Pol II - mrna synthesis
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1 Pol II - mrna synthesis Pol II, S. cerevisiae (12 subunits) - core by specific Rpb1-3, 9 and 11 - Rpb5-6, 8, 10 and 12 - shared by Pol I-III - specific subcomplex Rpb4/7 not essential - TF: transcription factors - associated factors RAP74, RAP30 (TFIIF) - auxiliary complexes: Mediator, SAGA Gnatt et al, Science, 2001 (Kornberg s lab) CTD: Tyr 1 Ser 2 Pro 3 Thr 4 Ser 5 Pro 6 Ser 7 26 (yeast) - 52 (human) repeats
2 Co-transcriptional mrna processing CTD posphorylation status Phospho-CTD Associated Proteins - transcription - chromatin structure - RNA processing (splicing, 3 end formation) - RNA export - RNA degradation - snrna modification - snornp biogenesis - DNA metabolism - protein synthesis and degradation Phatnani and Greenleaf, 2006
3 CAPPING H 2 N N N OH O N N + OH O O O O P O - O P O γ β α O - P O - O OH O N N OH O N NH NH 2 O - CH 3 7-methylguanosine 5-5 -triphosphate bridge (m 7 G) Co-transcriptional capping - occurs after the synthesis of nt of RNA - CE recruitment to CTD requires high Ser5-P GT/Ceg1-guanylyltransferase MT/Abd1-methyltransferase (promote early elongation) Cet1-RNA triphopshatase (inhibits re-initiation) CBC-cap binding complex Guo and Lima, Cur. Op.Str.Biol., 2005
4 Co-transcriptional mrna processing: SPLICING Exon1 Intron Exon2 Spliceosome Munoz et al., TiBS, 2009 pre-mrna: - m7g cap synthesis (Ser5-P) - spliceosome assembly - splicing, at least partially
5 Pre-mRNA SPLICING Cryo EM native spliceosome active center Alberts B, Bray D, Lewis J, et al., Molecular Biology of the Cell. 3rd edition;
6 de Almeida and Carmo-Fonseca, FEBS Lett, 2008
7 Pre-mRNA SPLICING: CIS ELEMENTS yeast human The consensus splicing sequences are not so conserved after all 5 Splice Site Branch Point A 3 Splice Site 5 Exon A 3 Exon 5 Splice Site 3 Splice Site Zbigniew Dominski, lectures 2008 Warf and Berglund, 2010, TiBS; Reddy, Ann.Rev.PlantBiol., 2007
8 Pre-mRNA SPLICING: TRANS ELEMENTS 5 snrnas U1, U2, U4, U5, U6 active center E G D3 F B D1 D2 Sm/Lsm snrnas pre-mrna::snrna base-pairing Warf and Berglund, 2010, TiBS; Reddy, Ann.Rev.PlantBiol., 2007
9 Chemistry of pre-mrna splicing and U2/U6 model
10 TRANSCRIPTION AND SPLICING CTD Ser-P and splicing Elongation rate and splicing Lenasi and Barboric, WIREsRNA, 2013
11 ALERNATIVE SPLICING (AS) communication between the 3 and 5 splice sites Reddy, Ann.Rev.PlantBiol., 2007; Chen and Manley, Nat.Rev.Mol.CellBiol., 2009
12 ALERNATIVE SPLICING (AS) Reddy, Annu. Rev. Plant Biol., 2007 Exons and introns often contain sequences that facilitate or inhibit splice site usage. These elements bind splicing activators or repressors. ESR exonic splicing regulatory elements ISR intronic splicing regulatory elements ESS/ISS exonic/intronic splicing silencers ESE/ISE - exonic/intronic splicing enhancers SR Ser/Arg rich proteins PTB polypyrimidine tract-binding proteins hnrnp heterogenous nuclear RNP AS occurs at the level of recognition of splice sites and other regulatory elements by RNA-binding proteins
13 Luco and Misteli, Curr Op Gene Dev, 2011 AS splicing CODE: chromatin, ncrnas, SF
14 CLEAVAGE AND POLYADENYLATION mrna ncrna Cleavage and polyadenylation complex (CP) (recruited at Ser2-P CTD) Jacquier, Nat. Rev. Genet, 2009 yeast metazoan the the Millevoi and Vagner, NAR, 2008
