Uniprot-TrEMBL)
p-SUPT5HProteinO00267 (Uniprot-TrEMBL)
pol

II

promoter:TFIID:TFIIA:TFIIB complex
ComplexR-HSA-109630 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF complex
ComplexR-HSA-109632 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF:TFIIE complex
ComplexR-HSA-75871 (Reactome)
pol II

promoter:TFIID

complex
ComplexR-HSA-109628 (Reactome)
pol II closed

pre-initiation

complex
ComplexR-HSA-109635 (Reactome)
pol II open

pre-initiation

complex
ComplexR-HSA-109876 (Reactome)
pol II transcription

complex containing 11 nucleotide long

transcript
ComplexR-HSA-75902 (Reactome)
pol II transcription

complex containing 3 Nucleotide long

transcript
ComplexR-HSA-75878 (Reactome)
pol II transcription

complex containing 4 nucleotide long

transcript
ComplexR-HSA-75881 (Reactome)
pol II transcription

complex containing 4-9 nucleotide long

transcript
ComplexR-HSA-75890 (Reactome)
pol II transcription

complex containing 9 nucleotide long

transcript
ComplexR-HSA-75882 (Reactome)
pol II transcription complexComplexR-HSA-109878 (Reactome)
template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end R-ALL-71063 (Reactome)
template DNA with

first transcript dinucleotide, opened to +8

position
R-ALL-109877 (Reactome)
template DNA with first transcript dinucleotide, opened to +8 position R-ALL-109877 (Reactome)
template DNA:11 nucleotide transcript hybrid R-ALL-75901 (Reactome)
template DNA:3 nucleotide transcript hybrid R-ALL-75858 (Reactome)
template DNA:30 nt transcript hybrid R-ALL-111260 (Reactome)
template DNA:4 nucleotide transcript hybrid R-ALL-75884 (Reactome)
template DNA:4-9

nucleotide

transcript hybrid
R-ALL-75897 (Reactome)
template DNA:4-9 nucleotide transcript hybrid R-ALL-75897 (Reactome)
template DNA:9 nucleotide transcript hybrid R-ALL-75888 (Reactome)
template:capped transcript hybrid R-ALL-113424 (Reactome)
upstream

mRNA

fragment:CPSF:PAP:PABPN1 complex
ComplexR-HSA-112164 (Reactome)
upstream intronless mRNA fragment R-ALL-112163 (Reactome)

Annotated Interactions

View all...
SourceTargetTypeDatabase referenceComment
3' end cleaved,

ligated exon

containing complex
ArrowR-HSA-72180 (Reactome)
ADPArrowR-HSA-75949 (Reactome)
AFF4ArrowR-HSA-113429 (Reactome)
AFF4R-HSA-112381 (Reactome)
ATPR-HSA-75949 (Reactome)
Aborted early elongation complexArrowR-HSA-113409 (Reactome)
Aborted elongation

complex after

arrest
ArrowR-HSA-112395 (Reactome)
Arrested processive elongation complexArrowR-HSA-113414 (Reactome)
Arrested processive elongation complexR-HSA-112395 (Reactome)
Arrested processive elongation complexR-HSA-113413 (Reactome)
CCNT1,CCNT2,CCNKR-HSA-112430 (Reactome)
CDK9R-HSA-112430 (Reactome)
CE:Pol II CTD:Spt5 complexArrowR-HSA-77073 (Reactome)
CF IArrowR-HSA-72180 (Reactome)
CF IArrowR-HSA-77592 (Reactome)
CF IIArrowR-HSA-72180 (Reactome)
CF IIArrowR-HSA-77592 (Reactome)
CTDP1ArrowR-HSA-113429 (Reactome)
CTDP1R-HSA-112383 (Reactome)
CTDP1mim-catalysisR-HSA-112383 (Reactome)
Cap Binding Complex (CBC)ArrowR-HSA-112381 (Reactome)
Capped

Intronless Histone

pre-mRNA:CBP80:CBP20:SLBP:ZFP100 Complex
R-HSA-77586 (Reactome)
Capped Intronless

Histone pre-mRNA:CBC:ZFP100

Complex
R-HSA-111437 (Reactome)
CstFArrowR-HSA-72180 (Reactome)
CstFArrowR-HSA-77592 (Reactome)
DNA containing Pol

II promoter with transcript with 2

or 3 nucleotides
ArrowR-HSA-75856 (Reactome)
DNA containing RNA

Polymerase II

promoter
R-HSA-109636 (Reactome)
DSIF complexArrowR-HSA-112434 (Reactome)
DSIF complexArrowR-HSA-113429 (Reactome)
DSIF complexR-HSA-113407 (Reactome)
DSIF:NELF:early elongation complexArrowR-HSA-113402 (Reactome)
DSIF:NELF:early elongation complexR-HSA-112381 (Reactome)
DSIF:NELF:early elongation complexR-HSA-113409 (Reactome)
EAF1ArrowR-HSA-113429 (Reactome)
EAF1R-HSA-112381 (Reactome)
EAF2ArrowR-HSA-113429 (Reactome)
EAF2R-HSA-112381 (Reactome)
ELLArrowR-HSA-113429 (Reactome)
ELLR-HSA-112381 (Reactome)
Early elongation

