CO-TRANSCRIPTIONAL PROCESSES: Pol II CTD
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All RNAs great and small Institute of Genetics and Biotechnology University of Warsaw HISTORY OF RNA Rinn and Chang, Ann. Rev. Biochem, 2012 RNA – aka My Favorite Molecule RNA form A helix - narrow inaccessible major groove (red) - shallow minor groove (green) - versatile and flexible - catalytically active (splicing, translation, modification) - self-sufficient? - labile (regulation of expression) - create complex 3D structures - specific and unspecific interactions with proteins and other RNAs „THE RNA WORLD” hypothesis „primordial soup” „prebiotic soup” pre-RNA world RNA world RNA+DNA+ proteins RNA+proteins RNA made via condensation RNA evolution- molecules RNA starts to join aminoacids from ribose and other organic learns to replicate and synthesises polypeptides substances and proteins Proteins aid RNA to replicate and make DNA and proteins take over major roles proteins. dsRNA evolves into stable DNA. as genetic information and enzymes RNA capacity - CATALYTIC RNAs Nobel 1989 RNA enzymes – RIBOZYMES -1981/82 Tom Cech - self-splicing in Tetrahymena rRNA -1982 Sidney Altman - bacterial RNaseP RNA subunit Thomas Cech Sidney Altman Tetrahymena group I self-splicing intron Escherichia coli RNaseP RNA mRNA SPLICING Nobel 1993 Phil Sharp Richard Roberts RNAi Nobel 2006 Andrew Fire Craig Mello RNAs – STRUCTURE AND FUNCTION Nobel 2009 Elizabeth Blackburn Venkatraman Ramakrishnan Jack Szostak Ada Yonath Carol Greider Thomas Steitz Telomerase - maintaing chromosome ends Crystal structure of the ribosome Hammerhead, RIBOZYMES Hairpin, HDV viroids, eukaryotes plant satellite RNA, 2007 viruses Nat. Rev. Genet., Nat. Rev. mRNA splicing-like , l organelles (fungi, plants), bacteria, archea Serganov and Pate and Serganov organelles (fungi, plants), bacteria, mitochondria (animals) 2+ Mechanism: nucleophilic attack of the ribose -OH group (H2O, Me ) on the phosphate Serganov and Patel, Nat Rev Genet, 2007; Evans et al, TiBS, 2006 RNase P RNA – a true enzyme enzyme a true – RNA P RNase tRNA processing,multiple turnover tRNA RNase P RNA RNA P RNase coli E. MODERN RNA WORLD RNA vestiges- catalytic RNAs with active centres made of RNA RIBOSOME - protein synthesis SPLICEOSOME - pre-mRNA splicing 5 snRNAs U1, U2, U4, U5, U6 active snRNP center U6 catalytic activity Ribosome, crystal structure Cryo EM Ditlev Brodersen, Venki Ramakrishnan C complex, Cryo EM Galej et al, Nature, 2016 SPLICEOSOME: pre-mRNA SPLICING pre-mRNA::snRNA D3 B Sm/Lsm G Luhrmann and Stark, Curr. Op. Str. Biol., 2009 base-pairing E D1 D2 F snRNPs SPLICEOSOME -ribonucleoprotein complex (RNP) organised around snRNAs RIBOSOME: TRANSLATION - mRNA - messenger, informative - tRNA - transfer, transport of aminoacids - rRNA - ribosome, translation machinery REGULATION OF GENE EXPRESSION translation 6 1) chromatin 5 degradation 2) transcription 7 splicing 4 3) RNA processing processing transcription 2 3 4) RNA export 5) translation (mRNA) 3 ncRNAs 1 6) protein stability 7) RNA degradation RNA • coding: mRNAs • non-coding: ncRNAs • stable • unstable • structural (rRNA, tRNA) • regulatory (si/miRNA) • polyadenylated • non-polyadenylated There are no „free” RNAs in the cell All cellular RNAs exist as ribonucleoprotein particles (RNPs) All RNA types are synthesised as precursors and undergo processing TRANSCRIPTION RNA Pol I RNA Pol II RNA Pol III A135 Rpb2 C128 AC40 Rpb3 AC40 Core subunits AC Rpb (similar in all) A190 Rpb1 C160 AC 19 11 19 5 Common 5 10 5 6 10 6 6 10 subunits 9 9 9 8 (same in all) 8 8 + 4 others + 2 others + 5 others tRNA, 5S rRNA, U6 ribosomal RNA mRNA , most snRNAs (U1, U2, U3, U4, U5, snRNA, U6atac snRNA, 35S precursor contains 7SK RNA, 7SL RNA, 18S, 5.8S and 25S subunits U11, U12, U4atac), snoRNAs, microRNAs, RNase P RNA, telomerase RNA RNase MRP RNA Zbigniew Dominski, lectures 2008 CO-TRANSCRIPTIONAL PROCESSES: Pol II CTD CTD posphorylation status Phospho-CTD Phatnani and Greenleaf, 2006 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 Nucleosome positioning The length of typical internal exons (grey boxes) is comparable to the DNA wrapped around a nucleosome. Nucleosome positioning relative to the transcription start site (TSS), transcription termination site (TTS) and, to a lesser extent, exons helps to define the boundaries of these elements, providing a platform for crosstalk between chromatin, transcription and splicing. Nucleosomes at introns are less stable (dased lines). A sleeping Pol II represents pausing events at splice sites (AG and GT). Consistent with nucleosome phasing over exons, slower transcription elongation has been measured over exonic sequences CO-TRANSCRIPTIONAL PROCESSES O CAPPING N NH OH OH N O O O N NH2 O O P O P O P O O γ - β - α - H2N N N O O O OH OH N N+ - O CH3 7-methylguanosine 5’-5’-triphosphate bridge (m7G) Co-transcriptional capping - occurs after the synthesis of 10-15 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 CO-TRANSCRIPTIONAL PROCESSES SPLICING Exon1 Exon2 Intron - spliceosome assembly (Ser5-P) - majority of splicing (up to 70-80%) cap Spliceosome Munoz et al., TiBS, 2009 pre-mRNA Wong et al., TiG, 2014 CO-TRANSCRIPTIONAL PROCESSES PRE-rRNA PROCESSING AND MODIFCATION nucleolus 70-80% of cellular transcription is for rRNA by Pol I 50% of Pol II transcription is for RP genes co-trx coupled co-trx cleavage Rnt1 cleavage and termination Granemman and Baserga, Curr.Op.CellBiol., 2005; Kos and Tollervey, Mol.Cell’10 40S small 60S large subunit subunit Co-transcriptional: - association of SSU subcomplexes 80S ribosome - pre-rRNA cleavages dividing small and large subunits (70%) - ribose modification (2’-O-methylation) CO-TRANSCRIPTIONAL PROCESSES 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) RNA binding RNA DEVH polymerase proteins helicase CO-TRANSCRIPTIONAL PROCESSES POL II TRANSCRIPTION TERMINATION mRNA hybrid allosteric- torpedo model ncRNA CP Cleavage and polyadenylation complex (CP) (recruited at Ser2-P CTD) Pap1 Luo and Bentley, Gene Dev, 2006 Nrd1/Nab3/Sen1-dependent termination (recruited at Ser5-P) ncRNA mRNA • sn/snoRNAs • CUTs • short mRNAs (< 600 nt) Jacquier, Nat. Rev. Genet 2009 CO-TRANSCRIPTIONAL PROCESSES POL I TRANSCRIPTION TERMINATION Nsi1/Re yeast Rnt1 b1 Pol I termination factors: Pol I 25S • DNA-binding protein Nsi1/Reb1 • Pol I subunit Rpa12 • endonuclease Rnt1 5’ • RFB binding protein Fob1 • 5’-3’ exonuclease Rat1/Rai1 Rat1/ Rai1 (torpedo mechanism) • RNA helicase Sen1 • Nrd1/Nab3 complex (??) mammalian transcript release element PTRF – release factor T-stretch + TTF-I pause site SETX – helicase, Sen1 homolog Richard and Manley, GeneDev., 2009 TTF-I – transcription termination factor I CO-TRANSCRIPTIONAL PROCESSES POL III TRANSCRIPTION TERMINATION Landrieux et al., EMBO J., al., et2006 Landrieux Richard and Manley, Gene Dev., 2009 C1, C2 core subunits Pol III EM structure (Pol pausing) C37-C53 subcomplex is situated across the cleft near RNA exit C11 (TFIIS) subunit of Pol III has intrinsic RNA cleavage activity important for Pol lll termination Fernadez-Tornero et al., Mol. Cell, 2007 CO-TRANSCRIPTIONAL PROCESSES mRNA EXPORT: GENE GATING in yeast Iglesias and Stutz, Stutz, Lett,FEBS2008 and Iglesias nucleus NUCLEAR PORE COMPLEX cytoplasm 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 POST-TRANSCRIPTIONAL PROCESSES Rex1 tRNA PROCESSING (yeast) Rrp6 tRNA precursors: 5’ leader 3’ leader - 5’ end by RNAse P D tRNase Z - 3’ end by tRNase Z RNase P acceptor stem - alternative 3’ pathway: exonucleolytic by Rex1 and Rrp6 anticodon 5’-3’ ligation pathway tRNA SPLICING yeast In the cytoplasm on the mitochondrial membrane cytoplasm splicing aminoacylation Hopper and Shaheen, TiBS,2008; Lopes et al, WIREsRNA, 2015 3’-5’ ligation pathway Archaea, vertebratesx POST-TRANSCRIPTIONAL PROCESSES tRNA can occur in the nucleus Functions of modifications: and in the cytoplasm • contributeMODIFICATION to folding • provide stability • facilitate alternative structures 2003 , GeneGev. • affect codon recognition (wobble bp) • (frameshifting) contribute to translation Phizicky tRNA CCA ADDITION Hopper and Hopper by tRNA nucleotidyl- transferase tRNA AMINOACYLATION by tRNA aminoacyl synthetases two classes: class I and class II 2001 etBiol.Chem., al, rer (aminoacylate 2’-OH or 3’-OH of A) u Sch COORDINATION: ALTERNATIVE SPLICING, CHROMATIN, ncRNAs, SPLICING FACTORS Luco and Misteli, Curr Op Gene Dev, 2011 Dev, Gene Op Curr Misteli, and Luco COORDINATION: SPLICING AND RNA DECAY Kilchert et al, Nat Rev Mol Cell biol, 2016 .