The terminal loop region controls microRNA processing by Drosha and Dicer

Nucleic Acids Research

Volumn 38, Issue 21, 2010, Pages 7689-7697

  Zhang, Xiaoxiao ^a   Zeng, Yan ^a,b  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DICER; MICRORNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR DROSHA; UNCLASSIFIED DRUG;

ARTICLE; CELL MATURATION; CONTROLLED STUDY; GENE INTERACTION; GENE MUTATION; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; IN VITRO STUDY; PRIORITY JOURNAL; RNA CLEAVAGE; RNA PROCESSING; RNA SEQUENCE; RNA STRUCTURE; TERMINAL LOOP REGION; TRANSCRIPTION REGULATION;

CELL LINE; HUMANS; MICRORNAS; MUTATION; RIBONUCLEASE III; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, DOUBLE-STRANDED;

EID: 78649870594     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq645     Document Type: Article

References (49)

1. Bartel, D. P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
2. Valencia-Sanchez, M. A., Liu, J., Hannon, G. J. and Parker, R. (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev., 20, 515-524.
3. Chekulaeva, M. and Filipowicz, W. (2009) Mechanisms of miRNA-mediated post-transcriptional regulation in animal cells. Curr. Opin. Cell Biol., 21, 452-460.
4. Ambros, V. (2004) The functions of animal microRNAs. Nature, 431, 350-355.
5. Garzon, R., Calin, G. A. and Croce, C. M. (2009) MicroRNAs in Cancer. Annu. Rev. Med., 60, 167-179.
6. Cullen, B. R. (2004) Transcription and processing of human microRNA precursors. Mol. Cell, 16, 861-865.
7. Lee, Y., Ahn, C., Han, J., Choi, H., Kim, J., Yim, J., Lee, J., Provost, P., Radmark, O., Kim, S. et al. (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature, 425, 415-419.
8. Denli, A. M., Tops, B., Plasterk, R. H. A., Ketting, R. F. and Hannon, G. J. (2004) Processing of pri-microRNAs by the microprocessor complex. Nature, 432, 231-235.
9. Gregory, R. I., Yan, K. P., Amuthan, G., Chendrimada, T., Doratotaj, B., Cooch, N. and Shiekhattar, R. (2004) The microprocessor complex mediates the genesis of microRNAs. Nature, 432, 235-240.
10. Han, J., Lee, Y., Yeom, K. H., Kim, Y. K., Jin, H. and Kim, V. N. (2004) The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev., 18, 3016-3027.
11. Landthaler, M., Yalcin, A. and 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.
12. Berezikov, E., Chung, W. J., Willis, J., Cuppen, E. and Lai, E. C. (2007) Mammalian mirtron genes. Mol. Cell, 28, 328-336.
13. Okamura, K., Hagen, J. W., Duan, H., Tyler, D. M. and Lai, E. C. (2007) The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell, 130, 89-100.
14. Ruby, J. G., Jan, C. H. and Bartel, D. P. (2007) Intronic microRNA precursors that bypass Drosha processing. Nature, 448, 83-86.
15. Babiarz, J. E., Ruby, J. G., Wang, Y., Bartel, D. P. and Blelloch, R. (2008) Mouse ES cells express endogenous shRNAs, siRNAs, and other microprocessor-independent, Dicer-dependent small RNAs. Genes Dev., 22, 2773-2785.
16. Bogerd, H. P., Karnowski, H. W., Cai, X., Shin, J., Pohlers, M. and Cullen, B. R. (2010) A mammalian herpesvirus uses noncanonical expression and processing mechanisms to generate viral microRNAs. Mol. Cell, 37, 135-142.
17. Yi, R., Qin, Y., Macara, I. G. and Cullen, B. R. (2003) Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev., 17, 3011-3016.
18. Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E. and Kutay, U. (2004) Nuclear export of microRNA precursors. Science, 303, 95-98.
19. Billy, E., Brondani, V., Zhang, H., Muller, U. and Filipowicz, W. (2001) Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc. Natl Acad. Sci. USA, 98, 14428-14433.
20. Grishok, A., Pasquinelli, A. E., Conte, D., Li, N., Parrish, S., Ha, I., Baillie, D. L., Fire, A., Ruvkun, G. and Mello, C. C. (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell, 106, 23-34.
21. Hutvagner, G., McLachlan, J., Pasquinelli, A. E., Balint, E., Tuschl, T. and Zamore, P. D. (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science, 293, 834-838.
22. Ketting, R. F., Haverkamp, T. H., van Luenen, H. G. and Plasterk, R. H. A. (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev., 15, 2654-2659.
23. Khvorova, A., Reynolds, A. and Jayasena, S. D. (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell, 115, 209-216.
