Structural Aspects of MicroRNA Biogenesis

IUBMB Life

Volumn 56, Issue 2, 2004, Pages 95-100

  Krol, Jacek ^a   Krzyzosiak, Wlodzimierz J ^a  

^a INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

Author keywords

Dicer specificity; miRNA biogenesis; miRNA length; miRNA precursor

Indexed keywords

GENE PRODUCT; MESSENGER RNA; MICRORNA; RNA PRECURSOR;

ARABIDOPSIS; CAENORHABDITIS ELEGANS; CELL FUNCTION; DEVELOPMENT; DROSOPHILA MELANOGASTER; EVOLUTION; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; HUMAN; MICRORNA GENE; NONHUMAN; ORGANOGENESIS; REVIEW; RNA GENE; RNA HYBRIDIZATION; RNA STRUCTURE; RNA SYNTHESIS;

ANIMALS; HUMANS; MICRORNAS; PROTEIN STRUCTURE, QUATERNARY; RIBONUCLEASE III; RNA PRECURSORS; SUBSTRATE SPECIFICITY;

ARABIDOPSIS; ARABIDOPSIS THALIANA; CAENORHABDITIS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; HOMO; HOMO SAPIENS; MELANOGASTER;

EID: 1842507232     PISSN: 15216543     EISSN: None     Source Type: Journal    
DOI: 10.1080/15216540410001670142     Document Type: Review

References (46)

