MicroRNA-encoding long non-coding RNAs

BMC Genomics

Volumn 9, Issue , 2008, Pages

  He, Shunmin ^a,c   Su, Hua ^a,c   Liu, Changning ^b,c   Skogerbø, Geir ^a   He, Housheng ^a   He, Dandan ^a   Zhu, Xiaopeng ^a   Liu, Tao ^a   Zhao, Yi ^b   Chen, Runsheng ^a  

^a INSTITUTE OF BIOPHYSICS   (China)

^b INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; UNTRANSLATED RNA;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE EXPRESSION; GENE FUNCTION; GENE LOCUS; GENETIC ALGORITHM; GENETIC CONSERVATION; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN MOTIF; RAT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; RNA TRANSCRIPTION; SEQUENCE ANALYSIS; ANIMAL; C57BL MOUSE; CHEMISTRY; CHROMOSOME MAP; COMPUTER PROGRAM; CONFORMATION; DNA MICROARRAY; FEMALE; GENETICS; MALE; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; PREGNANCY; RNA SPLICING;

RATTUS;

ANIMALS; BASE SEQUENCE; CHROMOSOME MAPPING; CONSERVED SEQUENCE; DATABASES, NUCLEIC ACID; FEMALE; MALE; MICE; MICE, INBRED C57BL; MICRORNAS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PREGNANCY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA SPLICING; RNA, UNTRANSLATED; SOFTWARE;

EID: 44649141308     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-236     Document Type: Article

References (52)

