The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans

Developmental Cell

Volumn 8, Issue 3, 2005, Pages 321-330

  Großhans, Helge ^a   Johnson, Ted ^a   Reinert, Kristy L ^a   Gerstein, Mark ^a   Slack, Frank J ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HORMONE RECEPTOR; MICRORNA; MUTANT PROTEIN; PROTEIN LET 7; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

3' UNTRANSLATED REGION; ARTICLE; CAENORHABDITIS ELEGANS; CELL DIFFERENTIATION; CELL LINEAGE; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENE MUTATION; GENE REPRESSION; GENETIC IDENTIFICATION; INTESTINE; LARVAL DEVELOPMENT; MORPHOGENESIS; NONHUMAN; ORTHOLOGY; PHENOTYPE; PHYLOGENY; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN TARGETING; SEQUENCE ANALYSIS; STEM CELL; SUBCUTANEOUS TISSUE; VENTRAL ROOT;

ANIMALS; BODY PATTERNING; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; INTESTINES; LARVA; MICRORNAS; RECEPTORS, CYTOPLASMIC AND NUCLEAR; TRANS-ACTIVATORS; TRANSCRIPTION FACTORS;

EID: 14644398601     PISSN: 15345807     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.devcel.2004.12.019     Document Type: Article

References (55)