complex with hyperphosphorylated

Pol II CTD
ArrowR-HSA-112381 (Reactome)
Early elongation

complex with hyperphosphorylated

Pol II CTD
R-HSA-112379 (Reactome)
Elongation complex prior to separationArrowR-HSA-113412 (Reactome)
Elongation complex prior to separationR-HSA-112396 (Reactome)
Elongation complex

with separated and uncleaved

transcript
ArrowR-HSA-112396 (Reactome)
Elongation complexArrowR-HSA-112379 (Reactome)
Elongation complexR-HSA-112385 (Reactome)
Elongin AR-HSA-112436 (Reactome)
Elongin B:C complexArrowR-HSA-112435 (Reactome)
Elongin B:C complexR-HSA-112436 (Reactome)
Elongin ComplexArrowR-HSA-112436 (Reactome)
Elongin ComplexArrowR-HSA-113429 (Reactome)
Elongin ComplexR-HSA-112379 (Reactome)
FACT complexArrowR-HSA-112429 (Reactome)
FACT complexArrowR-HSA-113429 (Reactome)
FACT complexR-HSA-112379 (Reactome)
GTF2BArrowR-HSA-73946 (Reactome)
GTF2BArrowR-HSA-75856 (Reactome)
GTF2BArrowR-HSA-75869 (Reactome)
GTF2BR-HSA-109637 (Reactome)
IWS1ArrowR-HSA-113429 (Reactome)
IWS1R-HSA-112379 (Reactome)
MLLT1ArrowR-HSA-113429 (Reactome)
MLLT1R-HSA-112381 (Reactome)
MLLT3ArrowR-HSA-113429 (Reactome)
MLLT3R-HSA-112381 (Reactome)
Mature

Intronless transcript derived Histone

mRNA:SLBP:CBP80:CBP20
ArrowR-HSA-77586 (Reactome)
Mature intronless

transcript derived Histone pre-mRNA:CBC

complex
ArrowR-HSA-111437 (Reactome)
NELF complexArrowR-HSA-112437 (Reactome)
NELF complexArrowR-HSA-113429 (Reactome)
NELF complexR-HSA-113402 (Reactome)
NELFAR-HSA-112437 (Reactome)
NELFBR-HSA-112437 (Reactome)
NELFCDR-HSA-112437 (Reactome)
NELFER-HSA-112437 (Reactome)
NTPArrowR-HSA-113402 (Reactome)
NTPArrowR-HSA-113412 (Reactome)
NTPArrowR-HSA-113429 (Reactome)
NTPR-HSA-111264 (Reactome)
NTPR-HSA-112385 (Reactome)
NTPR-HSA-113402 (Reactome)
NTPR-HSA-113412 (Reactome)
NTPR-HSA-75850 (Reactome)
NTPR-HSA-75861 (Reactome)
NTPR-HSA-75869 (Reactome)
NTPR-HSA-75873 (Reactome)
NTPR-HSA-76576 (Reactome)
P-TEFb complexArrowR-HSA-112430 (Reactome)
P-TEFb complexArrowR-HSA-113429 (Reactome)
P-TEFb complexR-HSA-112381 (Reactome)
P-TEFb complexmim-catalysisR-HSA-112381 (Reactome)
PAF1CArrowR-HSA-113429 (Reactome)
PAF1CR-HSA-112379 (Reactome)
PPiArrowR-HSA-111264 (Reactome)
PPiArrowR-HSA-75850 (Reactome)
PPiArrowR-HSA-75864 (Reactome)
PPiArrowR-HSA-75869 (Reactome)
PPiArrowR-HSA-75873 (Reactome)
PPiArrowR-HSA-76576 (Reactome)
Paused processive elongation complexArrowR-HSA-113411 (Reactome)
Paused processive elongation complexR-HSA-112392 (Reactome)
PiArrowR-HSA-75949 (Reactome)
Pol II Initiation

complex with phosphodiester-PPi

intermediate
ArrowR-HSA-75866 (Reactome)
Pol II Initiation

complex with phosphodiester-PPi

intermediate
R-HSA-75864 (Reactome)
Pol II Promoter Escape ComplexR-HSA-75856 (Reactome)
Pol II initiation complexArrowR-HSA-75861 (Reactome)
Pol II initiation complexR-HSA-75866 (Reactome)
Pol II transcription

complex containing extruded transcript

to +30
ArrowR-HSA-113430 (Reactome)
Pol II transcription

complex containing extruded transcript

to +30
R-HSA-77071 (Reactome)
Pol II transcription

complex containing extruded transcript

to +30
mim-catalysisR-HSA-77071 (Reactome)
Pol II transcription

complex containing

transcript to +30
ArrowR-HSA-111264 (Reactome)
Pol II transcription

complex containing

transcript to +30
R-HSA-113430 (Reactome)
Pol II transcription

complex with (ser5) phosphorylated CTD containing extruded

transcript to +30
ArrowR-HSA-77071 (Reactome)
Pol II transcription

complex with (ser5) phosphorylated CTD containing extruded

transcript to +30
R-HSA-77069 (Reactome)
Processive elongation complexArrowR-HSA-112385 (Reactome)
Processive elongation complexArrowR-HSA-112392 (Reactome)
Processive elongation complexArrowR-HSA-113413 (Reactome)
Processive elongation complexR-HSA-113411 (Reactome)
Processive elongation complexR-HSA-113412 (Reactome)
Processive elongation complexR-HSA-113414 (Reactome)
Processive elongation complexR-HSA-113429 (Reactome)
R-HSA-109636 (Reactome) Although TBP (TATA box binding factor) is necessary and sufficient for initiation of basal transcription, the other subunits of the general transcription factor TFIID, the TBP-associated factors, are required for response to transcriptional activators. TBP binds to the TATA box (a core promoter element), and bends the DNA 80 degrees toward the major groove. This conformation of TBP-TATA box provides the proper topology for the binding of the general transcription factor TFIIB.

