The pathway of miRNA maturation

Methods in Molecular Biology

Volumn 1095, Issue , 2014, Pages 3-10

  Sand, Michael ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

Dicer; Drosha; MicroRNA; Mirtron; Precursor microRNA; Primary microRNA

Indexed keywords

MICRORNA; RAN PROTEIN;

CHROMOSOME; EXON; HUMAN; INTRON; MATURATION; MICROPROCESSOR; NONHUMAN; PRIORITY JOURNAL; REVIEW; SIGNAL TRANSDUCTION;

ANIMALS; CYTOSOL; HUMANS; MICRORNAS; RIBONUCLEASE III; RNA CLEAVAGE; RNA, MESSENGER;

EID: 84934440051     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-703-7_1     Document Type: Review

References (59)

1. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang KC, Hallinan J, Mattick J, Hume DA, Lipovich L, Batalov S, Engstrom PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C (2005) Antisense transcription in the mammalian transcriptome. Science 309:1564-1566
2. Kim YK, Kim VN (2007) Processing of intronic microRNAs. EMBO J 26:775-783
3. Rodriguez A, Griffi ths-Jones S, Ashurst JL, Bradley A (2004) Identifi cation of mammalian microRNA host genes and transcription units. Genome Res 14:1902-1910
4. Borchert GM, Lanier W, Davidson BL (2006) RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol 13: 1097-1101
5. Lee Y, Jeon K, Lee JT, Kim S, Kim VN (2002) MicroRNA maturation: stepwise processing and subcellular localization. Embo J 21: 4663-4670
6. Sand M, Gambichler T, Sand D, Skrygan M, Altmeyer P, Bechara FG (2009) MicroRNAs and the skin: tiny players in the body's largest organ. J Dermatol Sci 53:169-175
7. Bhattacharyya M, Feuerbach L, Bhadra T, Lengauer T, Bandyopadhyay S (2012) MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection. Stat Appl Genet Mol Biol 11:1-25
8. He C, Li Z, Chen P, Huang H, Hurst LD, Chen J (2012) Young intragenic miRNAs are less coexpressed with host genes than old ones: implications of miRNA-host gene coevolution. Nucleic Acids Res 40:4002-4012
9. Li SC, Tang P, Lin WC (2007) Intronic microRNA: discovery and biological implications. DNA Cell Biol 26:195-207
10. Marco A, Hooks K, Griffi ths-Jones S (2012) Evolution and function of the extended miR-2 microRNA family. RNA Biol 9
11. Lau PW, MacRae IJ (2009) The molecular machines that mediate microRNA maturation. J Cell Mol Med 13:54-60
12. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, Shiekhattar R (2004) The Microprocessor complex mediates the genesis of microRNAs. Nature 432:235-240
13. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim VN (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425:415-419
14. Trabucchi M, Briata P, Filipowicz W, Rosenfeld MG, Ramos A, Gherzi R (2009) How to control miRNA maturation? RNA Biol 6:536-540
15. Fukuda T, Yamagata K, Fujiyama S, Matsumoto T, Koshida I, Yoshimura K, Mihara M, Naitou M, Endoh H, Nakamura T, Akimoto C, Yamamoto Y, Katagiri T, Foulds C, Takezawa S, Kitagawa H, Takeyama K, O'Malley BW, Kato S (2007) DEAD-box RNA helicase subunits of the Drosha complex are required for processing of rRNA and a subset of microRNAs. Nat Cell Biol 9:604-611
16. Davis BN, Hilyard AC, Lagna G, Hata A (2008) SMAD proteins control DROSHA-mediated microRNA maturation. Nature 454:56-61
17. Hata A, Davis BN (2010) Regulation of primiRNA processing through Smads. Adv Exp Med Biol 700:15-27
18. Davis BN, Hilyard AC, Nguyen PH, Lagna G, Hata A (2010) Smad proteins bind a conserved RNA sequence to promote microRNA maturation by Drosha. Mol Cell 39:373-384
19. Yang W, Chendrimada TP, Wang Q, Higuchi M, Seeburg PH, Shiekhattar R, Nishikura K (2006) Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol 13:13-21
20. Gruber JJ, Zatechka DS, Sabin LR, Yong J, Lum JJ, Kong M, Zong WX, Zhang Z, Lau CK, Rawlings J, Cherry S, Ihle JN, Dreyfuss G, Thompson CB (2009) Ars2 links the nuclear cap-binding complex to RNA interference and cell proliferation. Cell 138:328-339
21. Yamagata K, Fujiyama S, Ito S, Ueda T, Murata T, Naitou M, Takeyama K, Minami Y, O'Malley BW, Kato S (2009) Maturation of microRNA is hormonally regulated by a nuclear receptor. Mol Cell 36:340-347
22. Trabucchi M, Briata P, Garcia-Mayoral M, Haase AD, Filipowicz W, Ramos A, Gherzi R, Rosenfeld MG (2009) The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs. Nature 459:1010-1014
23. Trabucchi M, Briata P, Filipowicz W, Ramos A, Gherzi R, Rosenfeld MG (2011) KSRP promotes the maturation of a group of miRNA precuresors. Adv Exp Med Biol 700:36-42
24. Sakamoto S, Aoki K, Higuchi T, Todaka H, Morisawa K, Tamaki N, Hatano E, Fukushima A, Taniguchi T, Agata Y (2009) The NF90-NF45 complex functions as a negative regulator in the microRNA processing pathway. Mol Cell Biol 29:3754-3769
25. Suzuki HI, Yamagata K, Sugimoto K, Iwamoto T, Kato S, Miyazono K (2009) Modulation of microRNA processing by p53. Nature 460: 529-533