1. Ambros, V. (2001) MicroRNAs: tiny regulators with great potential. Cell 107, 823-826.
2. Lee, Y., Jeon, K., Lee, J-T., Kim, S., and Kim, V. N. (2002) microRNA maturation: stepwise processing and subcellular localization. EMBO J. 21, 4663-4670.
3. Lee, Y., Ahn, C., Han, J., Chol, 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.
4. Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E., and Kutay, U. (2003) Nuclear Export of MicroRNA Precursors. Science 20, 10.1126/ science. 1090599.
5. Hutvágner, 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.
6. Knight, S. W., and Bass, B. L. (2001) A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293, 2269-2271.
7. Lagos-Quintana, M., Rauhut, R., Lendlecker, W., and Tuschl, T. (2001) Identification of novel genes coding for small expressed RNAs. Science 294, 853-858.
8. Lau, N. C., Lim, L. P., Weinstein, E. G., and Bartel, D. P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858-862.
9. Lee, R., and Ambros, V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862-864.
10. Hutvágner, G., and Zamore, P. D. (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297, 2056-2060.
11. Hannon, G. J. (2002) RNA interference. Nature, 418, 244-251.
12. Bernstein, E., Caudy, A. A., Hammond, S. M., and Hannon, G. J. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363-366.
13. McManus, M. T., and Sharp, P. A. (2002) Gene silencing in mammals by small interfering RNAs. Nat. Rev. Genet. 3, 737-747.
14. Elbashir, S. M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., and Tuschl, T. (2001) Duplexes of 21-nucleotide RNAs mediated RNA interference in cultured mammalian cells. Nature 411, 494-498.
15. Rhoades, M. W., Reinhart, B. J., Lim, L. P., Burge, C. B., Bartel, B., and Bartel, D. P. (2002) Prediction of plant microRNA targets. Cell 110, 513-520.
16. Zeng, Y., Wagner, E. T., and Cullen, B. R. (2002) Both natural and designed microRNA can inhibit the expression of cognate mRNAs wnen expressed in human cells. Mol. Cell 9, 1327-1333.
17. Doench, J. G., Petersen, C. P., and Zamore, P. A. (2003) siRNAs can function as miRNAs. Genes Dev. 17, 438-442.
18. Mourelatos, Z., Destie, J., Paushkin, S., Sharma, A., Charroux, B., Abel, L., Rappsilber, J., Mann, M., and Dreyfuss, G. (2002) miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev. 16, 720-728.
19. Lai, E. C., Tomancak, P., Williams, R. W., and Rubin, G. M. (2003) Computational identification of Drosophila microRNA genes. Genome Biol. 4, R42.
20. Largos-Quintana, M., Rauhut, R., Meyer, J., Borkhardt, A., and Tuschl, T. (2003) New microRNAs from mouse and human. RNA 9, 175-179.
21. Aravin, A. A., Lagos-Quintana, M., Yalcin, A., Zavolan, M., Marks, D., Snyder, B., Gaasterland, T., Meyer, J., and Tuschl T. (2003) The small RNA profile during Drosophila melanogaster development. Dev Cell. 5, 337-350.
22. Rhoades, M. W., Reinhart, B. J., Lim, L. P., Burge, C. B., Bartel, B., and Bartel, D. P. (2002) Prediction of plant microRNA targets. Cell 110, 513-520.
23. Lim, L. P., Lau, N. C., Weinstein, E. G., Abdelhakim, A., Yekta, S., Rhoades, M. W., Burge, C. B., and Bartel, D. P. (2003) The microRNAs of Caenorhabditis elegans. Genes Dev. 17, 1-18.
24. Zamore, P. D. (2001) RNA interference: listening to the sound of silence. Nature Struc. Biol. 9, 746-750.
25. Tuschl, T. (2002) Expanding small RNA interference. Nature Biotech. 20, 446-448.
26. Brummelkamp, T. R., Bernards, R., and Agami, R. (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296, 550-553.
27. Provost, P., Dishart, D., Doucet, J., Frendewey, D., Samuelsson, B., and Radmark O. (2002) Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J. 21, 5864-5874.
28. 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.
29. Kawasaki, H., Suyama, E., Iyo, M., and Taira, K. (2003) siRNAs generated by recombinant human Dicer induce specific and significant but target site-independent gene silencing in human cells. Nucleic Acids Res. 31, 981-987.
30. Myers, J. W., Jones, J. T., Meyer, T., and Ferrell, J. E. (2003) Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing. Nature Biotech. 21, 324-328.
31. Pasquinelli, A. E., Reinhart, B. J., Slack, F., Martindale, M. Q., Kuroda, M. I., Maller, B., Hayward, D. C., Ball, E. E., Degan, B., Muller, P., et al. (2000) Conservation across animal phylogeny of the sequences and temporal regulation of the 21 nucleotide let-7 heterochronic regulatory RNA. Nature 408, 86-89.
32. Griffiths-Jones, S. (2004) The microRNA Registry. Nucleic Acids Res. 32, D109-D111.
33. Zeng, Y., and Cullen, B. R. (2003) Sequence requirements for microRNA processing and function in human cells. RNA 9, 112-123.
34. Chelladurai, B., Li, H., Zhang, K., and Nicholson, A. W. (1993) Mutational analysis of a ribonuclease III processing signal. Biochemistry 32, 75-49-7558.
35. Zhang, K., and Nicholson, A. W. (1997) Regulation of ribonuclease III processing by double-helical sequence antideterminants. Proc. Natl. Acad. Sci USA 94, 13437-13441.
36. Ketting, R. F., Fischer, S. E., Bernstein, E., Sijen, T., Hannon, G. J., and Plasterk, R. H. (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15, 2654-2659.
37. Khvorova, A., Reynolds, A., and Jayasena, S. D. (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209-216.
38. Schwarz, D. S., Hutvágner, 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.
39. Blaszczyk, J., Tropea, J. E., Bubunenko, M., Routzhan, K. M., Waugh, D. S., Court, D. L., and Ji, X. (2001) Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage. Structure 9, 1225-1236.
40. Zamore, P. D. (2002) Thirty-three years later, a glimpse at the ribonuclease III active sites. Mol. Cell 8, 1158-1160.
41. Lamontagne, B., and Elela, S. A. (2004) Evaluation of the RNA determinant for bacterial and yeast RNase III binding and cleavage. J. Biol. Chem. 279, 2231-2241.
42. Doyle, M., and Jantsch, M. F. (2002) New and old roles of the double-stranded RNA-binding domain. J. Struc. Biol. 140, 147-153.
43. Yan, K. S., Yan, S., Faroog, A., Han, A., Zeng, L., and Zhou, M.-M. (2003) Structure and conserved RNA binding of the PAZ domain. Nature 426, 468-474.
44. 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.
45. Campblell, F., Cassano, A., Anderson, V., and Harris, M. E. (2002) Pre-steady-state and stopped-flow fluorescence analysis of Escherichia coli ribonuclease III: insights into mechanism and conformational changes associated with binding and catalysis. J. Mol. Biol. 317, 21-40.
46. Zheng, X., and Bevilacqua, P. C. (2000) Straightening of bulged RNA by the double-stranded RNA-binding domain from the protein kinase PKR. Proc. Natl. Acad. Sci. U S A. 97, 14162-14167.