Mapping of Small RNAs in the Human ENCODE Regions

American Journal of Human Genetics

Volumn 82, Issue 4, 2008, Pages 971-981

  Borel, Christelle ^a   Gagnebin, Maryline ^a   Gehrig, Corinne ^a   Kriventseva, Evgenia V ^a   Zdobnov, Evgeny M ^a,b,c   Antonarakis, Stylianos E ^a  

^a UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; MICRORNA; RNA; TRANSCRIPTOME;

5' UNTRANSLATED REGION; ARTICLE; BINDING SITE; CELL FUNCTION; CELL STRAIN HEPG2; GENE FUNCTION; GENE MAPPING; HUMAN; HUMAN CELL; HUMAN GENOME; HYBRIDIZATION; INTRON; PRIORITY JOURNAL; RNA ANALYSIS; RNA TRANSCRIPTION; VALIDATION PROCESS;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; CELL LINE, TUMOR; CHROMOSOME MAPPING; GENOME, HUMAN; HUMANS; MICRORNAS; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSCRIPTION, GENETIC;

EID: 41549129240     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ajhg.2008.02.016     Document Type: Article

References (68)

1. Cheng J., Kapranov P., Drenkow J., Dike S., Brubaker S., Patel S., Long J., Stern D., Tammana H., Helt G., et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308 (2005) 1149-1154
2. Kapranov P., Drenkow J., Cheng J., Long J., Helt G., Dike S., and Gingeras T.R. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res. 15 (2005) 987-997
3. Kapranov P., Cawley S.E., Drenkow J., Bekiranov S., Strausberg R.L., Fodor S.P., and Gingeras T.R. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296 (2002) 916-919
4. Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., et al. The transcriptional landscape of the mammalian genome. Science 309 (2005) 1559-1563
5. Kapranov P., Cheng J., Dike S., Nix D.A., Duttagupta R., Willingham A.T., Stadler P.F., Hertel J., Hackermuller J., Hofacker I.L., et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316 (2007) 1484-1488
6. Moore T., Constancia M., Zubair M., Bailleul B., Feil R., Sasaki H., and Reik W. Multiple imprinted sense and antisense transcripts, differential methylation and tandem repeats in a putative imprinting control region upstream of mouse Igf2. Proc. Natl. Acad. Sci. USA 94 (1997) 12509-12514
7. Caudy A.A., Ketting R.F., Hammond S.M., Denli A.M., Bathoorn A.M., Tops B.B., Silva J.M., Myers M.M., Hannon G.J., and Plasterk R.H. A micrococcal nuclease homologue in RNAi effector complexes. Nature 425 (2003) 411-414
8. Tufarelli C., Stanley J.A., Garrick D., Sharpe J.A., Ayyub H., Wood W.G., and Higgs D.R. Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat. Genet. 34 (2003) 157-165
9. Munroe S.H., and Lazar M.A. Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA. J. Biol. Chem. 266 (1991) 22083-22086
10. Lee J.T., Davidow L.S., and Warshawsky D. Tsix, a gene antisense to Xist at the X-inactivation centre. Nat. Genet. 21 (1999) 400-404
11. Kumar M., and Carmichael G.G. Nuclear antisense RNA induces extensive adenosine modifications and nuclear retention of target transcripts. Proc. Natl. Acad. Sci. USA 94 (1997) 3542-3547
12. Lapidot M., and Pilpel Y. Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms. EMBO Rep. 7 (2006) 1216-1222
13. Prasanth K.V., and Spector D.L. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev. 21 (2007) 11-42
14. Consortium. EP (2004). The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306, 636-40.
15. Consortium E.P., Birney E., Stamatoyannopoulos J.A., Dutta A., Guigo R., Gingeras T.R., Margulies E.H., Weng Z., Snyder M., Dermitzakis E.T., et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 (2007) 799-816
16. Brudno M., Do C.B., Cooper G.M., Kim M.F., Davydov E., Green E.D., Sidow A., and Batzoglou S. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13 (2003) 721-731