24. Schwarz, D. S., Hutvagner, G., Du, T., Xu, Z., Aronin, N. and Zamore, P. D. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell, 115, 199-208.
25. Chendrimada, T. P., Gregory, R. I., Kumaraswamy, E., Norman, J., Cooch, N., Nishikura, K. and Shiekhattar, R. (2005) TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature, 436, 740-744.
26. Forstemann, K., Tomari, Y., Du, T., Vagin, V. V., Denli, A. M., Bratu, D. P., Klattenhoff, C., Theurkauf, W. E. and Zamore, P. D. (2005) Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol., 3, e236.
27. Gregory, R. I., Chendrimada, T. P., Cooch, N. and Shiekhattar, R. (2005) Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell, 123, 631-640.
28. Haase, A. D., Jaskiewicz, L., Zhang, H., Laine, S., Sack, R., Gatignol, A. and Filipowicz, W. (2005) TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep., 6, 961-967.
29. Maniataki, E. and Mourelatos, Z. (2005) A human, ATP-independent, RISC assembly machine fueled by pre-miRNA. Genes Dev., 19, 2979-2990.
30. Saito, K., Ishizuka, A., Siomi, H. and Siomi, M. C. (2005) Processing of pre-microRNAs by the Dicer-1-Loquacious complex in Drosophila cells. PLoS Biol., 3, e235.
31. Lee, Y., Hur, I., Park, S. Y., Kim, Y. K., Suh, M. R. and Kim, V. N. (2006) The role of PACT in the RNA silencing pathway. EMBO J., 25, 522-532.
32. Zeng, Y. and Cullen, B. R. (2003) Sequence requirements for microRNA processing and function in human cells. RNA, 9, 112-123.
33. Zeng, Y., Yi, R. and Cullen, B. R. (2005) Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J., 24, 138-148.
34. Zeng, Y. and Cullen, B. R. (2005) Single-stranded extensions on primary microRNA transcripts are required for Drosha cleavage. J. Biol. Chem., 280, 27595-27603.
35. Han, J., Lee, Y., Yeom, K. H., Nam, J. W., Heo, I., Rhee, J. K., Sohn, S. Y., Cho, Y., Zhang, B. T. and Kim, V. N. (2006) Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell, 125, 887-901.
36. Michlewski, G., Guil, S., Semple, C. A. and Caceres, J. F. (2008) Posttranscriptional regulation of miRNAs harboring conserved terminal loops. Mol. Cell, 32, 383-393.
37. Zeng, Y. and Cullen, B. R. (2006) Recognition and cleavage of primary microRNA transcripts. Methods Mol. Biol., 342, 49-56.
38. Zeng, Y. and Cullen, B. R. (2004) Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic Acids Res., 32, 4776-4785.
39. Macrae, I. J., Zhou, K., Li, F., Repic, A., Brooks, A. N., Cande, W. Z., Adams, P. D. and Doudna, J. A. (2006) Structural basis for double-stranded RNA processing by Dicer. Science, 311, 195-198.
40. Zhang, H., Kolb, F. A., Brondani, V., Billy, E. and Filipowicz, W. (2002) Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J., 21, 5875-5885.
41. Ma, E., MacRae, I. J., Kirsch, J. F. and Doudna, J. A. (2008) Autoinhibition of human dicer by its internal helicase domain. J. Mol. Biol., 380, 237-243.
42. Guil, S. and Caceres, J. F. (2007) The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nat. Struct. Mol. Biol., 14, 591-596.
43. Heo, I., Joo, C., Cho, J., Ha, M., Han, J. and Kim, V. N. (2008) Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Mol. Cell, 32, 276-284.
44. Newman, M. A., Thomson, J. M. and Hammond, S. M. (2008) Lin-28 interaction with the Let-7 precursor loop mediates regulated microRNA processing. RNA, 14, 1539-1549.
45. Rybak, A., Fuchs, H., Smirnova, L., Brandt, C., Pohl, E. E., Nitsch, R. and Wulczyn, F. G. (2008) A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment. Nat. Cell Biol., 10, 987-993.
46. Viswanathan, S. R., Daley, G. Q. and Gregory, R. I. (2008) Selective blockade of microRNA processing by Lin-28. Science, 320, 97-100.
47. Lehrbach, N. J., Armisen, J., Lightfoot, H. L., Murfitt, K. J., Bugaut, A., Balasubramanian, S. and Miska, E. (2009) LIN-28 and the poly(U) polymerase PUP-2 regulate let-7 microRNA processing in Caenorhabditis elegans. Nat. Struct. Mol. Biol., 16, 1016-1020.
48. Ruggiero, T., Trabucchi, M., De Santa, F., Zupo, S., Harfe, B. D., McManus, M. T., Rosenfeld, M. G., Briata, P. and Gherzi, R. (2009) LPS induces KH-type splicing regulatory protein-dependent processing of microRNA-155 precursors in macrophages. FASEB J., 23, 2898-2908.
49. Trabucchi, M., Briata, P., Garcia-Mayoral, M., Haase, A. D., Filipowicz, W., Ramos, A., Gherzi, R. and Rosenfeld, M. G. (2009) The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs. Nature, 459, 1010-1014.