Recruitment of TREX to the Transcription Machinery by Its Direct Binding to the Phospho-CTD of RNA Polymerase II
Messenger RNA (mRNA) synthesis and export are tightly linked, but the molecular mechanisms of this coupling are largely unknown. In Saccharomyces cerevisiae, the conserved TREX complex couples transcription to mRNA export and mediates mRNP formation. Here, we show that TREX is recruited to the transcription machinery by direct interaction of its subcomplex THO with the serine 2-serine 5 (S2/S5) diphosphorylated CTD of RNA polymerase II. S2 and/or tyrosine 1 (Y1) phosphorylation of the CTD is required for TREX occupancy in vivo, establishing a second interaction platform necessary for TREX recruitment in addition to RNA. Genome-wide analyses show that the occupancy of THO and the TREX components Sub2 and Yra1 increases from the 5′ to the 3′ end of the gene in accordance with the CTD S2 phosphorylation pattern. Importantly, in a mutant strain, in which TREX is recruited to genes but does not increase towards the 3′ end, the expression of long transcripts is specifically impaired. Thus, we show for the first time that a 5′-3′ increase of a protein complex is essential for correct expression of the genome. In summary, we provide insight into how the phospho-code of the CTD directs mRNP formation and export through TREX recruitment.
Vyšlo v časopise:
Recruitment of TREX to the Transcription Machinery by Its Direct Binding to the Phospho-CTD of RNA Polymerase II. PLoS Genet 9(11): e32767. doi:10.1371/journal.pgen.1003914
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1003914
Souhrn
Messenger RNA (mRNA) synthesis and export are tightly linked, but the molecular mechanisms of this coupling are largely unknown. In Saccharomyces cerevisiae, the conserved TREX complex couples transcription to mRNA export and mediates mRNP formation. Here, we show that TREX is recruited to the transcription machinery by direct interaction of its subcomplex THO with the serine 2-serine 5 (S2/S5) diphosphorylated CTD of RNA polymerase II. S2 and/or tyrosine 1 (Y1) phosphorylation of the CTD is required for TREX occupancy in vivo, establishing a second interaction platform necessary for TREX recruitment in addition to RNA. Genome-wide analyses show that the occupancy of THO and the TREX components Sub2 and Yra1 increases from the 5′ to the 3′ end of the gene in accordance with the CTD S2 phosphorylation pattern. Importantly, in a mutant strain, in which TREX is recruited to genes but does not increase towards the 3′ end, the expression of long transcripts is specifically impaired. Thus, we show for the first time that a 5′-3′ increase of a protein complex is essential for correct expression of the genome. In summary, we provide insight into how the phospho-code of the CTD directs mRNP formation and export through TREX recruitment.
Zdroje
1. FudaNJ, ArdehaliMB, LisJT (2009) Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature 461: 186–192.
2. ShandilyaJ, RobertsSG (2012) The transcription cycle in eukaryotes: From productive initiation to RNA polymerase II recycling. Biochimica et biophysica acta 1819: 391–400.
3. CheungAC, CramerP (2012) A movie of RNA polymerase II transcription. Cell 149: 1431–1437.
4. PeralesR, BentleyD (2009) “Cotranscriptionality”: the transcription elongation complex as a nexus for nuclear transactions. Mol Cell 36: 178–191.
5. ZhangDW, Rodriguez-MolinaJB, TietjenJR, NemecCM, AnsariAZ (2012) Emerging Views on the CTD Code. Genetics Research International 2012: 347214.
6. HeidemannM, HintermairC, VossK, EickD (2012) Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription. Biochimica et biophysica acta 1829 (1) 55–62.
7. MayerA, LidschreiberM, SiebertM, LeikeK, SodingJ, et al. (2010) Uniform transitions of the general RNA polymerase II transcription complex. Nature structural & molecular biology 17: 1272–1278.
8. KimH, EricksonB, LuoW, SewardD, GraberJH, et al. (2010) Gene-specific RNA polymerase II phosphorylation and the CTD code. Nature structural & molecular biology 17: 1279–1286.
9. TietjenJR, ZhangDW, Rodriguez-MolinaJB, WhiteBE, AkhtarMS, et al. (2010) Chemical-genomic dissection of the CTD code. Nat Struct Mol Biol 17: 1154–1161.
10. KimM, SuhH, ChoEJ, BuratowskiS (2009) Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7. J Biol Chem 284: 26421–26426.
11. MayerA, HeidemannM, LidschreiberM, SchreieckA, SunM, et al. (2012) CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II. Science 336: 1723–1725.
12. ChapmanRD, HeidemannM, AlbertTK, MailhammerR, FlatleyA, et al. (2007) Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7. Science 318: 1780–1782.
13. EgloffS, O'ReillyD, ChapmanRD, TaylorA, TanzhausK, et al. (2007) Serine-7 of the RNA polymerase II CTD is specifically required for snRNA gene expression. Science 318: 1777–1779.