1. J.E. Abrahante A.L. Daul M. Li M.L. Volk J.M. Tennessen E.A. Miller A.E. Rougvie The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs Dev. Cell 4 2003 625-637
2. M.N. Alder S. Dames J. Gaudet S.E. Mango Gene silencing in Caenorhabditis elegans by transitive RNA interference RNA 9 2003 25-32
3. A. Antebi J.G. Culotti E.M. Hedgecock daf-12 regulates developmental age and the dauer alternative in Caenorhabditis elegans Development 125 1998 1191-1205
4. A. Antebi W.H. Yeh D. Tait E.M. Hedgecock D.L. Riddle daf-12 encodes a nuclear receptor that regulates the dauer diapause and developmental age in C. elegans Genes Dev. 14 2000 1512-1527
5. W. Ao J. Gaudet W.J. Kent S. Muttumu S.E. Mango Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR Science 305 2004 1743-1746
6. D.P. Bartel MicroRNAs: Genomics, biogenesis, mechanism, and function Cell 116 2004 281-297
7. J. Boudeau A.F. Baas M. Deak N.A. Morrice A. Kieloch M. Schutkowski A.R. Prescott H.C. Clevers D.R. Alessi MO25α/β interact with STRADα/β enhancing their ability to bind, activate and localize LKB1 in the cytoplasm EMBO J. 22 2003 5102-5114
8. J. Bracht S. Hunter R. Eachus P. Weeks A.E. Pasquinelli Trans-splicing and polyadenylation of let-7 microRNA primary transcripts RNA 10 2004 1586-1594
9. G.A. Calin C. Sevignani C.D. Dumitru T. Hyslop E. Noch S. Yendamuri M. Shimizu S. Rattan F. Bullrich M. Negrini C.M. Croce Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers Proc. Natl. Acad. Sci. USA 101 2004 2999-3004
10. S. Chang R.J. Johnston Jr. C. Frokjaer-Jensen S. Lockery O. Hobert MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode Nature 430 2004 785-789
11. J.G. Doench P.A. Sharp Specificity of microRNA target selection in translational repression Genes Dev. 18, 2004 504-511
12. A.J. Enright B. John U. Gaul T. Tuschl C. Sander D.S. Marks MicroRNA targets in Drosophila Genome Biol. 5 2003 R1
13. A.G. Fraser R.S. Kamath P. Zipperlen M. Martinez-Campos M. Sohrmann J. Ahringer Functional genomic analysis of C. elegans chromosome I by systematic RNA interference Nature 408 2000 325-330
14. J. Gaudet S.E. Mango Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4 Science 295 2002 821-825
15. D. Gems A.J. Sutton M.L. Sundermeyer P.S. Albert K.V. King M.L. Edgley P.L. Larsen D.L. Riddle Two pleiotropic classes of daf-2 mutation affect larval arrest, adult behavior, reproduction and longevity in Caenorhabditis elegans Genetics 150 1998 129-155
16. I. Ha B. Wightman G. Ruvkun A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation Genes Dev. 10 1996 3041-3050
17. M. Han P.W. Sternberg let-60, a gene that specifies cell fates during C. elegans vulval induction, encodes a ras protein Cell 63 1990 921-931
18. P.J. Heid W.B. Raich R. Smith W.A. Mohler K. Simokat S.B. Gendreau J.H. Rothman J. Hardin The zinc finger protein DIE-1 is required for late events during epithelial cell rearrangement in C. elegans Dev. Biol. 236 2001 165-180
19. M.A. Horner S. Quintin M.E. Domeier J. Kimble M. Labouesse S.E. Mango pha-4, an HNF-3 homolog, specifies pharyngeal organ identity in Caenorhabditis elegans Genes Dev. 12 1998 1947-1952
20. B. John A.J. Enright A. Aravin T. Tuschl C. Sander D.S. Marks Human microRNA targets PLoS Biol. 2 2004 e363
21. S.M. Johnson S.Y. Lin F.J. Slack 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 2003 364-379
22. J.M. Kalb K.K. Lau B. Goszczynski T. Fukushige D. Moons P.G. Okkema J.D. McGhee pha-4 is Ce-fkh-1, a fork head/HNF-3α,β,γ homolog that functions in organogenesis of the C. elegans pharynx Development 125 1998 2171-2180
23. R.S. Kamath A.G. Fraser Y. Dong G. Poulin R. Durbin M. Gotta A. Kanapin N. Le Bot S. Moreno M. Sohrmann et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi Nature 421 2003 231-237
24. M. Kiriakidou P.T. Nelson A. Kouranov P. Fitziev C. Bouyioukos Z. Mourelatos A. Hatzigeorgiou A combined computational-experimental approach predicts human microRNA targets Genes Dev. 18 2004 1165-1178
25. M. Lagos-Quintana R. Rauhut W. Lendeckel T. Tuschl Identification of novel genes coding for small expressed RNAs Science 294 2001 853-858
26. M. Lagos-Quintana R. Rauhut A. Yalcin J. Meyer W. Lendeckel T. Tuschl Identification of tissue-specific microRNAs from mouse Curr. Biol. 12 2002 735-739
27. E.C. Lai Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation Nat. Genet. 30 2002 363-364
28. P.L. Larsen P.S. Albert D.L. Riddle Genes that regulate both development and longevity in Caenorhabditis elegans Genetics 139 1995 1567-1583
29. N.C. Lau L.P. Lim E.G. Weinstein D.P. Bartel An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans Science 294 2001 858-862
30. R.C. Lee V. Ambros An extensive class of small RNAs in Caenorhabditis elegans Science 294 2001 862-864
31. R.C. Lee R.L. Feinbaum V. Ambros The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 Cell 75 1993 843-854
32. B.P. Lewis I.H. Shih M.W. Jones-Rhoades D.P. Bartel C.B. Burge Prediction of mammalian microRNA targets Cell 115 2003 787-798
33. L.P. Lim M.E. Glasner S. Yekta C.B. Burge D.P. Bartel Vertebrate microRNA genes Science 299 2003 1540
34. L.P. Lim N.C. Lau E.G. Weinstein A. Abdelhakim S. Yekta M.W. Rhoades C.B. Burge D.P. Bartel The microRNAs of Caenorhabditis elegans Genes Dev. 17 2003 991-1008
35. S.Y. Lin S.M. Johnson M. Abraham M.C. Vella A. Pasquinelli C. Gamberi E. Gottlieb F.J. Slack The C. elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target Dev. Cell 4 2003 639-650
36. C. Llave K.D. Kasschau M.A. Rector J.C. Carrington Endogenous and silencing-associated small RNAs in plants Plant Cell 14 2002 1605-1619
37. D.G. Morton D.C. Shakes S. Nugent D. Dichoso W. Wang A. Golden K.J. Kemphues The Caenorhabditis elegans par-5 gene encodes a 14-3-3 protein required for cellular asymmetry in the early embryo Dev. Biol. 241 2002 47-58
38. E.G. Moss L. Tang Conservation of the heterochronic regulator Lin-28, its developmental expression and microRNA complementary sites Dev. Biol. 258 2003 432-442
39. E.G. Moss R.C. Lee V. Ambros 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
40. A.E. Pasquinelli B.J. Reinhart F. Slack M.Q. Martindale M.I. Kuroda B. Maller D.C. Hayward E.E. Ball B. Degnan P. Muller Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA Nature 408 2000 86-89
41. W.R. Pearson Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms Genomics 11 1991 635-650
42. B.J. Reinhart F.J. Slack M. Basson A.E. Pasquinelli J.C. Bettinger A.E. Rougvie H.R. Horvitz G. Ruvkun The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans Nature 403 2000 901-906
43. B.J. Reinhart E.G. Weinstein M.W. Rhoades B. Bartel D.P. Bartel MicroRNAs in plants Genes Dev. 16 2002 1616-1626
44. A.E. Rougvie Control of developmental timing in animals Nat. Rev. Genet. 2 2001 690-701
45. J.A. Simon J.W. Tamkun Programming off and on states in chromatin: mechanisms of Polycomb and trithorax group complexes Curr. Opin. Genet. Dev. 12 2002 210-218
46. F.J. Slack M. Basson Z. Liu V. Ambros H.R. Horvitz G. Ruvkun 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
47. T.F. Smith M.S. Waterman Identification of common molecular subsequences J. Mol. Biol. 147 1981 195-197
48. A. Stark J. Brennecke R.B. Russell S.M. Cohen Identification of Drosophila microRNA targets PLoS Biol. 1 2003 E60
49. L.D. Stein Z. Bao D. Blasiar T. Blumenthal M.R. Brent N. Chen A. Chinwalla L. Clarke C. Clee A. Coghlan et al. The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics PLoS Biol. 1 2003 E45
50. J. Takamizawa H. Konishi K. Yanagisawa S. Tomida H. Osada H. Endoh T. Harano Y. Yatabe M. Nagino Y. Nimura et al. Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival Cancer Res. 64 2004 3753-3756
51. L. Timmons A. Fire Specific interference by ingested dsRNA Nature 395 1998 854
52. B. Vandewalle A. Adenis L. Hornez F. Revillion J. Lefebvre 1,25-dihydroxyvitamin D3 receptors in normal and malignant human colorectal tissues Cancer Lett. 86 1994 67-73
53. B. Wightman I. Ha G. Ruvkun Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans Cell 75 1993 855-862
54. A. Yamashita T. Ohnishi I. Kashima Y. Taya S. Ohno Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay Genes Dev. 15 2001 2215-2228
55. K. Yasui I. Imoto Y. Fukuda A. Pimkhaokham Z.Q. Yang T. Naruto Y. Shimada Y. Nakamura J. Inazawa Identification of target genes within an amplicon at 14q12-q13 in esophageal squamous cell carcinoma Genes Chromosomes Cancer 32 2001 112-118