RNase III-independent microRNA biogenesis in mammalian cells

RNA

Volumn 18, Issue 12, 2012, Pages 2166-2173

  Maurin, Thomas ^a   Cazalla, Demián ^b,c   Yang, Jr Shiuan ^a   Bortolamiol Becet, Diane ^a   Lai, Eric C ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

Argonaute; MicroRNA; RNase III; Slicer

Indexed keywords

ARGONAUTE 2 PROTEIN; DICER; MICRORNA; RIBONUCLEASE III; SMALL INTERFERING RNA;

ANIMAL; ARTICLE; BIOGENESIS; COMPLEX FORMATION; IMMUNOPRECIPITATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA INTERFERENCE;

ANIMALS; ARGONAUTE PROTEINS; BASE SEQUENCE; CELL LINE; DEAD-BOX RNA HELICASES; ENDORIBONUCLEASES; GENE KNOCKOUT TECHNIQUES; HEK293 CELLS; HELA CELLS; HERPESVIRUS 2, SAIMIRIINE; HUMANS; MICE; MICRORNAS; RIBONUCLEASE III; RNA, SMALL NUCLEAR; RNA, VIRAL;

MAMMALIA;

EID: 84869840081     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.036194.112     Document Type: Article

References (52)

1. Ameres SL, Hung JH, Xu J, Weng Z, Zamore PD. 2011. Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins. RNA 17: 54-63.
2. Axtell MJ, Westholm JO, Lai EC. 2011. Vive la différence: Biogenesis and evolution of microRNAs in plants and animals. Genome Biol 12: 221. doi: 10.1186/gb-2011-12-4-221.
3. Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R. 2008. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev 22: 2773-2785.
4. Baillat D, Hakimi MA, Naar AM, Shilatifard A, Cooch N, Shiekhattar R. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell 123: 265-276.
5. Berezikov E, Chung W-J, Willis J, Cuppen E, Lai EC. 2007. Mammalian mirtron genes. Mol Cell 28: 328-336. (Pubitemid 47600007)
6. Bogerd HP, Karnowski HW, Cai X, Shin J, Pohlers M, Cullen BR. 2010. A mammalian herpesvirus uses non-canonical expression and processing mechanisms to generate viral microRNAs. Mol Cell 37: 135-142.
7. Cazalla D, Yario T, Steitz JA. 2010. Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA. Science 328: 1563-1566.
8. Cazalla D, Xie M, Steitz JA. 2011. A primate herpesvirus uses the integrator complex to generate viral microRNAs. Mol Cell 43: 982-992.
9. Cheloufi S, Dos Santos CO, Chong MM, Hannon GJ. 2010. A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature 465: 584-589.
10. Chung WJ, Agius P, Westholm JO, Chen M, Okamura K, Robine N, Leslie CS, Lai EC. 2011. Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans. Genome Res 21: 286-300.
11. Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson N, et al. 2010. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science 328: 1694-1698.
12. Czech B, Hannon GJ. 2010. Small RNA sorting: Matchmaking for Argonautes. Nat Rev Genet 12: 19-31.
13. Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, Dus M, Perrimon N, Kellis M, Wohlschlegel J, Sachidanandam R, et al. 2008. An endogenous siRNA pathway in Drosophila. Nature 453: 798-802.
14. Diederichs S, Haber DA. 2007. Dual role for Argonautes in microRNA processing and posttranscriptional regulation of microRNA expression. Cell 131: 1097-1108. (Pubitemid 350235019)
15. Ding SW, Voinnet O. 2007. Antiviral immunity directed by small RNAs. Cell 130: 413-426. (Pubitemid 47198311)
16. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811. (Pubitemid 28099681)
17. Flynt AS, Lai EC. 2008. Biological principles of microRNA-mediated regulation: Shared themes amid diversity. Nat Rev Genet 9: 831-842.
18. Flynt AS, Chung WJ, Greimann JC, Lima CD, Lai EC. 2010. microRNA biogenesis via splicing and exosome-mediated trimming in Drosophila. Mol Cell 38: 900-907.
19. Halic M, Moazed D. 2010. Dicer-independent primal RNAs trigger RNAi and heterochromatin formation. Cell 140: 504-516.
20. Havens MA, Reich AA, Duelli DM, Hastings ML. 2012. Biogenesis of mammalian microRNAs by a non-canonical processing pathway. Nucleic Acids Res 40: 4626-4640.
21. Hutvagner G, Simard MJ. 2008. Argonaute proteins: Key players in RNA silencing. Nat Rev Mol Cell Biol 9: 22-32.
22. Karginov FV, Cheloufi S, Chong MM, Stark A, Smith AD, Hannon GJ. 2010. Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Mol Cell 38: 781-788.
23. Kawamura Y, Saito K, Kin T, Ono Y, Asai K, Sunohara T, Okada T, Siomi MC, Siomi H. 2008. Drosophila endogenous small RNAs bind to Argonaute2 in somatic cells. Nature 453: 793-797. (Pubitemid 351793781)
24. Kennerdell JR, Carthew RW. 2000. Heritable gene silencing in Drosophila using double-stranded RNA. Nat Biotechnol 18: 896-898. (Pubitemid 30640919)
25. Ketting RF. 2011. The many faces of RNAi. Dev Cell 20: 148-161.