14. HsinJP, ShethA, ManleyJL (2011) RNAP II CTD phosphorylated on threonine-4 is required for histone mRNA 3′ end processing. Science 334: 683–686.
15. HintermairC, HeidemannM, KochF, DescostesN, GutM, et al. (2012) Threonine-4 of mammalian RNA polymerase II CTD is targeted by Polo-like kinase 3 and required for transcriptional elongation. The EMBO journal 31: 2784–2797.
16. StrasserK, MasudaS, MasonP, PfannstielJ, OppizziM, et al. (2002) TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417: 304–308.
17. ZenklusenD, VinciguerraP, WyssJC, StutzF (2002) Stable mRNP formation and export require cotranscriptional recruitment of the mRNA export factors Yra1p and Sub2p by Hpr1p. Mol Cell Biol 8241–8253.
18. LunaR, RondonAG, AguileraA (2012) New clues to understand the role of THO and other functionally related factors in mRNP biogenesis. Biochimica et biophysica acta 1819: 514–520.
19. KatahiraJ, YonedaY (2009) Roles of the TREX complex in nuclear export of mRNA. RNA Biol 6: 149–152.
20. Molina-Navarro MM, Martinez-Jimenez CP, Rodriguez-Navarro S (2011) Transcriptional Elongation and mRNA Export Are Coregulated Processes. Genetics Research International 2011 652461.
21. JohnsonSA, KimH, EricksonB, BentleyDL (2011) The export factor Yra1 modulates mRNA 3′ end processing. Nature structural & molecular biology 18: 1164–1171.
22. RougemailleM, DieppoisG, Kisseleva-RomanovaE, GudipatiRK, LemoineS, et al. (2008) THO/Sub2p functions to coordinate 3′-end processing with gene-nuclear pore association. Cell 135: 308–321.
23. Gomez-GonzalezB, Garcia-RubioM, BermejoR, GaillardH, ShirahigeK, et al. (2011) Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles. The EMBO journal 30: 3106–3119.
24. GaillardH, WellingerRE, AguileraA (2007) A new connection of mRNP biogenesis and export with transcription-coupled repair. Nucleic Acids Res 35: 3893–3906.
25. HurtE, LuoMJ, RotherS, ReedR, StrasserK (2004) Cotranscriptional recruitment of the serine-arginine-rich (SR)-like proteins Gbp2 and Hrb1 to nascent mRNA via the TREX complex. Proc Natl Acad Sci U S A 101: 1858–1862.
26. AbruzziKC, LacadieS, RosbashM (2004) Biochemical analysis of TREX complex recruitment to intronless and intron-containing yeast genes. Embo J 23: 2620–2631.
27. StrasserK, HurtE (2000) Yra1p, a conserved nuclear RNA-binding protein, interacts directly with Mex67p and is required for mRNA export. Embo J 19: 410–420.
28. ZenklusenD, VinciguerraP, StrahmY, StutzF (2001) The yeast hnRNP-Like proteins Yra1p and Yra2p participate in mRNA export through interaction with Mex67p. Mol Cell Biol 4219–4232.
29. GwizdekC, IglesiasN, RodriguezMS, Ossareh-NazariB, HobeikaM, et al. (2006) Ubiquitin-associated domain of Mex67 synchronizes recruitment of the mRNA export machinery with transcription. Proc Natl Acad Sci U S A 103: 16376–16381.
30. IglesiasN, TutucciE, GwizdekC, VinciguerraP, Von DachE, et al. (2010) Ubiquitin-mediated mRNP dynamics and surveillance prior to budding yeast mRNA export. Genes & development 24: 1927–1938.
31. GilbertW, GuthrieC (2004) The Glc7p nuclear phosphatase promotes mRNA export by facilitating association of Mex67p with mRNA. Molecular cell 13: 201–212.
32. MasonPB, StruhlK (2005) Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol Cell 17: 831–840.
33. ChanaratS, SeizlM, StrasserK (2011) The Prp19 complex is a novel transcription elongation factor required for TREX occupancy at transcribed genes. Genes & development 25: 1147–1158.
34. ChanaratS, Burkert-KautzschC, MeinelDM, StrasserK (2012) Prp19C and TREX: interacting to promote transcription elongationand mRNA export. Transcription 3: 8–12.
35. MacKellarAL, GreenleafAL (2011) Cotranscriptional association of mRNA export factor Yra1 with C-terminal domain of RNA polymerase II. The Journal of biological chemistry 286: 36385–36395.
36. LarochelleM, LemayJF, BachandF (2012) The THO complex cooperates with the nuclear RNA surveillance machinery to control small nucleolar RNA expression. Nucleic acids research 40: 10240–10253.
