A Whole-Genome RNAi Screen for C. elegans miRNA Pathway Genes

Current Biology

Volumn 17, Issue 23, 2007, Pages 2013-2022

  Parry, Devin H ^a   Xu, Jinling ^a   Ruvkun, Gary ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

RNA

Indexed keywords

CAENORHABDITIS ELEGANS PROTEIN; HELMINTH RNA; LET 7 MICRORNA, C ELEGANS; LET-7 MICRORNA, C ELEGANS; LIN 14 PROTEIN, C ELEGANS; LIN-14 PROTEIN, C ELEGANS; MESSENGER RNA; MICRORNA; NUCLEAR PROTEIN; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

ANIMAL; ARTICLE; BIOLOGY; CAENORHABDITIS ELEGANS; GENE EXPRESSION REGULATION; GENETICS; GENOME; GROWTH, DEVELOPMENT AND AGING; METABOLISM; RNA INTERFERENCE;

ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; GENOME, HELMINTH; MICRORNAS; NUCLEAR PROTEINS; RNA INTERFERENCE; RNA, HELMINTH; RNA, MESSENGER; RNA, SMALL INTERFERING;

CAENORHABDITIS ELEGANS;

EID: 36549001859     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2007.10.058     Document Type: Article

References (47)

1. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116 (2004) 281-297
2. Kloosterman W.P., and Plasterk R.H. The diverse functions of microRNAs in animal development and disease. Dev. Cell 11 (2006) 441-450
3. Grishok A., Pasquinelli A.E., Conte D., Li N., Parrish S., Ha I., Baillie D.L., Fire A., Ruvkun G., and Mello C.C. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106 (2001) 23-34
4. Bernstein E., Kim S.Y., Carmell M.A., Murchison E.P., Alcorn H., Li M.Z., Mills A.A., Elledge S.J., Anderson K.V., and Hannon G.J. Dicer is essential for mouse development. Nat. Genet. 35 (2003) 215-217
5. Wienholds E., Koudijs M.J., van Eeden F.J., Cuppen E., and Plasterk R.H. The microRNA-producing enzyme Dicer1 is essential for zebrafish development. Nat. Genet. 35 (2003) 217-218
6. 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. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408 (2000) 86-89
7. Reinhart B.J., Slack F.J., Basson M., Pasquinelli A.E., Bettinger J.C., Rougvie A.E., Horvitz H.R., and Ruvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403 (2000) 901-906
8. Lin S.Y., Johnson S.M., Abraham M., Vella M.C., Pasquinelli A., Gamberi C., Gottlieb E., and Slack F.J. The C. elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target. Dev. Cell 4 (2003) 639-650
9. Abrahante J.E., Daul A.L., Li M., Volk M.L., Tennessen J.M., Miller E.A., and Rougvie A.E. The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs. Dev. Cell 4 (2003) 625-637
10. Slack F.J., Basson M., Liu Z., Ambros V., Horvitz H.R., and Ruvkun G. 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 (2000) 659-669
11. Bracht J., Hunter S., Eachus R., Weeks P., and Pasquinelli A.E. Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. RNA 10 (2004) 1586-1594
12. Ketting R.F., Fischer S.E., Bernstein E., Sijen T., Hannon G.J., and Plasterk R.H. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15 (2001) 2654-2659
13. Hutvagner G., McLachlan J., Pasquinelli A.E., Balint E., Tuschl T., and Zamore P.D. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293 (2001) 834-838
14. Kennedy S., Wang D., and Ruvkun G. A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature 427 (2004) 645-649
15. Kim J.K., Gabel H.W., Kamath R.S., Tewari M., Pasquinelli A., Rual J.F., Kennedy S., Dybbs M., Bertin N., Kaplan J.M., et al. Functional genomic analysis of RNA interference in C. elegans. Science 308 (2005) 1164-1167
16. Rual J.F., Ceron J., Koreth J., Hao T., Nicot A.S., Hirozane-Kishikawa T., Vandenhaute J., Orkin S.H., Hill D.E., van den Heuvel S., and Vidal M. Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res. 14 (2004) 2162-2168
17. Kamath R.S., Fraser A.G., Dong Y., Poulin G., Durbin R., Gotta M., Kanapin A., Le Bot N., Moreno S., Sohrmann M., et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421 (2003) 231-237
18. Koonin E., Fedorova N., Jackson J., Jacobs A., Krylov D., Makarova K., Mazumder R., Mekhedov S., Nikolskaya A., Rao B., et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 5 (2004) R7
19. Moss E.G., Lee R.C., and Ambros V. The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell 88 (1997) 637-646
20. Polesskaya A., Cuvellier S., Naguibneva I., Duquet A., Moss E.G., and Harel-Bellan A. Lin-28 binds IGF-2 mRNA and participates in skeletal myogenesis by increasing translation efficiency. Genes Dev. 21 (2007) 1125-1138