26. Yu B, Bi L, Zheng B, Ji L, Chevalier D, Agarwal M, Ramachandran V, Li W, Lagrange T, Walker JC, Chen X (2008) The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc Natl Acad Sci USA 105:10073-10078
27. Kawahara Y, Mieda-Sato A (2012) TDP-43 promotes microRNA biogenesis as a component of the Drosha and Dicer complexes. Proc Natl Acad Sci USA 109:3347-3352
28. Winter J, Jung S, Keller S, Gregory RI, Diederichs S (2009) Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 11:228-234
29. Luciano DJ, Mirsky H, Vendetti NJ, Maas S (2004) RNA editing of a miRNA precursor. RNA 10:1174-1177
30. Blow MJ, Grocock RJ, van Dongen S, Enright AJ, Dicks E, Futreal PA, Wooster R, Stratton MR (2006) RNA editing of human microRNAs. Genome Biol 7:R27
31. Landthaler M, Yalcin A, Tuschl T (2004) The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol 14:2162-2167
32. Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN (2004) The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 18:3016-3027
33. Triboulet R, Gregory RI (2010) Autoregulatory mechanisms controlling the Microprocessor. Adv Exp Med Biol 700:56-66
34. Yeom KH, Lee Y, Han J, Suh MR, Kim VN (2006) Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing. Nucleic Acids Res 34: 4622-4629
35. Han J, Pedersen JS, Kwon SC, Belair CD, Kim YK, Yeom KH, Yang WY, Haussler D, Blelloch R, Kim VN (2009) Posttranscriptional crossregulation between Drosha and DGCR8. Cell 136:75-84
36. Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D (2006) Identifi cation and classifi cation of conserved RNA secondary structures in the human genome. PLoS Comput Biol 2:e33
37. Shenoy A, Blelloch R (2009) Genomic analysis suggests that mRNA destabilization by the microprocessor is specialized for the autoregulation of Dgcr8. PLoS One 4:e6971
38. Guttler T, Gorlich D (2011) Ran-dependent nuclear export mediators: a structural perspective. EMBO J 30:3457-3474
39. Bohnsack MT, Czaplinski K, Gorlich D (2004) Exportin 5 is a RanGTP-dependent dsRNAbinding protein that mediates nuclear export of pre-miRNAs. RNA 10:185-191
40. Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U (2004) Nuclear export of microRNA precursors. Science 303:95-98
41. Coutavas E, Ren M, Oppenheim JD, D'Eustachio P, Rush MG (1993) Characterization of proteins that interact with the cell-cycle regulatory protein Ran/TC4. Nature 366:585-587
42. Sand M, Skrygan M, Georgas D, Arenz C, Gambichler T, Sand D, Altmeyer P, Bechara FG (2011) Expression levels of the microRNA maturing microprocessor complex component DGCR8 and the RNA-induced silencing complex (RISC) components Argonaute-1, Argonaute-2, PACT, TARBP1, and TARBP2 in epithelial skin cancer. Mol Carcinog 51: 916-922
43. Wang HW, Noland C, Siridechadilok B, Taylor DW, Ma E, Felderer K, Doudna JA, Nogales E (2009) Structural insights into RNA processing by the human RISC-loading complex. Nat Struct Mol Biol 16:1148-1153
44. Ma E, MacRae IJ, Kirsch JF, Doudna JA (2008) Autoinhibition of human dicer by its internal helicase domain. J Mol Biol 380:237-243
45. Forman JJ, Legesse-Miller A, Coller HA (2008) A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci USA 105:14879-14884
46. Diederichs S, Haber DA (2007) Dual role for argonautes in microRNA processing and posttranscriptional regulation of microRNA expression. Cell 131:1097-1108
47. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115:199-208
48. Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209-216
49. Okamura K, Phillips MD, Tyler DM, Duan H, Chou YT, Lai EC (2008) The regulatory activity of microRNA species has substantial infl uence on microRNA and 3? UTR evolution. Nat Struct Mol Biol 15:354-363
50. Ro S, Park C, Young D, Sanders KM, Yan W (2007) Tissue-dependent paired expression of miRNAs. Nucleic Acids Res 35:5944-5953
51. 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
52. Czech B, Zhou R, Erlich Y, Brennecke J, Binari R, Villalta C, Gordon A, Perrimon N, Hannon GJ (2009) Hierarchical rules for Argonaute loading in Drosophila. Mol Cell 36:445-456
53. Ghildiyal M, Xu J, Seitz H, Weng Z, Zamore PD (2010) Sorting of Drosophila small silencing RNAs partitions microRNA strands into the RNA interference pathway. RNA 16:43-56
54. Okamura K, Liu N, Lai EC (2009) Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. Mol Cell 36:431-444
55. Westholm JO, Lai EC (2011) Mirtrons: microRNA biogenesis via splicing. Biochimie 93:1897-1904
56. Noland CL, Ma E, Doudna JA (2011) siRNA repositioning for guide strand selection by human Dicer complexes. Mol Cell 43:110-121
57. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901-906
58. Dalmay T (2008) Identifi cation of genes targeted by microRNAs. Biochem Soc Trans 36: 1194-1196
59. Miyoshi K, Miyoshi T, Siomi H (2010) Many ways to generate microRNA-like small RNAs: non-canonical pathways for microRNA production. Mol Genet Genomics 284:95-103