37. BatisseJ, BatisseC, BuddA, BottcherB, HurtE (2009) Purification of nuclear poly(A)-binding protein Nab2 reveals association with the yeast transcriptome and a messenger ribonucleoprotein core structure. The Journal of biological chemistry 284: 34911–34917.
38. FongN, OhmanM, BentleyDL (2009) Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing. Nature structural & molecular biology 16: 916–922.
39. WestML, CordenJL (1995) Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutations. Genetics 140: 1223–1233.
40. NissanTA, GalaniK, MacoB, TollerveyD, AebiU, et al. (2004) A pre-ribosome with a tadpole-like structure functions in ATP-dependent maturation of 60S subunits. Molecular cell 15: 295–301.
41. KroganNJ, PengWT, CagneyG, RobinsonMD, HawR, et al. (2004) High-definition macromolecular composition of yeast RNA-processing complexes. Molecular cell 13: 225–239.
42. LundeBM, ReichowSL, KimM, SuhH, LeeperTC, et al. (2010) Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain. Nature structural & molecular biology 17: 1195–1201.
43. LicatalosiDD, GeigerG, MinetM, SchroederS, CilliK, et al. (2002) Functional interaction of yeast pre-mRNA 3′ end processing factors with RNA polymerase II. Molecular cell 9: 1101–1111.
44. KimM, AhnSH, KroganNJ, GreenblattJF, BuratowskiS (2004) Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes. Embo J 23: 354–364.
45. van WervenFJ, TimmersHT (2006) The use of biotin tagging in Saccharomyces cerevisiae improves the sensitivity of chromatin immunoprecipitation. Nucleic acids research 34: e33.
46. KizerKO, PhatnaniHP, ShibataY, HallH, GreenleafAL, et al. (2005) A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. Molecular and cellular biology 25: 3305–3316.
47. VojnicE, SimonB, StrahlBD, SattlerM, CramerP (2006) Structure and carboxyl-terminal domain (CTD) binding of the Set2 SRI domain that couples histone H3 Lys36 methylation to transcription. The Journal of biological chemistry 281: 13–15.
48. DrouinS, LarameeL, JacquesPE, ForestA, BergeronM, et al. (2010) DSIF and RNA polymerase II CTD phosphorylation coordinate the recruitment of Rpd3S to actively transcribed genes. PLoS genetics 6: e1001173.
49. GovindCK, QiuH, GinsburgDS, RuanC, HofmeyerK, et al. (2010) Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes. Molecular cell 39: 234–246.
50. PenaA, GewartowskiK, MroczekS, CuellarJ, SzykowskaA, et al. (2012) Architecture and nucleic acids recognition mechanism of the THO complex, an mRNP assembly factor. The EMBO journal 31: 1605–1616.
51. LeiH, ZhaiB, YinS, GygiS, ReedR (2013) Evidence that a consensus element found in naturally intronless mRNAs promotes mRNA export. Nucleic acids research 41: 2517–2525.
52. CartySM, GoldstrohmAC, SuneC, Garcia-BlancoMA, GreenleafAL (2000) Protein-interaction modules that organize nuclear function: FF domains of CA150 bind the phosphoCTD of RNA polymerase II. Proceedings of the National Academy of Sciences of the United States of America 97: 9015–9020.
53. GoldstrohmAC, AlbrechtTR, SuneC, BedfordMT, Garcia-BlancoMA (2001) The transcription elongation factor CA150 interacts with RNA polymerase II and the pre-mRNA splicing factor SF1. Molecular and cellular biology 21: 7617–7628.
54. DavidCJ, BoyneAR, MillhouseSR, ManleyJL (2011) The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65-Prp19 complex. Genes & development 25: 972–983.
55. DermodyJL, DreyfussJM, VillenJ, OgundipeB, GygiSP, et al. (2008) Unphosphorylated SR-like protein Npl3 stimulates RNA polymerase II elongation. PloS one 3: e3273.
56. NagalakshmiU, WangZ, WaernK, ShouC, RahaD, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344–1349.
57. RotherS, BurkertC, BrungerKM, MayerA, KieserA, et al. (2010) Nucleocytoplasmic shuttling of the La motif-containing protein Sro9 might link its nuclear and cytoplasmic functions. Rna 16: 1393–1401.
58. LenstraTL, BenschopJJ, KimT, SchulzeJM, BrabersNA, et al. (2011) The specificity and topology of chromatin interaction pathways in yeast. Molecular cell 42: 536–549.
59. QiuH, HuC, GaurNA, HinnebuschAG (2012) Pol II CTD kinases Bur1 and Kin28 promote Spt5 CTR-independent recruitment of Paf1 complex. The EMBO journal 31: 3494–3505.
60. XuZ, WeiW, GagneurJ, PerocchiF, Clauder-MunsterS, et al. (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature 457: 1033–1037.
61. VentersBJ, WachiS, MavrichTN, AndersenBE, JenaP, et al. (2011) A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Molecular cell 41: 480–492.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
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