Primary microRNA transcripts are processed co-transcriptionally (original) (raw)

References

  1. Kim, V.N. MicroRNA biogenesis: coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 6, 376–385 (2005).
    Article CAS PubMed Google Scholar
  2. Basyuk, E., Suavet, F., Doglio, A., Bordonné, R. & Bertrand, E. Human let-7 stem-loop precursors harbour features of RNase III cleavage products. Nucleic Acids Res. 31, 6593–6597 (2003).
    Article CAS PubMed Google Scholar
  3. Denli, A.M., Tops, B.B.J., Plasterk, R.H.A., Ketting, R.F. & Hannon, G.J. Processing of primary microRNAs by the microprocessor complex. Nature 432, 231–235 (2004).
    Article CAS PubMed Google Scholar
  4. Gregory, R.I. et al. The Microprocessor complex mediates the genesis of microRNAs. Nature 432, 235–240 (2004).
    Article CAS PubMed Google Scholar
  5. Han, J. et al. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125, 887–901 (2006).
    Article CAS PubMed Google Scholar
  6. Lund, E., Güttinger, S., Calado, A., Dahlberg, J.E. & Kutay, U. Nuclear export of microRNA precursors. Science 303, 95–98 (2004).
    Article CAS PubMed Google Scholar
  7. Valencia-Sanchez, M.A., Liu, J., Hannon, G.J. & Parker, R. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev. 20, 515–524 (2006).
    Article CAS PubMed Google Scholar
  8. Hannon, G.J. RNA interference. Nature 418, 244–251 (2002).
    Article CAS PubMed Google Scholar
  9. Schwarz, D.S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208 (2003).
    Article CAS PubMed Google Scholar
  10. Lee, Y., Jeon, K., Lee, J.T., Kim, S. & Kim, V.N. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 21, 4663–4670 (2002).
    Article CAS PubMed Google Scholar
  11. Saini, H.K., Griffiths-Jones, S. & Enright, A.J. Genomic analysis of human microRNA transcripts. Proc. Natl. Acad. Sci. USA 104, 17719–17724 (2007).
    Article CAS PubMed Google Scholar
  12. Lagos-Quintana, M., Rauhut, R., Meyer, J., Borkhardt, A. & Tuschl, T. New microRNAs from mouse and human. RNA 9, 175–179 (2003).
    Article CAS PubMed Google Scholar
  13. Rodriguez, A., Griffiths-Jones, S., Ashurst, J.L. & Bradley, A. Identification of mammalian microRNA host genes and transcription units. Genome Res. 14, 1902–1910 (2004).
    Article CAS PubMed Google Scholar
  14. Kim, Y.K. & Kim, V.N. Processing of intronic microRNAs. EMBO J. 26, 775–783 (2007).
    Article CAS PubMed Google Scholar
  15. Baskerville, S. & Bartel, D.P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11, 241–247 (2005).
    Article CAS PubMed Google Scholar
  16. Smalheiser, N.R. EST analyses predict the existence of a population of chimeric microRNA precursor-mRNA transcripts expressed in normal human and mouse tissues. Genome Biol. 4, 403 (2003).
    Article PubMed Google Scholar
  17. Qu, L.H. et al. U24, a novel intron-encoded small nucleolar RNA with two 12 nt long, phylogenetically conserved complementarities to 28S rRNA. Nucleic Acids Res. 23, 2669–2676 (1995).
    Article CAS PubMed Google Scholar
  18. de Turris, V. et al. TOP promoter elements control the relative ratio of intron-encoded snoRNA versus spliced mRNA biosynthesis. J. Mol. Biol. 344, 383–394 (2004).
    Article CAS PubMed Google Scholar
  19. Hirose, T., Shu, M.D. & Steitz, J.A. Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells. Mol. Cell 12, 113–123 (2003).