21. Leung A.K., Calabrese J.M., and Sharp P.A. Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules. Proc. Natl. Acad. Sci. USA 103 (2006) 18125-18130
22. Horowitz D.S., and Abelson J. Stages in the second reaction of pre-mRNA splicing: the final step is ATP independent. Genes Dev. 7 (1993) 320-329
23. McKendrick L., Thompson E., Ferreira J., Morley S.J., and Lewis J.D. Interaction of eukaryotic translation initiation factor 4G with the nuclear cap-binding complex provides a link between nuclear and cytoplasmic functions of the m(7) guanosine cap. Mol. Cell. Biol. 21 (2001) 3632-3641
24. Izaurralde E., Lewis J., McGuigan C., Jankowska M., Darzynkiewicz E., and Mattaj I.W. A nuclear cap binding protein complex involved in pre-mRNA splicing. Cell 78 (1994) 657-668
25. Zhong W., and Sternberg P.W. Genome-wide prediction of C. elegans genetic interactions. Science 311 (2006) 1481-1484
26. 7G cap binding-like motif within human Ago2 represses translation. Cell 129 (2007) 1141-1151
27. Szymczyna B.R., Bowman J., McCracken S., Pineda-Lucena A., Lu Y., Cox B., Lambermon M., Graveley B.R., Arrowsmith C.H., and Blencowe B.J. Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processing. Genes Dev. 17 (2003) 461-475
28. D'Souza-Schorey C., and Chavrier P. ARF proteins: roles in membrane traffic and beyond. Nat. Rev. Mol. Cell Biol. 7 (2006) 347-358
29. Spiliotis E.T., and Nelson W.J. Here come the septins: novel polymers that coordinate intracellular functions and organization. J. Cell Sci. 119 (2006) 4-10
30. Rodriguez A.J., Seipel S.A., Hamill D.R., Romancino D.P., Di Carlo M., Suprenant K.A., and Bonder E.M. Seawi-a sea urchin piwi/argonaute family member is a component of MT-RNP complexes. RNA 11 (2005) 646-656
31. Blower M.D., Nachury M., Heald R., and Weis K. A Rae1-containing ribonucleoprotein complex is required for mitotic spindle assembly. Cell 121 (2005) 223-234
32. Sternberg, P.W. (2005). WormBook (http://www.wormbook.org).
33. Kao G., Tuck S., Baillie D., and Sundaram M.V. C. elegans SUR-6/PR55 cooperates with LET-92/protein phosphatase 2A and promotes Raf activity independently of inhibitory Akt phosphorylation sites. Development 131 (2004) 755-765
34. Johnson S.M., Grosshans H., Shingara J., Byrom M., Jarvis R., Cheng A., Labourier E., Reinert K.L., Brown D., and Slack F.J. RAS is regulated by the let-7 microRNA family. Cell 120 (2005) 635-647
35. Zhang H., Christoforou A., Aravind L., Emmons S.W., van den Heuvel S., and Haber D.A. The C. elegans Polycomb gene SOP-2 encodes an RNA binding protein. Mol. Cell 14 (2004) 841-847
36. Grishok A., Sinskey J.L., and Sharp P.A. Transcriptional silencing of a transgene by RNAi in the soma of C. elegans. Genes Dev. 19 (2005) 683-696
37. Zhang T., Sun Y., Tian E., Deng H., Zhang Y., Luo X., Cai Q., Wang H., Chai J., and Zhang H. RNA-binding proteins SOP-2 and SOR-1 form a novel PcG-like complex in C. elegans. Development 133 (2006) 1023-1033
38. Lu J., Getz G., Miska E.A., Alvarez-Saavedra E., Lamb J., Peck D., Sweet-Cordero A., Ebert B.L., Mak R.H., Ferrando A.A., et al. MicroRNA expression profiles classify human cancers. Nature 435 (2005) 834-838
39. Thomson J.M., Newman M., Parker J.S., Morin-Kensicki E.M., Wright T., and Hammond S.M. Extensive post-transcriptional regulation of microRNAs and its implications for cancer. Genes Dev. 20 (2006) 2202-2207
40. Ungar D., Oka T., Krieger M., and Hughson F.M. Retrograde transport on the COG railway. Trends Cell Biol. 16 (2006) 113-120
41. Reeves J.E., and Fried M. The surf-4 gene encodes a novel 30 kDa integral membrane protein. Mol. Membr. Biol. 12 (1995) 201-208
42. Hamelin M., Scott I.M., Way J.C., and Culotti J.G. The mec-7 beta-tubulin gene of Caenorhabditis elegans is expressed primarily in the touch receptor neurons. EMBO J. 11 (1992) 2885-2893
43. Hayes G.D., Frand A.R., and Ruvkun G. The mir-84 and let-7 paralogous microRNA genes of Caenorhabditis elegans direct the cessation of molting via the conserved nuclear hormone receptors NHR-23 and NHR-25. Development 133 (2006) 4631-4641
44. Lee R.C., Feinbaum R.L., and Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75 (1993) 843-854
45. Wightman B., Ha I., and Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75 (1993) 855-862
46. Timmons L., and Fire A. Specific interference by ingested dsRNA. Nature 395 (1998) 854
47. Reinhart B.J., and Ruvkun G. Isoform-specific mutations in the Caenorhabditis elegans heterochronic gene lin-14 affect stage-specific patterning. Genetics 157 (2001) 199-209