Transcriptional activators function by affecting the kinetics of binding of TBP to the promoter DNA.

R-HSA-109637 (Reactome) The general transcription factor TFIIB is a single polypeptide of approximately 35 kDa. There is a Zn-binding domain near the N terminus of TFIIB, and the C-terminal domain encompasses two imperfect repeats; between the N and C termini is a phylogenetically conserved region. The C terminus interacts with TBP and RNA Polymerase II, whereas the N terminus interacts with factor TFIIF and RNA polymerase II. TFIIB is a sequence-specific factor, and it interacts with the BRE element within the promoter.

TFIIB interacts with the Rpb1 subunit of RNA polymerase II to define transcription strat sites. Several activators directly bind TFIIB, and stimulate transcription. The N-terminus and the C-terminus can participate in intramolecular interactions, and this can be disrupted by specific activators by causing a conformational change in TFIIB.

TFIIA also binds the preinitiation complex along with TFIIB. However, TFIIA is not required for accurate initiation, but rather functions as a coactivator of transcription.

R-HSA-109638 (Reactome) The general transcription factor TFIIF has a high affinity for the RNA Polymerase II holoenzyme. TFIIF stabilizes the preinitiation complex, and suppresses non-specific binding of RNA Pol II to DNA, and is thus critical for start site recognition.
R-HSA-109639 (Reactome) The binding of TFIIH completes the assembly of the preinitiation complex (PIC) for RNA Polymerase II transcription. Although RNA polymerase binds the TATA box on the promoter DNA, no initiation of transcription occurs until TFIIH is bound to the PIC. TFIIH is the only factor with known enzymatic activities.
R-HSA-111264 (Reactome) RNA polymerase II transcription complexes are susceptible to transcriptional stalling and arrest, when extending nascent transcripts to 30-nt. This susceptibility depends on presence on down-stream DNA, the particular DNA-sequence of the template and presence of transcription factors. Transcription factor TFIIH remains associated to the RNA pol II elongation complex until position +30. At this stage transcription elongation factor TFIIS can rescue stalled transcription elongation complexes. The transcription bubble varies between 13- and 22-nt in size.
R-HSA-111437 (Reactome) Processing is initiated once the U7 snRNP is loaded onto the pre-mRNA. The pre-mRNA HDE makes base-pairing contacts with the 5�² end of U7 snRNA. Binding of the U7 snRNP to the pre-mRNA is stabilized by interactions between a U7 snRNP protein, hZFP100 and other trans-acting factors, including the factor that catalyzes the cleavage reaction, which have yet to be defined. The cleavage occurs in the presence of EDTA as does the cleavage reaction in polyadenylation, it is likely that this reaction is catalyzed by a protein. There may well be additional proteins associated with the U7 snRNP, since the in vitro processing occurs in the absence of SLBP, it is possible that all the other factors required for processing are associated with the active form of the U7 snRNP.
R-HSA-112379 (Reactome) At the beginning of this reaction, 1 molecule of 'FACT complex', 1 molecule of 'Elongin Complex', 1 molecule of 'Early elongation complex with hyperphosphorylated Pol II CTD', 1 molecule of 'TFIIH', 1 molecule of 'RNA polymerase II elongation factor ELL', and 1 molecule of 'TFIIS protein' are present. At the end of this reaction, 1 molecule of 'Elongation complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-112381 (Reactome) Cdk-9 is the kinase subunit of P-TEFb that phosphorylates Serine 2 on the heptapeptide repeats of Pol II CTD alleviating the negative action of DSIF-NELF complex. This reaction is considered to be a rate limiting step for processive elongation. P-TEFb complex, that has a DRB-sensitive cyclin-dependent kinase activity, is composed of ~43 kDa, Cdk9 kinase (PITALRE), and either Cyclin T1, Cyclin T2a, Cyclin T2b, or Cyclin K. The exact mechanism by which P-TEFb removes the inhibition of elongation by DSIF-NELF is not yet known. P-TEFb is also capable of phosphorylating Spt5 subunit of DSIF complex.
A P-TEFb complex (which contains only the Cyclin T1) is implicated in the efficient synthesis of human immunodeficiency virus-1 (HIV-1) transcripts. Cyclin T1 subunit of the P-TEFb(Cyclin T1:Cdk9) complex interacts with HIV-1 encoded Tat protein that binds to the transactivation response (TAR) element in the nascent HIV-1 transcript (reviewed in Price,2000).
The mechanism by which DSIF, NELF and P-TEFb or TAK/P-TEFb act together in Pol II-regulated elongation is yet to be fully understood. Various biochemical evidences point to a model in which DSIF and NELF negatively regulate elongation through interactions with polymerase containing a hypophosphorylated CTD. Subsequent phosphorylation of the Pol II CTD by P-TEFb might promote elongation by inhibiting interactions of DSIF and NELF with the elongation complex.

