Martinez E, Ge H, Tao Y, Yuan CX, Palhan V, Roeder RG.; ''Novel cofactors and TFIIA mediate functional core promoter selectivity by the human TAFII150-containing TFIID complex.''; PubMedEurope PMCScholia
Mandal SS, Cho H, Kim S, Cabane K, Reinberg D.; ''FCP1, a phosphatase specific for the heptapeptide repeat of the largest subunit of RNA polymerase II, stimulates transcription elongation.''; PubMedEurope PMCScholia
Dvir A, Conaway RC, Conaway JW.; ''A role for TFIIH in controlling the activity of early RNA polymerase II elongation complexes.''; PubMedEurope PMCScholia
Kibel A, Iliopoulos O, DeCaprio JA, Kaelin WG.; ''Binding of the von Hippel-Lindau tumor suppressor protein to Elongin B and C.''; PubMedEurope PMCScholia
Roeder RG.; ''Transcriptional regulation and the role of diverse coactivators in animal cells.''; PubMedEurope PMCScholia
Rosenfeld MG, Lunyak VV, Glass CK.; ''Sensors and signals: a coactivator/corepressor/epigenetic code for integrating signal-dependent programs of transcriptional response.''; PubMedEurope PMCScholia
Mousson F, Kolkman A, Pijnappel WW, Timmers HT, Heck AJ.; ''Quantitative proteomics reveals regulation of dynamic components within TATA-binding protein (TBP) transcription complexes.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Hernandez N.; ''Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Justice NJ, Jan YN.; ''Variations on the Notch pathway in neural development.''; PubMedEurope PMCScholia
Sims RJ, Belotserkovskaya R, Reinberg D.; ''Elongation by RNA polymerase II: the short and long of it.''; PubMedEurope PMCScholia
Pal M, McKean D, Luse DS.; ''Promoter clearance by RNA polymerase II is an extended, multistep process strongly affected by sequence.''; PubMedEurope PMCScholia
Holstege FC, Fiedler U, Timmers HT.; ''Three transitions in the RNA polymerase II transcription complex during initiation.''; PubMedEurope PMCScholia
Kadonaga JT.; ''Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Jawdekar GW, Henry RW.; ''Transcriptional regulation of human small nuclear RNA genes.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Wahle E, Rüegsegger U.; ''3'-End processing of pre-mRNA in eukaryotes.''; PubMedEurope PMCScholia
Van Arsdell SW, Weiner AM.; ''Human genes for U2 small nuclear RNA are tandemly repeated.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Maston GA, Evans SK, Green MR.; ''Transcriptional regulatory elements in the human genome.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Kamakaka RT, Bulger M, Kadonaga JT.; ''Potentiation of RNA polymerase II transcription by Gal4-VP16 during but not after DNA replication and chromatin assembly.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Chen J, Wagner EJ.; ''snRNA 3' end formation: the dawn of the Integrator complex.''; PubMedEurope PMCScholia
O'Reilly D, Kuznetsova OV, Laitem C, Zaborowska J, Dienstbier M, Murphy S.; ''Human snRNA genes use polyadenylation factors to promote efficient transcription termination.''; PubMedEurope PMCScholia
Takagaki Y, Manley JL.; ''Complex protein interactions within the human polyadenylation machinery identify a novel component.''; PubMedEurope PMCScholia
Zhao J, Hyman L, Moore C.; ''Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis.''; PubMedEurope PMCScholia
Schultz P, Fribourg S, Poterszman A, Mallouh V, Moras D, Egly JM.; ''Molecular structure of human TFIIH.''; PubMedEurope PMCScholia
Zhou Z, Licklider LJ, Gygi SP, Reed R.; ''Comprehensive proteomic analysis of the human spliceosome.''; PubMedEurope PMCScholia
Egloff S, Dienstbier M, Murphy S.; ''Updating the RNA polymerase CTD code: adding gene-specific layers.''; PubMedEurope PMCScholia
Orphanides G, Lagrange T, Reinberg D.; ''The general transcription factors of RNA polymerase II.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Barolo S, Posakony JW.; ''Three habits of highly effective signaling pathways: principles of transcriptional control by developmental cell signaling.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Morris DP, Michelotti GA, Schwinn DA.; ''Evidence that phosphorylation of the RNA polymerase II carboxyl-terminal repeats is similar in yeast and humans.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Egloff S, Murphy S.; ''Role of the C-terminal domain of RNA polymerase II in expression of small nuclear RNA genes.''; PubMedEurope PMCScholia
Aso T, Lane WS, Conaway JW, Conaway RC.; ''Elongin (SIII): a multisubunit regulator of elongation by RNA polymerase II.''; PubMedEurope PMCScholia
Baillat D, Wagner EJ.; ''Integrator: surprisingly diverse functions in gene expression.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Louvi A, Artavanis-Tsakonas S.; ''Notch signalling in vertebrate neural development.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Goodrich JA, Tjian R.; ''Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Shilatifard A, Conaway RC, Conaway JW.; ''The RNA polymerase II elongation complex.''; PubMedEurope PMCScholia
Fiedler U, Marc Timmers HT.; ''Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Lin X, Taube R, Fujinaga K, Peterlin BM.; ''P-TEFb containing cyclin K and Cdk9 can activate transcription via RNA.''; PubMedEurope PMCScholia
Conaway RC, Conaway JW.; ''ATP activates transcription initiation from promoters by RNA polymerase II in a reversible step prior to RNA synthesis.''; PubMedEurope PMCScholia
Blazek E, Mittler G, Meisterernst M.; ''The mediator of RNA polymerase II.''; PubMedEurope PMCScholia
Wang W, Carey M, Gralla JD.; ''Polymerase II promoter activation: closed complex formation and ATP-driven start site opening.''; PubMedEurope PMCScholia
Hoffmann A, Roeder RG.; ''Cloning and characterization of human TAF20/15. Multiple interactions suggest a central role in TFIID complex formation.''; PubMedEurope PMCScholia
Rossignol M, Kolb-Cheynel I, Egly JM.; ''Substrate specificity of the cdk-activating kinase (CAK) is altered upon association with TFIIH.''; PubMedEurope PMCScholia
