MicroRNAs in search of a target

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 71, Issue , 2006, Pages 129-134

  Stefani, G ^a   Slack, F ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAENORHABDITIS ELEGANS PROTEIN; LET 7 MICRORNA, C ELEGANS; LET-7 MICRORNA, C ELEGANS; LIN 14 PROTEIN, C ELEGANS; LIN-14 PROTEIN, C ELEGANS; MICRORNA; NUCLEAR PROTEIN; RNA INDUCED SILENCING COMPLEX; UNCLASSIFIED DRUG;

ANIMAL; BIOLOGY; CAENORHABDITIS ELEGANS; GENE; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; REVIEW; ARTICLE; BIOINFORMATICS; GENE CONTROL; GENE EXPRESSION; GENE TARGETING; MOLECULAR RECOGNITION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE HOMOLOGY;

ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; GENES, HELMINTH; HUMANS; MICRORNAS; NUCLEAR PROTEINS; RNA-INDUCED SILENCING COMPLEX;

EID: 34250624953     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2006.71.032     Document Type: Conference Paper

References (69)

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.
2. Ambros V. 1989. A hierarchy of regulatory genes controls a larvato-adult developmental switch in C. elegans. Cell 57: 49.
3. Arava Y., Wang Y., Storey J.D., Liu C.L., Brown P.O., and Herschlag D. 2003. Genomewide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 100: 3889.
4. Bagga S., Bracht J., Hunter S., Massirer K., Holtz J., Eachus R., and Pasquinelli A.E. 2005. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122: 553.
5. Bartel D.P. and Chen C.Z. 2004. Micromanagers of gene expression: The potentially widespread influence of metazoan microRNAs. Nat. Rev. Genet. 5: 396.
6. Bhattacharyya S.N., Habermacher R., Martine U., Closs E.I., and Filipowicz W. 2006. Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell 125: 1111.
7. Brengues M., Teixeira D., and Parker R. 2005. Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies. Science 310: 486.
8. Brennecke J., Stark A., Russell R.B., and Cohen S.M. 2005. Principles of microRNA-target recognition. PLoS Biol. 3: e85.
9. Brown V., Jin P., Ceman S., Darnell J.C., O'Donnell W.T., Tenenbaum S.A., Jin X., Feng Y., Wilkinson K.D., Keene J.D., et al. 2001. Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. Cell 107: 477.
10. Chalfie M., Horvitz H.R., and Sulston J.E. 1981. Mutations that lead to reiterations in the cell lineages of C. elegans. Cell 24: 59.
11. Chen X. 2004. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 2022.
12. Cimmino A., Calin G.A., Fabbri M., Iorio M.V., Ferracin M., Shimizu M., Wojcik S.E., Aqeilan R.I., Zupo S., Dono M., et al. 2005. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc. Natl. Acad. Sci. 102: 13944.
13. Ding L., Spencer A., Morita K., and Han M. 2005. The developmental timing regulator AIN-1 interacts with miRISCs and may target the argonaute protein ALG-1 to cytoplasmic P bodies in C. elegans. Mol. Cell 19: 437.
14. Dinkova T.D., Keiper B.D., Korneeva N.L., Aamodt E.J., and Rhoads R.E. 2005. Translation of a small subset of Caenorhabditis elegans mRNAs is dependent on a specific eukaryotic translation initiation factor 4E isoform. Mol. Cell. Biol. 25: 100.
15. Doench J.G. and Sharp P.A. 2004. Specificity of microRNA target selection in translational repression. Genes Dev. 18: 504.
16. Dreyfuss G., Kim V.N., and Kataoka N. 2002. Messenger-RNAbinding proteins and the messages they carry. Nat. Rev. Mol. Cell Biol. 3: 195.
17. Farh K.K., Grimson A., Jan C., Lewis B.P., Johnston W.K., Lim L.P., Burge C.B., and Bartel D.P. 2005. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310: 1817.
18. Galban S., Fan J., Martindale J.L., Cheadle C., Hoffman B., Woods M.P., Temeles G., Brieger J., Decker J., and Gorospe M. 2003. von Hippel-Lindau protein-mediated repression of tumor necrosis factor alpha translation revealed through use of cDNA arrays. Mol. Cell. Biol. 23: 2316.