17. Washietl S., Hofacker I.L., Lukasser M., Huttenhofer A., and Stadler P.F. Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat. Biotechnol. 23 (2005) 1383-1390
18. Margulies E.H., Blanchette M., Haussler D., and Green E.D. Identification and characterization of multi-species conserved sequences. Genome Res. 13 (2003) 2507-2518
19. Washietl S., Hofacker I.L., and Stadler P.F. Fast and reliable prediction of noncoding RNAs. Proc. Natl. Acad. Sci. USA 102 (2005) 2454-2459
20. Bonnet E., Wuyts J., Rouze P., and Van de Peer Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20 (2004) 2911-2917
21. Berezikov E., Guryev V., van de Belt J., Wienholds E., Plasterk R.H., and Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120 (2005) 21-24
22. Yousef M., Nebozhyn M., Shatkay H., Kanterakis S., Showe L.C., and Showe M.K. Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier. Bioinformatics 22 (2006) 1325-1334
23. Chambon P. A decade of molecular biology of retinoic acid receptors. FASEB J. 10 (1996) 940-954
24. Vu D., Marin P., Walzer C., Cathieni M.M., Bianchi E.N., Saidji F., Leuba G., Bouras C., and Savioz A. Transcription regulator LMO4 interferes with neuritogenesis in human SH-SY5Y neuroblastoma cells. Brain Res. Mol. Brain Res. 115 (2003) 93-103
25. Yin Y., Zhao Y., Wang J., Liu C., Chen S., Chen R., and Zhao H. antiCODE: a natural sense-antisense transcripts database. BMC Bioinformatics 8 (2007) 319
26. Ambros V. microRNAs: tiny regulators with great potential. Cell 107 (2001) 823-826
27. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116 (2004) 281-297
28. Lim L.P., Glasner M.E., Yekta S., Burge C.B., and Bartel D.P. Vertebrate microRNA genes. Science 299 (2003) 1540
29. Michael M.Z., van Holst S.M.O.C., Pellekaan N.G., Young G.P., and James R.J. Reduced accumulation of specific microRNAs in colorectal neoplasia. Mol. Cancer Res. 1 (2003) 882-891
30. Fu H., Tie Y., Xu C., Zhang Z., Zhu J., Shi Y., Jiang H., Sun Z., and Zheng X. Identification of human fetal liver miRNAs by a novel method. FEBS Lett. 579 (2005) 3849-3854
31. Babajko S., and Binoux M. Modulation by retinoic acid of insulin-like growth factor (IGF) and IGF binding protein expression in human SK-N-SH neuroblastoma cells. Eur. J. Endocrinol. 134 (1996) 474-480
32. Matsumoto K., Gaetano C., Daughaday W.H., and Thiele C.J. Retinoic acid regulates insulin-like growth factor II expression in a neuroblastoma cell line. Endocrinology 130 (1992) 3669-3676
33. Ueno T., Suita S., and Zaizen Y. Retinoic acid induces insulin-like growth factor II expression in a neuroblastoma cell line. Cancer Lett. 71 (1993) 177-182
34. Dvir A. Promoter escape by RNA polymerase II. Biochim. Biophys. Acta 1577 (2002) 208-223
35. Wang X., Spangler L., and Dvir A. Promoter escape by RNA polymerase II. Downstream promoter DNA is required during multiple steps of early transcription. J. Biol. Chem. 278 (2003) 10250-10256
36. Carninci P., Sandelin A., Lenhard B., Katayama S., Shimokawa K., Ponjavic J., Semple C.A., Taylor M.S., Engstrom P.G., Frith M.C., et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet. 38 (2006) 626-635
37. Sandelin A., Carninci P., Lenhard B., Ponjavic J., Hayashizaki Y., and Hume D.A. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat. Rev. Genet. 8 (2007) 424-436
38. Kawaji H., Frith M.C., Katayama S., Sandelin A., Kai C., Kawai J., Carninci P., and Hayashizaki Y. Dynamic usage of transcription start sites within core promoters. Genome Biol. 7 (2006) R118
39. Brodsky A.S., Meyer C.A., Swinburne I.A., Hall G., Keenan B.J., Liu X.S., Fox E.A., and Silver P.A. Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biol. 6 (2005) R64