1. Carninci P Kasukawa T Katayama S Gough J Frith MC Maeda N Oyama R Ravasi T Lenhard B Wells C Kodzius R Shimokawa K Bajic VB Brenner SE Batalov S Forrest AR Zavolan M Davis MJ Wilming LG Aidinis V Allen JE Ambesi-Impiombato A Apweiler R Aturaliya RN Bailey TL Bansal M Baxter L Beisel KW Bersano T Bono H Chalk AM Chiu KP Choudhary V Christoffels A Clutterbuck DR Crowe ML Dalla E Dalrymple BP de Bono B Della Gatta G di Bernardo D Down T Engstrom P Fagiolini M Faulkner G Fletcher CF Fukushima T Furuno M Futaki S Gariboldi M Georgii-Hemming P Gingeras TR Gojobori T Green RE Gustincich S Harbers M Hayashi Y Hensch TK Hirokawa N Hill D Huminiecki L Iacono M Ikeo K Iwama A Ishikawa T Jakt M Kanapin A Katoh M Kawasawa Y Kelso J Kitamura H Kitano H Kollias G Krishnan SP Kruger A Kummerfeld SK Kurochkin IV Lareau LF Lazarevic D Lipovich L Liu J Liuni S McWilliam S Madan Babu M Madera M Marchionni L Matsuda H Matsuzawa S Miki H Mignone F Miyake S Morris K Mottagui-Tabar S Mulder N Nakano N Nakauchi H Ng P Nilsson R Nishiguchi S et al. The transcriptional landscape of the mammalian genome Science 2005, 309(5740):1559-1563 10.1126/science.1112014 16141072
2. Ota T Suzuki Y Nishikawa T Otsuki T Sugiyama T Irie R Wakamatsu A Hayashi K Sato H Nagai K Kimura K Makita H Sekine M Obayashi M Nishi T Shibahara T Tanaka T Ishii S Yamamoto J Saito K Kawai Y Isono Y Nakamura Y Nagahari K Murakami K Yasuda T Iwayanagi T Wagatsuma M Shiratori A Sudo H Hosoiri T Kaku Y Kodaira H Kondo H Sugawara M Takahashi M Kanda K Yokoi T Furuya T Kikkawa E Omura Y Abe K Kamihara K Katsuta N Sato K Tanikawa M Yamazaki M Ninomiya K Ishibashi T Yamashita H Murakawa K Fujimori K Tanai H Kimata M Watanabe M Hiraoka S Chiba Y Ishida S Ono Y Takiguchi S Watanabe S Yosida M Hotuta T Kusano J Kanehori K Takahashi-Fujii A Hara H Tanase TO Nomura Y Togiya S Komai F Hara R Takeuchi K Arita M Imose N Musashino K Yuuki H Oshima A Sasaki N Aotsuka S Yoshikawa Y Matsunawa H Ichihara T Shiohata N Sano S Moriya S Momiyama H Satoh N Takami S Terashima Y Suzuki O Nakagawa S Senoh A Mizoguchi H Goto Y Shimizu F Wakebe H Hishigaki H Watanabe T et al. Complete sequencing and characterization of 21,243 full-length human cDNAs Nat Genet 2004, 36(1):40-45 10.1038/ng1285 14702039
3. Erdmann VA Szymanski M Hochberg A de Groot N Barciszewski J Collection of mRNA-like non-coding RNAs Nucleic Acids Res 1999, 27(1);192-195 148132 9847177 10.1093/nar/27.1.192
4. Bertone P Stolc V Royce TE Rozowsky JS Urban AE Zhu X Rinn JL Tongprasit W Samanta M Weissman S Gerstein M Snyder M Global identification of human transcribed sequences with genome tiling arrays Science 2004, 306(5705):2242-2246 10.1126/science.1103388 15539566
5. Marahrens Y Loring J Jaenisch R Role of the Xist gene in X chromosome choosing Cell 1998, 92(5):657-664 10.1016/S0092-8674(00)81133-2 9506520
6. Young TL Matsuda T Cepko CL The noncoding RNA taurine upregulated gene 1 is required for differentiation of the murine retina Curr Biol 2005, 15(6):501-512 10.1016/j.cub.2005.02.027 15797018
7. Willingham AT Orth AP Batalov S Peters EC Wen BG Aza-Blanc P Hogenesch JB Schultz PG A strategy for probing the function of noncoding RNAs finds a repressor of NFAT Science 2005, 309(5740):1570-1573 10.1126/ science.1115901 16141075
8. Lee Y Ahn C Han J Choi H Kim J Yim J Lee J Provost P Radmark O Kim S Kim VN The nuclear RNase III Drosha initiates microRNA processing Nature 2003, 425(6956):415-419 10.1038/nature01957 14508493
9. Cullen BR Transcription and processing of human microRNA precursors Mol Cell 2004, 16(6):861-865 10.1016/j.molcel.2004.12.002 15610730
10. Bartel DP MicroRNAs: Genomics, biogenesis, mechanism, and function Cell 2004, 116(2):281-297 10.1016/S0092-8674(04)00045-5 14744438
11. Bohnsack MT Czaplinski K Gorlich D Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs Rna 2004, 10(2):185-191 1370530 14730017 10.1261/rna.5167604
12. Yi R Qin Y Macara IG Cullen BR Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs Genes Dev 2003, 17(24):3011-3016 305252 14681208 10.1101/gad.1158803
13. Saito K Ishizuka A Siomi H Siomi MC Processing of pre-microRNAs by the Dicer-1-Loquacious complex in Drosophila cells PLoS Biol 2005, 3(7):e235 1141268 15918769 10.1371/journal.pbio.0030235
14. Lee YS Nakahara K Pham JW Kim K He Z Sontheimer EJ Carthew RW Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways Cell 2004, 117(1):69-81 10.1016/S0092-8674(04)00261-2 15066283
15. Pham JW Pellino JL Lee YS Carthew RW Sontheimer EJ A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila Cell 2004, 117(1):83-94 10.1016/S0092-8674(04)00258-2 15066284
16. Lee Y Kim M Han J Yeom KH Lee S Baek SH Kim VN MicroRNA genes are transcribed by RNA polymerase II Embo J 2004, 23(20):4051-4060 524334 15372072 10.1038/sj.emboj.7600385
17. Rodriguez A Griffiths-Jones S Ashurst JL Bradley A Identification of mammalian microRNA host genes and transcription units Genome Res 2004, 14(10A):1902-1910 524413 15364901 10.1101/gr.2722704
18. Kapranov P Cheng J Dike S Nix DA Duttagupta R Willingham AT Stadler PF Hertel J Hackermueller J Hofacker IL Bell I Cheung E Drenkow J Dumais E Patel S Helt G Ganesh M Ghosh S Piccolboni A Sementchenko V Tammana H Gingeras TR RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription Science 2007 17510325