R-HSA-112383 (Reactome) FCP1 dephosphorylates RNAP II in ternary elongation complexes as well as in solution and is thought to function in the recycling of RNAP II during the transcription cycle. Biochemical experiments suggest that human FCP1 targets CTDs that are phosphorylated at serine 2 (CTD-serine 2) and/or CTD-serine 5. It is also observed to stimulate elongation independent of its catalytic activity. Dephosphorylation of Ser2 - phosphorylated Pol II results in hypophosphorylated form that disengages capping enzymes (CE).
R-HSA-112385 (Reactome) High-resolution structures of free, catalytically active yeast Pol II and of an elongating form reveal that Pol II elongation complex includes features like:
- RNA-DNA hybrid, an unwound template ahead of 3'-OH terminus of growing transcript and an exit groove at the base of the CTD, possibly for dynamic interaction of processing and transcriptional factors.
- a cleft or channel created by Rpb1 and Rpb2 subunits to accommodate DNA template, extending to Mg2+ ion located deep in the enzyme core
-a 50 kDa "clamp" with open confirmation in free polymerase, allowing entry of DNA strands but closed in the processive elongation phase.
The clamp is composed of portions of Rpb1,Rpb2 and Rpb3 , five loops or "switches" that change from unfolded to well-folded structures stabilizing the elongation complex, and a long "bridging helix" that emanates from Rpb1 subunit, crossing near the Mg2+ ion. The bridging helix is thought to "bend" to push on the base pair at the 3'-end of RNA-DNA hybrid like a ratchet, translocating Pol II along the DNA (Cramer et al.,2001; Gnatt et al.,2001).In addition to its dynamic biochemical potential, Pol II possess a repertoire of functions to serve as a critical platform of recruiting and coordinating the actions of a host of additional enzyme and proteins involved in various pathways.

R-HSA-112392 (Reactome) Recovery from pausing occurs spontaneously after a variable length of time as the enzyme spontaneously slides forward again. This renders the transcript's 3'-OH terminus realigned with the catalytic Mg2+ site of the enzyme. TFIIS is capable of excising the nascent transcript at 2 or 3 nucleotides upstream of the transcript's 3'-end to reinitiate processive elongation (reviewed by Shilatifard et al., 2003).
R-HSA-112395 (Reactome) At the beginning of this reaction, 1 molecule of 'Arrested processive elongation complex' is present. At the end of this reaction, 1 molecule of 'Aborted elongation complex after arrest' is present.

This reaction takes place in the 'nucleus'.

R-HSA-112396 (Reactome) At the beginning of this reaction, 1 molecule of 'Elongation complex prior to separation' is present. At the end of this reaction, 1 molecule of 'Elongation complex with separated and uncleaved transcript' is present.

This reaction takes place in the 'nucleus'.

R-HSA-112429 (Reactome) At the beginning of this reaction, 1 molecule of 'FACT 140 kDa subunit', and 1 molecule of 'FACT 80 kDa subunit' are present. At the end of this reaction, 1 molecule of 'FACT complex' is present.

This reaction takes place in the 'nucleus' (Kamakaka et al.1993, Orphanides et al.1998).

R-HSA-112430 (Reactome) At the beginning of this reaction, 1 molecule of 'Cdk 9 protein', 1 molecule of 'Cyclin T1', and 1 molecule of 'Cyclin T2' are present. At the end of this reaction, 1 molecule of 'P-TEFb complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-112434 (Reactome) At the beginning of this reaction, 1 molecule of 'SUPT5H protein', and 1 molecule of 'SPT4H1 protein' are present. At the end of this reaction, 1 molecule of 'DSIF complex' is present (Wada et al. 1998).

This reaction takes place in the 'nucleus'.

R-HSA-112435 (Reactome) At the beginning of this reaction, 1 molecule of 'Elongin B protein', and 1 molecule of 'Elongin C protein' are present. At the end of this reaction, 1 molecule of 'Elongin B:C complex' is present. This reaction takes place in the 'nucleus' (Aso et al., 1995; Duan et al., 1995b; Kibel et al., 1995).
R-HSA-112436 (Reactome) At the beginning of this reaction, 1 molecule of 'Elongin A1 protein', and 1 molecule of 'Elongin B:C complex' are present. At the end of this reaction, 1 molecule of 'Elongin Complex' is present.

This reaction takes place in the 'nucleus' (Kibel et al. 1995, Aso et al. 1995, Duan et al. 1995).

R-HSA-112437 (Reactome) At the beginning of this reaction, 1 molecule of 'NELF-A protein', 1 molecule of 'RD protein', 1 molecule of 'NELF-B protein', and 1 molecule of 'NELF-C/D protein' are present. At the end of this reaction, 1 molecule of 'NELF complex' is present(Yamaguchi et al.1999).

This reaction takes place in the 'nucleus'.