    Article CAS PubMed Google Scholar
  20. Richard, P., Kiss, A.M., Darzacq, X. & Kiss, T. Cotranscriptional recognition of human intronic box H/ACA snoRNAs occurs in a splicing-independent manner. Mol. Cell. Biol. 26, 2540–2549 (2006).
    Article CAS PubMed Google Scholar
  21. Yang, P.K. et al. Cotranscriptional recruitment of the pseudouridylsynthetase Cbf5p and of the RNA binding protein Naf1p during H/ACA snoRNP assembly. Mol. Cell. Biol. 25, 3295–3304 (2005).
    Article CAS PubMed Google Scholar
  22. Fazi, F. et al. A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPα regulates human granulopoiesis. Cell 123, 819–831 (2005).
    Article CAS PubMed Google Scholar
  23. Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. Identification of novel genes coding for small expressed RNAs. Science 294, 853–858 (2001).
    Article CAS PubMed Google Scholar
  24. Lee, Y. et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23, 4051–4060 (2004).
    Article CAS PubMed Google Scholar
  25. Glover-Cutter, K., Kim, S., Espinosa, J. & Bentley, D.L. RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nat. Struct. Mol. Biol. 15, 71–78 (2008).
    Article CAS PubMed Google Scholar
  26. Yeom, K.H., Lee, Y., Han, J., Suh, M.R. & Kim, V.N. Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing. Nucleic Acids Res. 34, 4622–4629 (2006).
    Article CAS PubMed Google Scholar
  27. Dye, M.J., Gromak, N. & Proudfoot, N.J. Exon tethering in transcription by RNA polymerase II. Mol. Cell 21, 849–859 (2006).
    Article CAS PubMed Google Scholar
  28. Gromak, N., Talotti, G., Proudfoot, N.J. & Pagani, F. Modulating alternative splicing by cotranscriptional cleavage of nascent intronic RNA. RNA 14, 359–366 (2007).
    Article PubMed Google Scholar
  29. Kluiver, J. et al. Regulation of pri-microRNA BI transcription and processing in Burkitt lynphoma. Oncogene 26, 3769–3776 (2007).
    Article CAS PubMed Google Scholar
  30. Thomson, J.M. et al. Extensive post-transcriptional regulation of microRNA and its implication for cancer. Genes Dev. 20, 2202–2207 (2006).
    Article CAS PubMed Google Scholar
  31. West, S., Gromak, N. & Proudfoot, N.J. Human 5′ → 3′ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. Nature 432, 522–525 (2004).
    Article CAS PubMed Google Scholar
  32. West, S., Proudfoot, N.J. & Dye, M. Molecular dissection of mammalian RNA polymerase II transcriptional termination. Mol. Cell 29, 600–610 (2008).
    Article CAS PubMed Google Scholar
  33. West, S., Gromak, N., Norbury, C.J. & Proudfoot, N.J. Adenylation and exosome-mediated degradation of cotranscriptionally cleaved pre-messenger RNA in human cells. Mol. Cell 21, 437–443 (2006).
    Article CAS PubMed Google Scholar
  34. Wuarin, J. & Schibler, U. Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing. Mol. Cell. Biol. 14, 7219–7225 (1994).
    Article CAS PubMed Google Scholar
  35. Zhou, H. & Lin, K. Excess of microRNAs in large and very 5′ biased introns. Biochem. Biophys. Res. Commun. 368, 709–715 (2008).
    Article CAS PubMed Google Scholar
  36. Kampa, D. et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14, 331–342 (2004).
    Article CAS PubMed Google Scholar
  37. Clark, T.A. et al. Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol. 8, R64 (2007).
    Article PubMed Google Scholar
  38. Proudfoot, N.J., Furger, A. & Dye, M.J. Integrating mRNA processing with transcription. Cell 108, 501–512 (2002).
    Article CAS PubMed Google Scholar
  39. Ryman, K., Fong, N., Bratt, E., Bentley, D.L. & Ohman, M. The C-terminal domain of RNA Pol II helps ensure that editing precedes splicing of the GluR-B transcript. RNA 13, 1071–1078 (2007).