15 TRANSCRIPTION TERMINATION: hybrid allosteric- torpedo model CP Luo and Bentley, Gene Dev, 2006 Pap1 3 -end processing factors are recruited to Ser2-P CTD at 3 end of genes via CID (CTD-interacting domain) of Pcf11 for CP and Rtt103 for Rat1 5-3 exonuclease and its activator Rai1. Pcf11 and Rat1 coordinately contribute to the recruitment of 3 - end processing factors
16 Nrd1/Nab3/Sen1-dependent TERMINATION CTD Pol II Nrd1/Nab3/Sen1 complex sn/snornas CUTs (Ser5-P) short mrnas (< 600 nt) ncrna mrna Jacquier, Nat. Rev. Genet 2009
17 HISTONE mrna 3 end FORMATION (nonpolyadenylated, metazoa, unique) SL structure endonuclease unique Sm/Lsm10/11 Dominski and Marzluff, Gene, 2007 U7 snrnp Histone pre-mrna contains conserved stem-loop (SL) structure, recognized by the SLBP (SL-binding protein) SLBP, ZFP100 and HDE (histone downstream element) stabilize the binding of U7 U7 snrnp, specificaly Lsm11, recruits cleavage factors and the cleavage by endonuclease CPSF-73 generates mature 3 end of histone mrna
18 POLYMERASE BACKTRACKING Polymerase backtracking in genome stability Double-strand break (DSB) formation as a result of codirectional collisions between the replisome and backtracked RNA polymerase in bacteria. Transcript cleavage factor (Gre) prevents polymerase backtracking and R loop formation, preserving genome integrity. Nudlerr, Cell, 2013
19 sn/snorna processing (small nuclear and nucleolar RNAs) 3 and 5 processing Fatica et al., EMBO, 2000 Rat1/Xrn1 Rnt1 RNP proteins Rnt1 RNA precursor RNP proteins RNA precursor termination
20 sn/snorna processing AAAAAAAAAAA AAAAAAAAAAA Exosome: 3-5 exo/endo-nuclease complex; 10 core components (RNA BP) catalytically active hydrolytic Dis3/Rrp44 (RNase II) nuclear cofactors- RNA BP Rrp47, nuclease Rrp6 (RNase D), RNA helicase Mtr4 cytoplasmic cofactors- Ski2-3-8 complex (RNA helicase Ski2), GTPase Ski7 subtrates- processing and/or degradation of almost all RNAs TRAMP: nuclear surveillance Trf4/5 + Air1/2 + Mtr4 poly(a) polymerase RNA binding proteins RNA DEVH helicase
21 RNA EXPORT Röther and Sträßer, Nuclear Transport,2009
22 Strambio-De-Castillia et al., Nat.Rev.Mol.Cel.Biol,2007 mrna EXPORT ALL FACTORS
23 Co-transcriptional mrna EXPORT: GENE GATING (yeast) nucleus cytoplasm NUCLEAR PORE COMPLEX Iglesias and Stutz, FEBS Lett, 2008 SAGA histone acetyltransferase complex (including Spt, Ada, Gcn5); trx activation THO mrnp biogenesis and export: Hpr1, Mft1, Tho2 and Thp2 (human THOC1-7) TREX transcription-export complex: THO/Sub2/Yra1, interacts with NPC via Mex67-Mtr2 TREX-2 transcription-export complex: Cdc31/Thp1/Sac3 and Sus1 from SAGA TREX-2 and TREX complexes link transcription (Pol II via THO, initiation complex SAGA via Sus1) to export receptors (Mex67, Yra1) and Nuclear Pore Complex
24 Köhler and Hurt, Nat.Rev.Mol.Cel.Biol,2007 EXPORT of other RNAs
25 Mature mrna: TRANSLATION eif3 EJC PABP1 m 7 GpppG eif4e eif4g 5 UTR AUG UAA 3 UTR AAAAAAAAAAAAA nts UTR- UNTRANSLATED REGION EJC- EXON JUNCTION COMPLEX eif4e eif3 m 7 Gppp 40S met 40S met met met met UAC AUG eif4g 60S A A Pab1p A A A A A UAA eif4e interacts with m7g cap to form translationally active mrna: cap dependent translation circular mrna protects agains degradation and stimulates translation eif4e/eif4g/pab recruits small ribosomal subunit trna-bound 40S scans mrna to locate START
26 THE RIBOSOME Three trna binding sites: A site = amino-acyl trna binding site P site = peptidyl-trna binding site E site = exit site
27 Schmeing and Ramakrishnan, Nature, 2009 THE RIBOSOME
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