R-HSA-113402 (Reactome) NELF complex is a ~ 300 kDa multiprotein complex composed of 5 peptides (A - E): ~66,61,59,58 and 46 kDa. All these peptides are required for NELF-mediated inhibition of Pol II elongation. NELF complex has been reported to bind to the pre-formed DSIF:RNA Pol II complex that may act as a scaffold for its binding. NELF-A is suspected to be involved in Wolf-Hirschhorn syndrome.
Binding of DSIF:NELF to RNA Pol II CTD results in abortive termination of early elongation steps by the growing transcripts.
R-HSA-113407 (Reactome) DSIF is a heterodimer consisting of hSPT4 (human homolog of yeast Spt4- p14) and hSPT5 (human homolog of yeast Spt5-p160). DSIF association with Pol II may be enabled by Spt5 binding to Pol II creating a scaffold for NELF binding (Wada et al.,1998). Spt5 subunit of DSIF can be phosphorylated by P-TEFb.
R-HSA-113409 (Reactome) In the early elongation phase, shorter transcripts typically of ~30 nt in length are generated due to random termination of elongating nascent transcripts. This abortive cessation of elongation has been observed mainly in the presence of DSIF-NELF bound to Pol II complex. (Reviewed in Conaway et al.,2000; Shilatifard et al., 2003 ).
R-HSA-113411 (Reactome) Pol II pausing is believed to result from reversible backtracking of the Pol II enzyme complex by ~2 to 4 nucleotides. This leads to misaligned 3'-OH terminus that is unable to be an acceptor for the incoming NTPs in synthesis of next phosphodiester bond (reviewed by Shilatifard et al., 2003).
R-HSA-113412 (Reactome) At the beginning of this reaction, 1 molecule of 'Processive elongation complex', and 1 molecule of 'NTP' are present. At the end of this reaction, 1 molecule of 'Elongation complex prior to separation', and 1 molecule of 'NTP' are present.

This reaction takes place in the 'nucleus'.

R-HSA-113413 (Reactome) TFIIS reactivates arrested RNA Pol II directly interacting with the enzyme resulting in endonucleolytic excision of nascent transcript ~7-14 nucleotides upstream of the 3' end. This reaction is catalyzed by the catalytic site and results in the generation of a new 3'-OH terminus that could be used for re-extension from the correctly base paired site (reviewed by Shilatifard et al., 2003).
R-HSA-113414 (Reactome) RNA Pol II arrest is believed to be a result of irreversible backsliding of the enzyme by ~7-14 nucleotides. It is suggested that, arrest leads to extrusion of displaced transcripts 3'-end through the small pore near the Mg2+ ion. Pol II arrest may lead to abortive termination of elongation due to irreversible trapping of the 3'-end of the displaced transcript in the pore (reviewed by Shilatifard et al., 2003).
R-HSA-113429 (Reactome) At the beginning of this reaction, 1 molecule of 'Processive elongation complex' is present. At the end of this reaction, 1 molecule of 'DSIF complex', 1 molecule of 'FACT complex', 1 molecule of 'RNA Polymerase II holoenzyme complex (hyperphosphorylated)', 1 molecule of 'damaged DNA substrate:nascent mRNA hybrid', 1 molecule of 'Elongin Complex', 1 molecule of 'FCP1P protein', 1 molecule of 'P-TEFb complex', 1 molecule of 'NELF complex', 1 molecule of 'RNA polymerase II elongation factor ELL', 1 molecule of 'NTP', 1 molecule of 'TFIIS protein', and 1 molecule of 'TFIIF' are present.

This reaction takes place in the 'nucleus' (Woudstra et al. 2002).

R-HSA-113430 (Reactome) At the beginning of this reaction, 1 molecule of 'Pol II transcription complex containing transcript to +30' is present. At the end of this reaction, 1 molecule of 'Pol II transcription complex containing extruded transcript to +30' is present.

This reaction takes place in the 'nucleus' (Buratowski 2009).
R-HSA-72180 (Reactome) Endonucleolytic cleavage separates the pre-mRNA into an upstream fragment destined to become the mature mRNA, and a downstream fragment that is rapidly degraded. Cleavage depends on two signals in the RNA, a highly conserved hexanucleotide, AAUAAA, 10 to 30 nucleotides upstream of the cleavage site, and a poorly conserved GU- or U-rich downstream element. Additional sequences, often upstream of AAUAAA, can enhance the efficiency of the reaction. Cleavage occurs most often after a CA dinucleotide. A single gene can have more than one 3' processing site.

Cleavage is preceded by the assembly of a large processing complex, the composition of which is poorly defined. ATP, but not its hydrolysis, is required for assembly. Cleavage at the 3'-end of mRNAs depends on a number of protein factors. CPSF, a heterotetramer, binds specifically to the AAUAAA sequence. The heterotrimer CstF binds the downstream element. CF I, which appears to be composed of two subunits, one of several related larger polypeptides and a common smaller one, also binds RNA, but with unknown specificity. RNA recognition by these proteins is cooperative. Cleavage also requires CF II, composed of at least two subunits, and poly(A) polymerase, the enzyme synthesizing the poly(A) tail in the second step of the reaction. The polypeptide catalyzing the hydrolysis of the phosphodiester bond remains to be identified.

Cleavage produces a 3'-OH on the upstream fragment and a 5'-phosphate on the downstream fragment. At some unknown point after cleavage, the downstream RNA fragment, CstF, CF I and CF II are thought to be released, whereas CPSF and poly(A) polymerase remain to carry out polyadenylation.