19. Giraldez A.J., Mishima Y., Rihel J., Grocock R.J., Van Dongen S., Inoue K., Enright A.J., and Schier A.F. 2006. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312: 75.
20. Grosshans H., Johnson T., Reinert K.L., Gerstein M., and Slack F.J. 2005. The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. Dev. Cell 8: 321.
21. Humphreys D.T., Westman B.J., Martin D.I., and Preiss T. 2005. MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function. Proc. Natl. Acad. Sci. 102: 16961.
22. Jakymiw A., Lian S., Eystathioy T., Li S., Satoh M., Hamel J.C., Fritzler M.J., and Chan E.K. 2005. Disruption of GW bodies impairs mammalian RNA interference. Nat. Cell Biol. 7: 1267.
23. Jing Q., Huang S., Guth S., Zarubin T., Motoyama A., Chen J., Di Padova F., Lin S.C., Gram H., and Han J. 2005. Involvement of microRNA in AU-rich element-mediated mRNA instability. Cell 120: 623.
24. Johannes G., Carter M.S., Eisen M.B., Brown P.O., and Sarnow P. 1999. Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc. Natl. Acad. Sci. 96: 13118.
25. 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.
26. Lagos-Quintana M., Rauhut R., Lendeckel W., and Tuschl T. 2001. Identification of novel genes coding for small expressed RNAs. Science 294: 853.
27. Lai E.C. 2002. Micro RNAs are complementary to 3′UTR sequence motifs that mediate negative post-transcriptional regulation. Nat. Genet. 30: 363.
28. 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.
29. Lee R.C. and Ambros V. 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862.
30. 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.
31. Lewis B.P., Burge C.B., and Bartel D.P. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15.
32. Lewis B.P., Shih I.H., Jones-Rhoades M.W., Bartel D.P., and Burge C.B. 2003. Prediction of mammalian microRNA targets. Cell 115: 787.
33. Lim L.P., Glasner M.E., Yekta S., Burge C.B., and Bartel D.P. 2003a. Vertebrate microRNA genes. Science 299: 1540.
34. Lim L.P., Lau N.C., Weinstein E.G., Abdelhakim A., Yekta S., Rhoades M.W., Burge C.B., and Bartel D.P. 2003b. The microRNAs of Caenorhabditis elegans. Genes Dev. 17: 991-1008.
35. Lim L.P., Lau N.C., Garrett-Engele P., Grimson A., Schelter J.M., Castle J., Bartel D.P., Linsley P.S., and Johnson J.M. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769.
36. Liu J., Valencia-Sanchez M.A., Hannon G.J., and Parker R. 2005a. MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nat. Cell Biol. 7: 719.
37. Liu J., Rivas F.V., Wohlschlegel J., Yates J.R., III, Parker R., and Hannon G.J. 2005b. A role for the P-body component GW182 in microRNA function. Nat. Cell Biol. 7: 1261.
38. Nakamoto M., Jin P., O'Donnell W.T., and Warren S.T. 2005. Physiological identification of human transcripts translationally regulated by a specific microRNA. Hum. Mol. Genet. 14: 3813.
39. Novina C.D. and Sharp P.A. 2004. The RNAi revolution. Nature 430: 161.
40. O'Donnell K.A., Wentzel E.A., Zeller K.I., Dang C.V., and Mendell J.T. 2005. c-Myc-regulated microRNAs modulate E2F1 expression. Nature 435: 839.
41. Olsen P.H. and Ambros V. 1999. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol. 216: 671.
42. Pasquinelli A.E., Reinhart B.J., Slack F., Martindale M.Q., Kuroda M.I., Maller B., Hayward D.C., Ball E.E., Degnan B., Muller P., et al. 2000. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408: 86.
43. Petersen C.P., Bordeleau M.E., Pelletier J., and Sharp P.A. 2006. Short RNAs repress translation after initiation in mammalian cells. Mol. Cell 21: 533.
44. Pillai R.S., Bhattacharyya S.N., Artus C.G., Zoller T., Cougot N., Basyuk E., Bertrand E., and Filipowicz W. 2005. Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science 309: 1573.