26. Lai EC. 2003. microRNAs: Runts of the genome assert themselves. Curr Biol 13: R925-R936. (Pubitemid 37502516)
27. Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G, Tuschl T. 2004. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell 15: 185-197. (Pubitemid 38950966)
28. Miyoshi K, Miyoshi T, Hartig JV, Siomi H, Siomi MC. 2010. Molecular mechanisms that funnel RNA precursors into endogenous small-interfering RNA and microRNA biogenesis pathways in Drosophila. RNA 16: 506-515.
29. O'Carroll D, Mecklenbrauker I, Das PP, Santana A, Koenig U, Enright AJ, Miska EA, Tarakhovsky A. 2007. A Slicer-independent role for Argonaute 2 in hematopoiesis and the microRNA pathway. Genes Dev 21: 1999-2004. (Pubitemid 47267286)
30. Okamura K, Hagen JW, Duan H, Tyler DM, Lai EC. 2007. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130: 89-100. (Pubitemid 47031325)
31. Okamura K, Chung W-J, Ruby JG, Guo H, Bartel DP, Lai EC. 2008. The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature 453: 803-806. (Pubitemid 351793790)
32. Okamura K, Robine N, Liu Y, Liu Q, Lai EC. 2011. R2D2 organizes small regulatory RNA pathways in Drosophila. Mol Cell Biol 31: 884-896.
33. Paddison PJ, Caudy AA, Bernstein E, Hannon GJ, Conklin DS. 2002. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev 16: 948-958. (Pubitemid 34408544)
34. Parker JS, Roe SM, Barford D. 2004. Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J 23: 4727-4737. (Pubitemid 40069703)
35. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. 2006. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20: 3407-3425. (Pubitemid 44969159)
36. Rosa MD, Gottlieb E, Lerner MR, Steitz JA. 1981. Striking similarities are exhibited by two small Epstein-Barr virus-encoded ribonucleic acids and the adenovirus-associated ribonucleic acids VAI and VAII. Mol Cell Biol 1: 785-796. (Pubitemid 12174755)
37. Ruby JG, Jan CH, Bartel DP. 2007. Intronic microRNA precursors that bypass Drosha processing. Nature 448: 83-86. (Pubitemid 47037009)
38. Scherer LJ, Frank R, Rossi JJ. 2007. Optimization and characterization of tRNA-shRNA expression constructs. Nucleic Acids Res 35: 2620-2628. (Pubitemid 47073675)
39. Sibley CR, Seow Y, Saayman S, Dijkstra KK, El Andaloussi S, Weinberg MS, Wood MJ. 2012. The biogenesis and characterization of mammalian microRNAs of mirtron origin. Nucleic Acids Res 40: 438-448.
40. Song JJ, Smith SK, Hannon GJ, Joshua-Tor L. 2004. Crystal structure of Argonaute and its implications for RISC Slicer activity. Science 305: 1434-1437. (Pubitemid 39167656)
41. Tan GS, Garchow BG, Liu X, Yeung J, Morris JP 4th, Cuellar TL, McManus MT, Kiriakidou M. 2009. Expanded RNA-binding activities of mammalian Argonaute 2. Nucleic Acids Res 37: 7533-7545.
42. Vazquez F, Blevins T, Ailhas J, Boller T, Meins F Jr. 2008. Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Res 36: 6429-6438.
43. Westholm JO, Lai EC. 2011. Mirtrons: microRNA biogenesis via splicing. Biochimie 93: 1897-1904.
44. Westholm JO, Ladewig E, Okamura K, Robine N, Lai EC. 2012. Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs. RNA 18: 177-192.
45. Yang JS, Lai EC. 2011. Alternative miRNA biogenesis pathways and the interpretation of core miRNA pathway mutants. Mol Cell 43: 892-903.
46. Yang JS, Maurin T, Robine N, Rasmussen KD, Jeffrey KL, Chandwani R, Papapetrou EP, Sadelain M, O'Carroll D, Lai EC. 2010. Conserved vertebrate mir-451 provides a platform for Dicer-independent, Ago2-mediated microRNA biogenesis. Proc Natl Acad Sci 107: 15163-15168.
47. Yang JS, Phillips MD, Betel D, Mu P, Ventura A, Siepel AC, Chen KC, Lai EC. 2011. Widespread regulatory activity of vertebrate microRNA*species. RNA 17: 312-326.
48. Yang JS, Maurin T, Lai EC. 2012. Functional parameters of Dicer-independent microRNA biogenesis. RNA 18: 945-957.
49. Yi R, O'Carroll D, Pasolli HA, Zhang Z, Dietrich FS, Tarakhovsky A, Fuchs E. 2006. Morphogenesis in skin is governed by discrete sets of differentially expressed microRNAs. Nat Genet 38: 356-362.
50. Yuan YR, Pei Y, Ma JB, Kuryavyi V, Zhadina M, Meister G, Chen HY, Dauter Z, Tuschl T, Patel DJ. 2005. Crystal structure of A. aeolicus Argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Mol Cell 19: 405-419. (Pubitemid 41078780)
51. Zhang W, Gao S, Zhou X, Xia J, Chellappan P, Zhang X, Jin H. 2010. Multiple distinct small RNAs originate from the same microRNA precursors. Genome Biol 11: R81. doi: 10.1186/gb-2010-11-8-r81.
52. Zhang H, Maniar JM, Fire AZ. 2011. "Inc-miRs": Functional intron-interrupted miRNA genes. Genes Dev 25: 1589-1594.