R-HSA-73946 (Reactome) At the beginning of this reaction, 1 molecule of 'pol II transcription complex' is present. At the end of this reaction, 1 molecule of 'TFIIA', 1 molecule of 'TFIIH', 1 molecule of 'TFIIE', 1 molecule of 'TFIID', 1 molecule of 'TFIIB', 1 molecule of 'RNA Polymerase II (unphosphorylated):TFIIF complex', and 1 molecule of 'template DNA with first transcript dinucleotide, opened to +8 position' are present.

This reaction takes place in the 'nucleus'.

R-HSA-75095 (Reactome) Factor TFIIE enters the preinitiation complex after TFIIF recruits RNA Polymerase II. TFIIE is composed of two subunits of 56 kDA and 34 kDa. TFIIE facilitates the recruitment of factor TFIIH to the preinitiation complex, and it also stimulates the phosphorylation of the RNA Polymerase II CTD by TFIIH.
R-HSA-75850 (Reactome) Formation of the second phosphodiester bond creates a 3-nt product. This short transcript is still loosely associated with the RNA polymerase II initiation complex and can dissociate to yield abortive products, which are not further extended. The transcription complex still requires continued ATP-hydrolysis by TFIIH and remains sensitive to single-stranded oligo-nucleotide inhibition.

The open region (“transcription bubble�) expands concomitant with the site of RNA-extension. In this case this region spans positions -9 to +3.

R-HSA-75856 (Reactome) At the beginning of this reaction, 1 molecule of 'Pol II Promoter Escape Complex' is present. At the end of this reaction, 1 molecule of 'TFIIA', 1 molecule of 'TFIIH', 1 molecule of 'TFIIE', 1 molecule of 'TFIID', 1 molecule of 'TFIIB', 1 molecule of 'RNA Polymerase II (unphosphorylated):TFIIF complex', and 1 molecule of 'DNA containing Pol II promoter with transcript with 2 or 3 nucleotides' are present.

This reaction takes place in the 'nucleus'.

R-HSA-75861 (Reactome) At the beginning of this reaction, 1 molecule of 'pol II open pre-initiation complex', and 2 molecules of 'NTP' are present. At the end of this reaction, 1 molecule of 'Pol II initiation complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-75862 (Reactome) At the beginning of this reaction, 1 molecule of 'pol II open pre-initiation complex' is present. At the end of this reaction, 1 molecule of 'pol II closed pre-initiation complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-75864 (Reactome) At the beginning of this reaction, 1 molecule of 'Pol II Initiation complex with phosphodiester-PPi intermediate' is present. At the end of this reaction, 1 molecule of 'pyrophosphate', and 1 molecule of 'pol II transcription complex' are present.

This reaction takes place in the 'nucleus'.

R-HSA-75866 (Reactome) At the beginning of this reaction, 1 molecule of 'Pol II initiation complex' is present. At the end of this reaction, 1 molecule of 'Pol II Initiation complex with phosphodiester-PPi intermediate' is present.

This reaction takes place in the 'nucleus'.

R-HSA-75869 (Reactome) Formation of the third phosphodiester bond creates a 4-nt product. This commits the initiation complex to promoter escape. The short 4-nt transcript is still loosely associated with the RNA polymerase II initiation complex and can dissociate to yield abortive products, which are not further extended. Inhibition of ATP-hydrolysis by TFIIH does not lead to collapse of the open region any longer. The transcription complex has lost the sensitivity to single-stranded oligo-nucleotide inhibition. However, ATP-hydrolysis and TFIIH are required for efficient promoter escape. The open region ("transcription bubble") expands concomitant with the site of RNA-extension. In this case this region spans positions -9 to +4.
R-HSA-75873 (Reactome) Formation of the second phosphodiester bond creates a 3-nt product. This transcript is still loosely associated with the RNA polymerase II initiation complex and can dissociate to yield abortive products, which are not further extended. At this stage pausing by RNA polymerase II may result in repeated slippage and reextension of the nascent RNA. The transcription complex still requires continued ATP-hydrolysis by TFIIH for efficient promoter escape. Basal transcription factor TFIIE dissociates from the initiation complex before position +10.

Basal transcription factor TFIIF may reassociate and can stimulate transcription elongation at multiple stages. The open region (“transcription bubble�) expands concomitant with the site of RNA-extension, eventually reaching an open region from -9 to +9.

R-HSA-75891 (Reactome) At the beginning of this reaction, 1 molecule of 'pol II transcription complex containing 4-9 nucleotide long transcript' is present. At the end of this reaction, 1 molecule of 'template DNA:4-9 nucleotide transcript hybrid', 1 molecule of 'TFIIH', 1 molecule of 'TFIIE', and 1 molecule of 'RNA Polymerase II (unphosphorylated):TFIIF complex' are present.

This reaction takes place in the 'nucleus'.

R-HSA-75949 (Reactome) After assembly of the complete RNA polymerase II-preinitiation complex, the next step is separation of the two DNA strands. This isomerization step is known as the closed-to-open complex transition and occurs prior to the initiation of mRNA synthesis. In the RNA polymerase II system this step requires the hydrolysis of ATP or dATP into Pi and ADP or dADP (in contrast to the other RNA polymerase systems) and is catalyzed by the XPB subunit of TFIIH. The region of the promoter, which becomes single-stranded , spans from –10 to +2 relative to the transcription start site.