19. Griffiths-Jones S Grocock RJ van Dongen S Bateman A Enright AJ miRBase: microRNA sequences, targets and gene nomenclature Nucleic Acids Res 2006:34 Database issue D140-4 1347474 16381832 10.1093/nar/gkj112
20. Lee Y Jeon K Lee JT Kim S Kim VN MicroRNA maturation: Stepwise processing and subcellular localization Embo J 2002, 21(17):4663-4670 126204 12198168 10.1093/emboj/cdf476
21. Sewer A Paul N Landgraf P Aravin A Pfeffer S Brownstein MJ Tuschl T van Nimwegen E Zavolan M Identification of clustered microRNAs using an ab initio prediction method BMC Bioinformatics 2005, 6:267 1315341 16274478 10.1186/1471-2105-6-267
22. Xue C Li F He T Liu GP Li Y Zhang X Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine BMC Bioinformatics 2005, 6:310 1360673 16381612 10.1186/ 1471-2105-6-310
23. Jiang P Wu H Wang W Ma W Sun X Lu Z MiPred: Classification of real and pseudo microRNA precursors using random forest prediction model with combined features Nucleic Acids Res 2007 35 Web Server issue W339-44 1933124 17553836 10.1093/nar/gkm368
24. LUO Ming-Yong TIAN Zhi-Gang WANG Ying-Xiong XU Zhi ZHANG Liang CHENG Jing Construction and application of a microarray for profiling microRNA expression Progress in Biochemistry and Biophysics 2007, 34(1):1-11
25. Chen C Ridzon DA Broomer AJ Zhou Z Lee DH Nguyen JT Barbisin M Xu NL Mahuvakar VR Andersen MR Lao KQ Livak KJ Guegler KJ Real-time quantification of microRNAs by stem-loop RT-PCR Nucleic Acids Res 2005, 33(20):e179 1292995 16314309 10.1093/nar/gni178
26. Bono H Yagi K Kasukawa T Nikaido I Tominaga N Miki R Mizuno Y Tomaru Y Goto H Nitanda H Shimizu D Makino H Morita T Fujiyama J Sakai T Shimoji T Hume DA Hayashizaki Y Okazaki Y Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays Genome Res 2003, 13(6B):1318-1323 403653 12819129 10.1101/gr.1075103
27. Siepel A Bejerano G Pedersen JS Hinrichs AS Hou M Rosenbloom K Clawson H Spieth J Hillier LW Richards S Weinstock GM Wilson RK Gibbs RA Kent WJ Miller W Haussler D Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes Genome Res 2005, 15(8):1034-1050 1182216 16024819 10.1101/gr.3715005
28. Numata K Kanai A Saito R Kondo S Adachi J Wilming LG Hume DA Hayashizaki Y Tomita M Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection Genome Res 2003, 13(6B):1301-1306 403720 12819127 10.1101/gr.1011603
29. Hirsch J Lefort V Vankersschaver M Boualem A Lucas A Thermes C d'Aubenton-Carafa Y Crespi M Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts Plant Physiol 2006, 140(4):1192-1204 1435803 16500993 10.1104/ pp.105.073817
30. Bartolomei MS Zemel S Tilghman SM Parental imprinting of the mouse H19 gene Nature 1991, 351(6322):153-155 10.1038/351153a0 1709450
31. Obernosterer G Leuschner PJF Alenius M Marinez J Post-transcriptional regulation of microRNA expression RNA 2006, 12:1161-1167 1484437 16738409 10.1261/rna.2322506
32. Bracht J Hunter S Eachus R Weeks P Pasquinelli AE Trans-splicing and polyadenylation of let-7 microRNA primary transcripts Rna 2004, 10(10):1586-1594 1370645 15337850 10.1261/rna.7122604
33. Thomson JM Parker J Perou CM Hammond SM A custom microarray platform for analysis of microRNA gene expression Nat Methods 2004, 1(1):47-53 10.1038/nmeth704 15782152
34. Wulczyn FG Smirnova L Rybak A Brandt C Kwidzinski E Ninnemann O Strehle M Seiler A Schumacher S Nitsch R Post-transcriptional regulation of the let-7 microRNA during neural cell specification FASEB J 2007, 21(2):415-426 10.1096/fj.06-6130com 17167072
35. Costa FF Non-coding RNAs: Lost in translation? Gene 2006 17113247
36. Willingham AT Gingeras TR TUF love for "junk" DNA Cell 2006, 125(7):1215-1220 10.1016/j.cell.2006.06.009 16814704
37. Huttenhofer A Schattner P Polacek N Non-coding RNAs: Hope or hype? Trends Genet 2005, 21(5):289-297 10.1016/j.tig.2005.03.007 15851066
38. FAMTOM3 database http://fantom3.gsc.riken.jp/
39. miRBase database http://microrna.sanger.ac.uk/
40. UCSC http://genome.ucsc.edu/
41. READ database http://read.gsc.riken.go.jp/
42. PhastCons http://hgdownload.cse.ucsc.edu/goldenPath/mm7/phastCons17Scores
43. WebLogo http://weblogo.berkeley.edu/
44. I.L. Hofacker WF P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster Fast Folding and Comparison of RNA Secondary Structures. Monatshefte f Chemie 1994, 125:167-188 10.1007/BF00818163
45. M. Zuker PS Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information Nucl Acid Res 1981, 9:133-148 10.1093/nar/9.1.133
46. Lim LP Lau NC Weinstein EG Abdelhakim A Yekta S Rhoades MW Burge CB Bartel DP The microRNAs of Caenorhabditis elegans Genes Dev 2003, 17(8):991-1008 196042 12672692 10.1101/gad.1074403
47. Zeng Y Cullen BR Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences J Biol Chem 2005, 280(30);27595-27603 10.1074/jbc.M504714200 15932881
48. Bailey TL Elkan C The value of prior knowledge in discovering motifs with MEME Proc Int Conf Intell Syst Mol Biol 1995, 3:21-29 7584439
49. NCBI http://www.ncbi.nlm.nih.gov/
50. Watanabe T Takeda A Mise K Okuno T Suzuki T Minami N Imai H Stage-specific expression of microRNAs during Xenopus development FEBS Lett 2005, 579(2):318-324 10.1016/j.febslet.2004.11.067 15642338
51. eBioMed http://www.ebiomed.org/pub/mencrna.htm
52. Crooks GE Hon G Chandonia JM Brenner SE WebLogo: A sequence logo generator Genome Res 2004, 14(6):1188-1190 419797 15173120 10.1101/ gr.849004