    Article CAS PubMed Google Scholar
  40. Kim, M. et al. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature 432, 517–522 (2004).
    Article CAS PubMed Google Scholar
  41. Gromak, N., West, S. & Proudfoot, N.J. Pause sites promote transcriptional termination of mammalian RNA polymerase II. Mol. Cell. Biol. 26, 3986–3996 (2006).
    Article CAS PubMed Google Scholar
  42. Dye, M.J., Gromak, N., Haussecker, D., West, S. & Proudfoot, N.J. Turnover and function of noncoding RNA polymerase II transcripts. Cold Spring Harb. Symp. Quant. Biol. 71, 275–284 (2006).
    Article CAS PubMed Google Scholar
  43. Danin-Kreiselman, M., Lee, C.Y. & Chanfreau, G. RNAse III-mediated degradation of unspliced pre-mRNAs and lariat introns. Mol. Cell 11, 1279–1289 (2003).
    Article CAS PubMed Google Scholar
  44. Kiss, T. SnoRNP biogenesis meets Pre-mRNA splicing. Mol. Cell 23, 775–776 (2006).
    Article CAS PubMed Google Scholar
  45. Shiohama, A., Sasaki, T., Noda, S., Minoshima, S. & Shimizu, N. Nucleolar localization of DGCR8 and identification of eleven DGCR8-associated proteins. Exp. Cell Res. 313, 4196–4207 (2007).
    Article CAS PubMed Google Scholar
  46. Guil, S. & Cáceres, J.F. The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nat. Struct. Mol. Biol. 14, 591–596 (2007).
    Article CAS PubMed Google Scholar
  47. Wagner, E.J. & Garcia-Blanco, M.A. RNAi-mediated PTB depletion leads to enhanced exon definition. Mol. Cell 10, 943–949 (2002).
    Article CAS PubMed Google Scholar
  48. Forsberg, E.C. et al. Developmentally dynamic histone acetylation pattern of a tissue-specific chromatin domain. Proc. Natl. Acad. Sci. USA 97, 14494–14499 (2000).
    Article CAS PubMed Google Scholar
  49. Ballarino, M., Morlando, M., Pagano, F., Fatica, A. & Bozzoni, I. The cotranscriptional assembly of snoRNPs controls the biosynthesis of H/ACA snoRNAs in Saccharomyces cerevisiae. Mol. Cell. Biol. 25, 5396–5403 (2005).
    Article CAS PubMed Google Scholar
  50. Haussecker, D. & Proudfoot, N. J. Dicer-dependent turnover of intergenic transcripts from the human β-globin gene cluster. Mol. Cell. Biol. 25, 9724–9733 (2005).
    Article CAS PubMed Google Scholar
  51. Dye, M.J. & Proudfoot, N.J. Terminal exon definition occurs cotranscriptionally and promotes termination of RNA polymerase II. Mol. Cell 3, 371–378 (1999).
    Article CAS PubMed Google Scholar
  52. Griffiths-Jones, S. The microRNA Registry. Nucleic Acids Res. 32, D109–D111 (2004).
    Article CAS PubMed Google Scholar
  53. Kent, W.J. BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).
    Article CAS PubMed Google Scholar
  54. Megraw, M., Sethupathy, P., Corda, B. & Hatzigeorgiou, A.G. miRGen: a database for the study of animal microRNA genomic organization and function. Nucleic Acids Res. 35, D149–D155 (2007).
    Article CAS PubMed Google Scholar
  55. Dye, M.J. & Proudfoot, N.J. Multiple transcript cleavage precedes polymerase release in termination by RNA polymerase II. Cell 105, 669–681 (2001).
    Article CAS PubMed Google Scholar
  56. Pawlicki, J.M. & Steitz, J.A. Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production. J. Cell Biol. 182, 61–76 (2008).
    Article CAS PubMed Google Scholar

Download references