Negative supercoiling in the promoter region probably induces transient opening events and can alleviate requirement of TFIIE, TFIIH and ATP-hydrolysis for open complex formation. ATP is also used in this step by the cdk7-subunit of TFIIH to phosphorylate the heptad repeats of the C-terminal domain of the largest subunit of RNA polymerase II (RPB1) on serine-2

R-HSA-76576 (Reactome) Formation of phosphodiester bonds nine and ten creates RNA products, which do not dissociate from the RNA pol II initiation complex. The transcription complex has enter the productive elongation phase. TFIIH and ATP-hydrolysis are required for efficient promoter escape. The open region (“transcription bubble�) expands concomitant with the site of RNA-extension. The region upstream from the transcription start site (-9 to -3) collapses to the double-stranded state. TFIIH remains associated to the RNA pol II initiation complex.
R-HSA-77068 (Reactome) At the beginning of this reaction, 1 molecule of 'RNA Pol II with phosphorylated CTD: CE complex' is present. At the end of this reaction, 1 molecule of 'RNA Pol II with phosphorylated CTD: CE complex with activated GT' is present.

This reaction takes place in the 'nucleus'.

R-HSA-77069 (Reactome) At the beginning of this reaction, 1 molecule of 'mRNA capping enzyme', and 1 molecule of 'Pol II transcription complex with (ser5) phosphorylated CTD containing extruded transcript to +30' are present. At the end of this reaction, 1 molecule of 'RNA Pol II with phosphorylated CTD: CE complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-77071 (Reactome) Phosphorylation of serine 5 residue at the CTD of pol II largest subunit is an important step signaling the end of initiation and escape into processive elongation processes. Cdk7 protein subunit of TFIIH phosphorylates RNA Pol II CTD serine 5 residues on its heptad repeats (Buratowski 2009).
R-HSA-77073 (Reactome) The capping enzyme interacts with the Spt5 subunit of transcription elongation factor DSIF. This interaction may couple the capping reaction with promoter escape or elongation, thereby acting as a "checkpoint" to assure that capping has occurred before the polymerase proceeds to make the rest of the transcript (Gonatopoulos-Pournatzis et al.2011).
R-HSA-77586 (Reactome) Processing is initiated once the SLBP (bound to the stem loop) and the U7 snRNP (bound to the HDE) are both loaded onto the pre-mRNA. The pre-mRNA HDE makes base-pairing contacts with the 5�² end of U7 snRNA. Binding of the U7 snRNP to the pre-mRNA is stabilized by interactions between a U7 snRNP protein, hZFP100 and SLBP. It should be noted that there must be other trans-acting factors, including the factor that catalyzes the cleavage reaction, which have yet to be defined. The cleavage occurs in the presence of EDTA as does the cleavage reaction in polyadenylation, it is likely that this reaction is catalyzed by a protein. There may well be additional proteins associated with the U7 snRNP, and since in some conditions in vitro processing occurs in the absence of SLBP, it is possible that all the other factors required for processing are associated with the active form of the U7 snRNP.
R-HSA-77592 (Reactome) The polypeptide catalyzing the hydrolysis of the phosphodiester bond remains to be identified. Cleavage produces a 3'-OH on the upstream fragment and a 5'-phosphate on the downstream fragment. At some unknown point after cleavage, the downstream fragment, CstF, CF I and CF II are thought to be released, whereas CPSF and poly(A) polymerase remain to carry out polyadenylation.
RNA

Pol II

(hypophosphorylated) complex bound to DSIF protein
ArrowR-HSA-113407 (Reactome)
RNA

Pol II

(hypophosphorylated) complex bound to DSIF protein
R-HSA-113402 (Reactome)
RNA

Pol II

(hypophosphorylated):capped pre-mRNA complex
ArrowR-HSA-112383 (Reactome)
RNA

Pol II

(hypophosphorylated):capped pre-mRNA complex
R-HSA-113407 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
ArrowR-HSA-73946 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
ArrowR-HSA-75856 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
ArrowR-HSA-75891 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
R-HSA-109638 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
mim-catalysisR-HSA-111264 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
mim-catalysisR-HSA-75850 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
mim-catalysisR-HSA-75869 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
mim-catalysisR-HSA-75873 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
mim-catalysisR-HSA-76576 (Reactome)
RNA

Polymerase II holoenzyme complex

(hyperphosphorylated)
ArrowR-HSA-113429 (Reactome)
RNA Pol II with

phosphorylated CTD: CE complex with

activated GT
ArrowR-HSA-77068 (Reactome)
RNA Pol II with

phosphorylated CTD: CE complex with

activated GT
R-HSA-77073 (Reactome)
RNA Pol II with

phosphorylated CTD:

CE complex
ArrowR-HSA-77069 (Reactome)
RNA Pol II with

phosphorylated CTD:

CE complex
R-HSA-77068 (Reactome)
RNGTTR-HSA-77069 (Reactome)
RNMTR-HSA-77073 (Reactome)
SSRP1R-HSA-112429 (Reactome)
SUPT16HR-HSA-112429 (Reactome)
SUPT4H1R-HSA-112434 (Reactome)
SUPT6HArrowR-HSA-113429 (Reactome)
SUPT6HR-HSA-112379 (Reactome)
Spliced mRNA:CBC:EJC:TREXR-HSA-72180 (Reactome)
TCEA1ArrowR-HSA-113429 (Reactome)
TCEA1R-HSA-112379 (Reactome)
TCEB1R-HSA-112435 (Reactome)
TCEB2R-HSA-112435 (Reactome)
TFIIAArrowR-HSA-73946 (Reactome)
TFIIAArrowR-HSA-75856 (Reactome)
TFIIAArrowR-HSA-75873 (Reactome)
TFIIAR-HSA-109637 (Reactome)
TFIIDArrowR-HSA-73946 (Reactome)
TFIIDArrowR-HSA-75856 (Reactome)
TFIIDArrowR-HSA-75873 (Reactome)
TFIIDR-HSA-109636 (Reactome)
TFIIEArrowR-HSA-73946 (Reactome)
TFIIEArrowR-HSA-75856 (Reactome)
TFIIEArrowR-HSA-75873 (Reactome)
TFIIEArrowR-HSA-75891 (Reactome)
TFIIER-HSA-75095 (Reactome)
TFIIFArrowR-HSA-113429 (Reactome)
TFIIHArrowR-HSA-112383 (Reactome)
TFIIHArrowR-HSA-112385 (Reactome)
TFIIHArrowR-HSA-73946 (Reactome)
TFIIHArrowR-HSA-75856 (Reactome)
TFIIHArrowR-HSA-75891 (Reactome)
TFIIHR-HSA-109639 (Reactome)
TFIIHR-HSA-112379 (Reactome)
TFIIHR-HSA-112383 (Reactome)
TFIIHmim-catalysisR-HSA-75850 (Reactome)
TFIIHmim-catalysisR-HSA-75869 (Reactome)
TFIIHmim-catalysisR-HSA-75949 (Reactome)
U7 snRNP:ZNF473ArrowR-HSA-111437 (Reactome)
U7 snRNP:ZNF473ArrowR-HSA-77586 (Reactome)
capped

pre-mRNA:CBC:RNA Pol II (phosphorylated)

complex
R-HSA-112383 (Reactome)
damaged DNA

substrate:nascent

mRNA hybrid
ArrowR-HSA-113429 (Reactome)
downstream

intronless mRNA

fragment
ArrowR-HSA-77592 (Reactome)
intronless pre-mRNA cleavage complexR-HSA-77592 (Reactome)
mRNA 3'-end cleavage factormim-catalysisR-HSA-72180 (Reactome)
p-SUPT5HR-HSA-112434 (Reactome)
p-SUPT5HR-HSA-77073 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB complex
ArrowR-HSA-109637 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB complex
R-HSA-109638 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF complex
ArrowR-HSA-109638 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF complex
R-HSA-75095 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF:TFIIE complex
ArrowR-HSA-75095 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF:TFIIE complex
R-HSA-109639 (Reactome)
pol II

promoter:TFIID

complex
ArrowR-HSA-109636 (Reactome)
pol II

promoter:TFIID

complex
R-HSA-109637 (Reactome)
pol II closed

pre-initiation

complex
ArrowR-HSA-109639 (Reactome)
pol II closed

pre-initiation

complex
ArrowR-HSA-75862 (Reactome)
pol II closed

pre-initiation

complex
R-HSA-75949 (Reactome)
pol II open

pre-initiation

complex
ArrowR-HSA-75949 (Reactome)
pol II open

pre-initiation

complex
R-HSA-75861 (Reactome)
pol II open

pre-initiation

complex
R-HSA-75862 (Reactome)
pol II transcription

complex containing 11 nucleotide long

transcript
ArrowR-HSA-76576 (Reactome)
pol II transcription

complex containing 11 nucleotide long

transcript
R-HSA-111264 (Reactome)
pol II transcription

complex containing 3 Nucleotide long

transcript
ArrowR-HSA-75850 (Reactome)
pol II transcription

complex containing 3 Nucleotide long

transcript
R-HSA-75869 (Reactome)
pol II transcription

complex containing 4 nucleotide long

transcript
ArrowR-HSA-75869 (Reactome)
pol II transcription

complex containing 4 nucleotide long

transcript
R-HSA-75873 (Reactome)
pol II transcription

complex containing 4-9 nucleotide long

transcript
R-HSA-75891 (Reactome)
pol II transcription

complex containing 9 nucleotide long

transcript
ArrowR-HSA-75873 (Reactome)
pol II transcription

complex containing 9 nucleotide long

transcript
R-HSA-76576 (Reactome)
pol II transcription complexArrowR-HSA-75864 (Reactome)
pol II transcription complexR-HSA-73946 (Reactome)
pol II transcription complexR-HSA-75850 (Reactome)
template DNA with

first transcript dinucleotide, opened to +8

position
ArrowR-HSA-73946 (Reactome)
template DNA:4-9

nucleotide

transcript hybrid
ArrowR-HSA-75891 (Reactome)
upstream

mRNA

fragment:CPSF:PAP:PABPN1 complex
ArrowR-HSA-77592 (Reactome)
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