45. Poy M.N., Eliasson L., Krutzfeldt J., Kuwajima S., Ma X., Macdonald P.E., Pfeffer S., Tuschl T., Rajewsky N., Rorsman P., and Stoffel M. 2004. A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432: 226.
46. Preiss T., Baron-Benhamou J., Ansorge W., and Hentze M.W. 2003. Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock. Nat. Struct. Biol. 10: 1039.
47. Rajasekhar V.K., Viale A., Socci N.D., Wiedmann M., Hu X., and Holland E.C. 2003. Oncogenic Ras and Akt signaling contribute to glioblastoma formation by differential recruitment of existing mRNAs to polysomes. Mol. Cell 12: 889.
48. Rajewsky N. 2006. microRNA target predictions in animals. Nat. Genet. (suppl. 1) 38: S8.
49. Rajewsky N. and Socci N.D. 2004. Computational identification of microRNA targets. Dev. Biol. 267: 529.
50. 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.
51. Rigoutsos I., Huynh T., Miranda K., Tsirigos A., McHardy A., and Platt D. 2006. Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. Proc. Natl. Acad. Sci. 103: 6605.
52. Saxena S., Jonsson Z.O., and Dutta A. 2003. Small RNAs with imperfect match to endogenous mRNA repress translation. Implications for off-target activity of small inhibitory RNA in mammalian cells. J. Biol. Chem. 278: 44312.
53. Schratt G.M., Nigh E.A., Chen W.G., Hu L., and Greenberg M.E. 2004. BDNF regulates the translation of a select group of mRNAs by a mammalian target of rapamycin-phosphatidylinositol 3-kinase-dependent pathway during neuronal development. J. Neurosci. 24: 7366.
54. Seggerson K., Tang L., and Moss E.G. 2002. Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Dev. Biol. 243: 215.
55. Sheth U. and Parker R. 2003. Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science 300: 805.
56. Sood P., Krek A., Zavolan M., Macino G., and Rajewsky N. 2006. Cell-type-specific signatures of microRNAs on target mRNA expression. Proc. Natl. Acad. Sci. 103: 2746.
57. Stark A., Brennecke J., Russell R.B., and Cohen S.M. 2003. Identification of Drosophila microRNA targets. PLoS Biol. 1: E60.
58. Stark A., Brennecke J., Bushati N., Russell R.B., and Cohen S.M. 2005. Animal microRNAs confer robustness to gene expression and have a significant impact on 3?UTR evolution. Cell 123: 1133.
59. 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.
60. Vella M.C., Reinert K., and Slack F.J. 2004a. Architecture of a validated microRNA::target interaction. Chem. Biol. 11: 1619.
61. Vella M.C., Choi E.Y., Lin S.Y., Reinert K., and Slack F.J. 2004b. The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3′UTR. Genes Dev. 18: 132.
62. 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.
63. Wightman B., Burglin T.R., Gatto J., Arasu P., and Ruvkun G. 1991. Negative regulatory sequences in the lin-14 3′-untranslated region are necessary to generate a temporal switch during Caenorhabditis elegans development. Genes Dev. 5: 1813.
64. Wu L., Fan J., and Belasco J.G. 2006. MicroRNAs direct rapid deadenylation of mRNA. Proc. Natl. Acad. Sci. 103: 4034.
65. Xie X., Lu J., Kulbokas E.J., Golub T.R., Mootha V., Lindblad-Toh K., Lander E.S., and Kellis M. 2005. Systematic discovery of regulatory motifs in human promoters and 3′UTRs by comparison of several mammals. Nature 434: 338.
66. Yekta S., Shih I.H., and Bartel D.P. 2004. MicroRNA-directed cleavage of HOXB8 mRNA. Science 304: 594.
67. Zamore P.D. and Haley B. 2005. Ribo-gnome: The big world of small RNAs. Science 309: 1519.
68. Zeng Y., Yi R., and Cullen B.R. 2003. MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc. Natl. Acad. Sci. 100: 9779.
69. Zong Q., Schummer M., Hood L., and Morris D.R. 1999. Messenger RNA translation state: The second dimension of high-throughput expression screening. Proc. Natl. Acad. Sci. 96: 10632.