Identification of specific let-7 microRNA binding complexes in Caenorhabditis elegans

RNA

Volumn 14, Issue 10, 2008, Pages 2104-2114

  Chan, Shih Peng ^a   Ramaswamy, Gopalakrishna ^b   Choi, Eun Young ^c   Slack, Frank J ^a  

^a YALE UNIVERSITY   (United States)

^b Caterpillar Logistics Services India Pvt Ltd   (India)

^c UNIVERSITY OF KENTUCKY   (United States)

Author keywords

let 7; miRNA; RISC; siRNA

Indexed keywords

BINDING PROTEIN; LET 7 MICRORNA; MICRORNA; PROTEIN P40; RIBONUCLEOPROTEIN; RNA BINDING PROTEIN; RNA INDUCED SILENCING COMPLEX; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; CAENORHABDITIS ELEGANS; COMPLEX FORMATION; CONTROLLED STUDY; CROSS LINKING; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; RNA BINDING; RNA SEQUENCE;

ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; MICRORNAS; MUTATION; RIBONUCLEOPROTEINS; RNA-INDUCED SILENCING COMPLEX;

CAENORHABDITIS ELEGANS;

EID: 52949098752     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.551208     Document Type: Article

References (42)

1. Abbott, A.L., Alvarez-Saavedra, E., Miska, E.A., Lau, N.C., Bartel, D.P., Horvitz, H.R., and Ambros, V. 2005. The let-7 microRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev. Cell 9: 403-414.
2. Ambros, V. 2001. microRNAs: Tiny regulators with great potential. Cell 107: 823-826.
3. Banerjee, D. and Slack, F. 2002. Control of developmental timing by small temporal RNAs: A paradigm for RNA-mediated regulation of gene expression. Bioessays 24: 119-129.
4. Bartel, D.P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
5. 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.
6. 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. 98: 14428-14433.
7. Calin, G.A., Liu, C.G., Sevignani, C., Ferracin, M., Felli, N., Dumitru, C.D., Shimizu, M., Cimmino, A., Zupo, S., Dono, M., et al. 2004a. MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc. Natl. Acad. Sci. 101: 11755-11760.
8. Calin, G.A., Sevignani, C., Dumitru, C.D., Hyslop, T., Noch, E., Yendamuri, S., Shimizu, M., Rattan, S., Bullrich, F., Negrini, M., et al. 2004b. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc. Natl. Acad. Sci. 101: 2999-3004.
9. Caudy, A.A., Myers, M., Hannon, G.J., and Hammond, S.M. 2002. Fragile X-related protein and VIG associate with the RNA interference machinery. Genes & Dev. 16: 2491-2496.
10. Caudy, A.A., Ketting, R.F., Hammond, S.M., Denli, A.M., Bathoorn, A.M., Tops, B.B., Silva, J.M., Myers, M.M., Hannon, G.J., and Plasterk, R.H. 2003. A micrococcal nuclease homologue in RNAi effector complexes. Nature 425: 411-414.
11. 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.
12. Grosshans, H. and Slack, F.J. 2002. Micro-RNAs: Small is plentiful. J. Cell Biol. 156: 17-21.
13. Hammond, S.M., Bernstein, E., Beach, D., and Hannon, G.J. 2000. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404: 293-296.
14. Hammond, S.M., Boettcher, S., Caudy, A.A., Kobayashi, R., and Hannon, G.J. 2001. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293: 1146-1150.
15. Hutvágner, G. and Zamore, P.D. 2002. A microRNA in a multiple-turnover RNAi enzyme complex. Science 297: 2056-2060.
16. 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.
17. Hutvágner, G., Simard, M.J., Mello, C.C., and Zamore, P.D. 2004. Sequence-specific inhibition of small RNA function. PLoS Biol. 2: e98. doi: 10.1371/journal.pbio.0020098.
18. Johnson, S.M., Lin, S.Y., and Slack, F.J. 2003. The time of appearance of the C. elegans let-7 microRNA is transcriptionally controlled utilizing a temporal regulatory element in its promoter. Dev. Biol. 259: 364-379.
19. Johnson, S.M., Grosshans, H., Shingara, J., Byrom, M., Jarvis, R., Cheng, A., Labourier, E., Reinert, K.L., Brown, D., and Slack, F.J. 2005. RAS is regulated by the let-7 microRNA family. Cell 120: 635-647.
20. Ketting, R.F., Haverkamp, T.H., van Luenen, H.G., and Plasterk, R.H. 1999. mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell 99: 133-141.
21. 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.
22. Lee, R.C., Feinbaum, R.L., and Ambros, V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
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: 991-1008.
24. Liu, J., Carmell, M.A., Rivas, F.V., Marsden, C.G., Thomson, J.M., Song, J.J., Hammond, S.M., Joshua-Tor, L., and Hannon, G.J. 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305: 1437-1441.
25. Martinez, J., Patkaniowska, A., Urlaub, H., Luhrmann, R., and Tuschl, T. 2002. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110: 563-574.
26. Meister, G., Landthaler, M., Patkaniowska, A., Dorsett, Y., Teng, G., and Tuschl, T. 2004. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15: 185-197.
27. Mourelatos, Z., Dostie, 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.
28. Nykanen, A., Haley, B., and Zamore, P.D. 2001. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107: 309-321.
29. Pasquinelli, A.E. and Ruvkun, G. 2002. Control of developmental timing by microRNAs and their targets. Annu. Rev. Cell Dev. Biol. 18: 495-513.
30. Pham, J.W., Pellino, J.L., Lee, Y.S., Carthew, R.W., and Sontheimer, E.J. 2004. A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell 117: 83-94.
31. Reinhart, B.J., Slack, F.J., Basson, M., Pasquinelli, A.E., Bettinger, J.C., Rougvie, A.E., Horvitz, H.R., and Ruvkun, G. 2000. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906.
32. Slack, F.J., Basson, M., Liu, Z., Ambros, V., Horvitz, H.R., and Ruvkun, G. 2000. The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol. Cell 5: 659-669.
33. Stiernagle, T. 1999. Maintenance of C. elegans. In C. elegans: A practical approach (ed. I.A. Hope), pp. 51-67. Oxford University Press, New York.
34. Tabara, H., Sarkissian, M., Kelly, W.G., Fleenor, J., Grishok, A., Timmons, L., Fire, A., and Mello, C.C. 1999. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99: 123-132.
35. Takamizawa, J., Konishi, H., Yanagisawa, K., Tomida, S., Osada, H., Endoh, H., Harano, T., Yatabe, Y., Nagino, M., Nimura, Y., et al. 2004. Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res. 64: 3753-3756.
36. Tomari, Y., Du, T., Haley, B., Schwarz, D.S., Bennett, R., Cook, H.A., Koppetsch, B.S., Theurkauf, W.E., and Zamore, P.D. 2004. RISC assembly defects in the Drosophila RNAi mutant armitage. Cell 116: 831-841.
37. Tops, B.B., Plasterk, R.H., and Ketting, R.F. 2006. The Caenorhabditis elegans Argonautes ALG-1 and ALG-2: Almost identical yet different. Cold Spring Harb. Symp. Quant. Biol. 71: 189-194.
38. 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.
39. Vella, M.C., Choi, E.Y., Lin, S.Y., Reinert, K., and Slack, F.J. 2004. The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 39UTR. Genes & Dev. 18: 132-137.
40. Viswanathan, S.R., Daley, G.Q., and Gregory, R.I. 2008. Selective blockade of microRNA processing by Lin28. Science 320: 97-100.
41. Wightman, B., Ha, I., and Ruvkun, G. 1993. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855-862.
42. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415.