Orphanides G, LeRoy G, Chang CH, Luse DS, Reinberg D.; ''FACT, a factor that facilitates transcript elongation through nucleosomes.''; PubMedEurope PMCScholia
Egloff S, O'Reilly D, Murphy S.; ''Expression of human snRNA genes from beginning to end.''; PubMedEurope PMCScholia
Pavelitz T, Bailey AD, Elco CP, Weiner AM.; ''Human U2 snRNA genes exhibit a persistently open transcriptional state and promoter disassembly at metaphase.''; PubMedEurope PMCScholia
Malik S, Roeder RG.; ''Dynamic regulation of pol II transcription by the mammalian Mediator complex.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Buratowski S.; ''Progression through the RNA polymerase II CTD cycle.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Parvin JD, Sharp PA.; ''DNA topology and a minimal set of basal factors for transcription by RNA polymerase II.''; PubMedEurope PMCScholia
Fiedler U, Timmers HT.; ''Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation.''; PubMedEurope PMCScholia
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.''; PubMedEurope PMCScholia
Bernstein LB, Manser T, Weiner AM.; ''Human U1 small nuclear RNA genes: extensive conservation of flanking sequences suggests cycles of gene amplification and transposition.''; PubMedEurope PMCScholia
Kugel JF, Goodrich JA.; ''Translocation after synthesis of a four-nucleotide RNA commits RNA polymerase II to promoter escape.''; PubMedEurope PMCScholia
Hernandez N.; ''TBP, a universal eukaryotic transcription factor?''; PubMedEurope PMCScholia
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.
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.
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.
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.
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.
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.
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.
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.
Processing is initiated once the U7 snRNP is loaded onto the pre-mRNA. The pre-mRNA HDE makes base-pairing contacts with the 5′ 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.
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.
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.
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).
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.
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).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 ).
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).
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.
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).
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).
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.
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).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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
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.
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.
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.
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).
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.
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′ 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.
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
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DataNodes
ligated exon
containing complexcomplex after
arrestIntronless Histone
pre-mRNA:CBP80:CBP20:SLBP:ZFP100 ComplexHistone pre-mRNA:CBC:ZFP100
ComplexII promoter with transcript with 2
or 3 nucleotidesPolymerase II
promotercomplex with hyperphosphorylated
Pol II CTDwith separated and uncleaved
transcriptIntronless transcript derived Histone
mRNA:SLBP:CBP80:CBP20transcript derived Histone pre-mRNA:CBC
complexcomplex with phosphodiester-PPi
intermediatecomplex containing extruded transcript
to +30complex containing
transcript to +30complex with (ser5) phosphorylated CTD containing extruded
transcript to +30Pol II
(hypophosphorylated) complex bound to DSIF proteinPol II
(hypophosphorylated):capped pre-mRNA complexPolymerase II
(unphosphorylated):TFIIF complexPolymerase II holoenzyme complex
(hyperphosphorylated)phosphorylated CTD: CE complex with
activated GTphosphorylated CTD:
CE complexpre-mRNA:CBC:RNA Pol II (phosphorylated)
complexsubstrate:nascent
mRNA hybridintronless mRNA
fragmentII
promoter:TFIID:TFIIA:TFIIB complexII
promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF complexII
promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF:TFIIE complexpromoter:TFIID
complexpre-initiation
complexpre-initiation
complexcomplex containing 11 nucleotide long
transcriptcomplex containing 3 Nucleotide long
transcriptcomplex containing 4 nucleotide long
transcriptcomplex containing 4-9 nucleotide long
transcriptcomplex containing 9 nucleotide long
transcriptfirst transcript dinucleotide, opened to +8
positionnucleotide
transcript hybridmRNA
fragment:CPSF:PAP:PABPN1 complexAnnotated Interactions
ligated exon
containing complexcomplex after
arrestIntronless Histone
pre-mRNA:CBP80:CBP20:SLBP:ZFP100 ComplexHistone pre-mRNA:CBC:ZFP100
ComplexII promoter with transcript with 2
or 3 nucleotidesPolymerase II
promotercomplex with hyperphosphorylated
Pol II CTDcomplex with hyperphosphorylated
Pol II CTDwith separated and uncleaved
transcriptIntronless transcript derived Histone
mRNA:SLBP:CBP80:CBP20transcript derived Histone pre-mRNA:CBC
complexcomplex with phosphodiester-PPi
intermediatecomplex with phosphodiester-PPi
intermediatecomplex containing extruded transcript
to +30complex containing extruded transcript
to +30complex containing
transcript to +30complex containing
transcript to +30complex with (ser5) phosphorylated CTD containing extruded
transcript to +30complex with (ser5) phosphorylated CTD containing extruded
transcript to +30Transcriptional activators function by affecting the kinetics of binding of TBP to the promoter DNA.
