New human and mouse microRNA genes found by homology search

FEBS Journal

Volumn 272, Issue 1, 2005, Pages 59-73

  Weber, Michel J ^a  

^a Université Paul Sabatier   (France)

Author keywords

Antisense transcript; Genomic localization; Human genome; MicroRNA; Mouse genome; mRNA degradation; RNA interference

Indexed keywords

COMPLEMENTARY RNA; GLYCERIC ACID; MESSENGER RNA; PHOSPHOTRANSFERASE; RNA;

ARTICLE; ENZYME STABILITY; GENE; GENE LOCATION; GENETIC CONSERVATION; INTRON; PRIORITY JOURNAL; RNA DEGRADATION; RNA INTERFERENCE; SEQUENCE HOMOLOGY;

ANIMALS; BASE SEQUENCE; HUMANS; INTRONS; MICE; MICRORNAS; MOLECULAR SEQUENCE DATA; RATS; SEQUENCE HOMOLOGY, NUCLEIC ACID; TRANSCRIPTION, GENETIC;

EID: 11444251652     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1432-1033.2004.04389.x     Document Type: Article

References (57)

1. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S & Kim VN (2003) The nuclear RNase III Drosha initiates micro RNA processing. Nature 425, 415-419.
2. Park W, Li J, Song R, Messing J & Chen X (2002) CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol 12, 1484-1495.
3. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B & Bartel DP (2002) MicroRNAs in plants. Genes Dev 16, 1616-1626.
4. Lund E, Guttinger S, Calado A, Dahlberg JE & Kutay U (2004) Nuclear export of microRNA precursors. Science 303, 95-98.
5. Bohnsack MT, Czaplinski K & Gorlich D (2004) Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 10, 185-191.
6. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.
7. Carrington JC & Ambros V (2003) Role of microRNAs in plant and animal development. Science 301, 336-338.
8. Lai EC (2003) microRNAs: runts of the genome assert themselves. Curr Biol 13, R925-R936.
9. Lee RC, Feinbaum RL & Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854.
10. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR & Ruvkun G (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901-906.
11. Lai EC, Tomancak P, Williams RW & Rubin GM (2003) Computational identification of Drosophila microRNA genes. Genome Biol 4, R42.
12. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB & Bartel DP (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17, 991-1008.
13. Lim LP, Glasner ME, Yekta S, Burge CB & Bartel DP (2003) Vertebrate microRNA genes. Science 299, 1540.
14. Lagos-Quintana M, Rauhut R, Lendeckel W & Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294, 853-858.
15. Griffiths-Jones S, Bateman A, Marshall M, Khanna A & Eddy SR (2003) Rfam: an RNA family database. Nucleic Acids Res 31, 439-441.
16. Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM & Ruvkun G (2004) Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci USA 101, 360-365.
17. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, et al. (2003) The UCSC Genome Browser Database, Nucleic Acids Res 31, 51-54.
18. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M et al. (2003) A uniform system for micro-RNA annotation. RNA 9, 277-279.
19. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W & Tuschl T (2002) Identification of tissue-specific microRNAs from mouse. Curr Biol 12, 735-739.
20. Schwarz DS, Du Hutvagner GT, Xu Z, Aronin N & Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199-208.
21. Doench JG & Sharp PA (2004) Specificity of micro-RNA target selection in translational repression. Genes Dev 18, 504-511.
22. Bejanin S, Cervini R, Mallet J & Berrard S (1994) A unique gene organization for two cholinergic markers, choline acetyltransferase and a putative vesicular transporter of acetylcholine. J Biol Chem 269, 21944-21947.
23. Conrad C, Vianna C, Freeman M & Davies P (2002) A polymorphic gene nested within an intron of the tau gene: implications for Alzheimer's disease. Proc Natl Acad Sci USA 99, 7751-7756.
24. Gauwerky CE, Huebner K, Isobe M, Nowell PC & Croce CM (1989) Activation of MYC in a masked t (8; 17) translocation results in an aggressive B-cell leukemia. Proc Natl Acad Sci USA 86, 8867-8871.
25. Bardwell JC, Regnier P, Chen SM, Nakamura Y, Grunberg-Manago M & Court DL (1989) Autoregulation of RNase III operon by mRNA processing. EMBO J 8, 3401-3407.
26. Regnier P & Grunberg-Manago M (1989) Cleavage by RNase III in the transcripts of the met Y-nus-A-infB operon of Escherichia coli releases the tRNA and initiates the decay of the downstream mRNA. J Mol Biol 210, 293-302.
27. Seitz H, Youngson N, Lin SP, Dalbert S, Paulsen M, Bachellerie JP, Ferguson-Smith AC & Cavaille J (2003) Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene. Nat Genet 34, 261-262.
28. Yekta S, Shih IH & Bartel DP (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science 304, 594-596.
29. Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M & Dreyfuss G (2002) miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 16, 720-728.
30. Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A & Tuschl T (2003) New microRNAs from mouse and human. RNA 9, 175-179.
31. Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noch E, Yendamuri S, Shimizu M, Rattan S, Bullrich F, Negrini M & Croce CM (2004) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci USA 101, 2999-3004.
32. Lee Y, Jeon K, Lee JT, Kim S & Kim VN (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 21, 4663-4670.
33. Cavaille J, Vitali P, Basyuk E, Huttenhofer A & Bachellerie JP (2001) A novel brain-specific box C/D small nucleolar RNA processed from tandemly repeated introns of a noncoding RNA gene in rats. J Biol Chem 276, 26374-26383.
34. Cavaille J, Seitz H, Paulsen M, Ferguson-Smith AC & Bachellerie JP (2002) Identification of tandemly-repeated C/D snoRNA genes at the imprinted human 14q32 domain reminiscent of those at the Prader-Willi/Angelman syndrome region. Hum Mol Genet 11, 1527-1538.
35. Tycowski KT, Shu MD & Steitz JA (1996) A mammalian gene with introns instead of exons generating stable RNA products. Nature 379, 464-466.
36. Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B, Gaasterland T, Meyer J & Tuschl T (2003) The small RNA profile during Drosophila melanogaster development. Dev Cell 5, 337-350.
37. Sempere LF, Sokol NS, Dubrovsky EB, Berger EM & Ambros V (2003) Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broad-complex gene activity. Dev Biol 259, 9-18.
38. Bashirullah A, Pasquinelli AE, Kiger AA, Perrimon N, Ruvkun G & Thummel CS (2003) Coordinate regulation of small temporal RNAs at the onset of Drosophila metamorphosis. Dev Biol 259, 1-8.
39. Lin SP, Youngson N, Takada S, Seitz H, Reik W, Paulsen M, Cavaille J & Ferguson-Smith AC (2003) Asymmetric regulation of imprinting on the maternal and paternal chromosomes at the Dlk1-Gt12 imprinted cluster on mouse chromosome 12. Nat Genet 35, 97-102.
40. Chen CZ, Li L, Lodish HF & Bartel DP (2004) Micro-RNAs modulate hematopoietic lineage differentiation. Science 303, 83-86.
41. Houbaviy HB, Murray MF & Sharp PA (2003) Embryonic stem cell-specific MicroRNAs. Dev Cell 5, 351-358.
42. Kiss T (2002) Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109, 145-148.
43. Bachellerie JP, Cavaille J & Huttenhofer A (2002) The expanding snoRNA world. Biochimie 84, 775-790.
44. Weinstein LB & Steitz JA (1999) Guided tours: from precursor snoRNA to functional snoRNP. Curr Opin Cell Biol 11, 378-384.
45. Caffarelli E, Arese M, Santoro B, Fragapane P & Bozzoni I (1994) In vitro study of processing of the intron-encoded U16 small nucleolar RNA in Xenopus laevis. Mol Cell Biol 14, 2966-2974.
46. Caffarelli E, Fatica A, Prislei S, De Gregorio E, Fragapane P & Bozzoni I (1996) Processing of the intron-encoded U16 and U18 snoRNAs: the conserved C and D boxes control both the processing reaction and the stability of the mature snoRNA. EMBO J 15, 1121-1131.
47. Fragapane P, Prislei S, Michienzi A, Caffarelli E & Bozzoni I (1993) A novel small nucleolar RNA (U16) is encoded inside a ribosomal protein intron and originates by processing of the pre-mRNA. EMBO J 12, 2921-2928.
48. Villa T, Ceradini F, Presutti C & Bozzoni I (1998) Processing of the intron-encoded U18 small nucleolar RNA in the yeast Saccharomyces cerevisiae relies on both exo- and endonucleolytic activities. Mol Cell Bio. 18, 3376-3383.
49. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP & Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115, 787-798.
50. Stark A, Brennecke J, Russell RB & Cohen SM (2003) Identification of Drosophila MicroRNA Targets. Plos Biol 1, E60.
51. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z & Hatzigeorgiou A (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18, 1165-1178.
52. Rodriguez A, Griffiths-Jones S, Ashurst JL & Bradley A (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res 14, 1902-1910.
53. Seitz H, Royo H, Bortolin ML, Lin SP, Ferguson-Smith AC & Cavaille V (2004) A large imprinted microRNA gene cluster at the mouse Dlk1-Gt12 domain. Genome Res 14, 1741-1748.
54. Kent WJ (2002) BLAT - the BLAST-like alignment tool. Genome Res 12, 656-664.
55. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406-3415.
56. Corpet F (1988) Multiple sequence alignment with hier-archical clustering. Nucleic Acids Res 16, 10881-10890.
57. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM & Haussler D (2002) The human genome browser at UCSC. Genome Res 12, 996-1006.