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.
This reaction takes place in the 'nucleus'.
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.
- 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.
This reaction takes place in the 'nucleus'.
This reaction takes place in the 'nucleus'.
This reaction takes place in the 'nucleus'.
This reaction takes place in the 'nucleus'.
This reaction takes place in the 'nucleus'.
This reaction takes place in the 'nucleus'.
This reaction takes place in the 'nucleus'.
This reaction takes place in the 'nucleus'.
Binding of DSIF:NELF to RNA Pol II CTD results in abortive termination of early elongation steps by the growing transcripts.
This reaction takes place in the 'nucleus'.
This reaction takes place in the 'nucleus'.
This reaction takes place in the 'nucleus' (Buratowski 2009).
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.
This reaction takes place in the 'nucleus'.
The open region (“transcription bubble�) expands concomitant with the site of RNA-extension. In this case this region spans positions -9 to +3.
This reaction takes place in the 'nucleus'.
This reaction takes place in the 'nucleus'.
This reaction takes place in the 'nucleus'.
This reaction takes place in the 'nucleus'.
This reaction takes place in the 'nucleus'.
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.
This reaction takes place in the 'nucleus'.
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
This reaction takes place in the 'nucleus'.
This reaction takes place in the 'nucleus'.
Pol II
(hypophosphorylated) complex bound to DSIF proteinPol II
(hypophosphorylated) complex bound to DSIF proteinPol II
(hypophosphorylated):capped pre-mRNA complexPol II
(hypophosphorylated):capped pre-mRNA complexPolymerase II
(unphosphorylated):TFIIF complexPolymerase II
(unphosphorylated):TFIIF complexPolymerase II
(unphosphorylated):TFIIF complexPolymerase II
(unphosphorylated):TFIIF complexPolymerase II
(unphosphorylated):TFIIF complexPolymerase II
(unphosphorylated):TFIIF complexPolymerase II
(unphosphorylated):TFIIF complexPolymerase II
(unphosphorylated):TFIIF complexPolymerase II
(unphosphorylated):TFIIF complexPolymerase II holoenzyme complex
(hyperphosphorylated)phosphorylated CTD: CE complex with
activated GTphosphorylated CTD: CE complex with
activated GTphosphorylated CTD:
CE complexphosphorylated CTD:
CE complexpre-mRNA:CBC:RNA Pol II (phosphorylated)
complexsubstrate:nascent
mRNA hybridintronless mRNA
fragmentII
promoter:TFIID:TFIIA:TFIIB complexII
promoter:TFIID:TFIIA:TFIIB complexII
promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF complexII
promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF complexII
promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF:TFIIE complexII
promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF:TFIIE complexpromoter:TFIID
complexpromoter:TFIID
complexpre-initiation
complexpre-initiation
complexpre-initiation
complexpre-initiation
complexpre-initiation
complexpre-initiation
complexcomplex containing 11 nucleotide long
transcriptcomplex containing 11 nucleotide long
transcriptcomplex containing 3 Nucleotide long
transcriptcomplex containing 3 Nucleotide long
transcriptcomplex containing 4 nucleotide long
transcriptcomplex containing 4 nucleotide long
transcriptcomplex containing 4-9 nucleotide long
transcriptcomplex containing 9 nucleotide long
transcriptcomplex containing 9 nucleotide long
transcriptfirst transcript dinucleotide, opened to +8
positionnucleotide
transcript hybridmRNA
fragment:CPSF:PAP:PABPN1 complex