40. Bai L., Santangelo T.J., and Wang M.D. Single-molecule analysis of RNA polymerase transcription. Annu. Rev. Biophys. Biomol. Struct. 35 (2006) 343-360
41. Dye M.J., Gromak N., and Proudfoot N.J. Exon tethering in transcription by RNA polymerase II. Mol. Cell 21 (2006) 849-859
42. Wu Y., Zhang Y., and Zhang J. Distribution of exonic splicing enhancer elements in human genes. Genomics 86 (2005) 329-336
43. Yelin R., Dahary D., Sorek R., Levanon E.Y., Goldstein O., Shoshan A., Diber A., Biton S., Tamir Y., Khosravi R., et al. Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol. 21 (2003) 379-386
44. Chen J., Sun M., Kent W.J., Huang X., Xie H., Wang W., Zhou G., Shi R.Z., and Rowley J.D. Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res. 32 (2004) 4812-4820
45. Sun M., Hurst L.D., Carmichael G.G., and Chen J. Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity. Genome Res. 16 (2006) 922-933
46. Lehner B., Williams G., Campbell R.D., and Sanderson C.M. Antisense transcripts in the human genome. Trends Genet. 18 (2002) 63-65
47. Prescott E.M., and Proudfoot N.J. Transcriptional collision between convergent genes in budding yeast. Proc. Natl. Acad. Sci. USA 99 (2002) 8796-8801
48. Hastings M.L., Milcarek C., Martincic K., Peterson M.L., and Munroe S.H. Expression of the thyroid hormone receptor gene, erbAalpha, in B lymphocytes: alternative mRNA processing is independent of differentiation but correlates with antisense RNA levels. Nucleic Acids Res. 25 (1997) 4296-4300
49. Hastings M.L., Ingle H.A., Lazar M.A., and Munroe S.H. Post-transcriptional regulation of thyroid hormone receptor expression by cis-acting sequences and a naturally occurring antisense RNA. J. Biol. Chem. 275 (2000) 11507-11513
50. Thenie A.C., Gicquel I.M., Hardy S., Ferran H., Fergelot P., Le Gall J.Y., and Mosser J. Identification of an endogenous RNA transcribed from the antisense strand of the HFE gene. Hum. Mol. Genet. 10 (2001) 1859-1866
51. Aravin A.A., Naumova N.M., Tulin A.V., Vagin V.V., Rozovsky Y.M., and Gvozdev V.A. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr. Biol. 11 (2001) 1017-1027
52. Aravin A.A., Klenov M.S., Vagin V.V., Bantignies F., Cavalli G., and Gvozdev V.A. Dissection of a natural RNA silencing process in the Drosophila melanogaster germ line. Mol. Cell. Biol. 24 (2004) 6742-6750
53. Aravin A.A., Lagos-Quintana M., Yalcin A., Zavolan M., Marks D., Snyder B., Gaasterland T., Meyer J., and Tuschl T. The small RNA profile during Drosophila melanogaster development. Dev. Cell 5 (2003) 337-350
54. Vagin V.V., Sigova A., Li C., Seitz H., Gvozdev V., and Zamore P.D. A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313 (2006) 320-324
55. Saito K., Nishida K.M., Mori T., Kawamura Y., Miyoshi K., Nagami T., Siomi H., and Siomi M.C. Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. Genes Dev. 20 (2006) 2214-2222
56. Watanabe T., Takeda A., Tsukiyama T., Mise K., Okuno T., Sasaki H., Minami N., and Imai H. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev. 20 (2006) 1732-1743
57. Aravin A., Gaidatzis D., Pfeffer S., Lagos-Quintana M., Landgraf P., Iovino N., Morris P., Brownstein M.J., Kuramochi-Miyagawa S., Nakano T., et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442 (2006) 203-207
58. Girard A., Sachidanandam R., Hannon G.J., and Carmell M.A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442 (2006) 199-202
59. Grivna S.T., Pyhtila B., and Lin H. MIWI associates with translational machinery and PIWI-interacting RNAs (piRNAs) in regulating spermatogenesis. Proc. Natl. Acad. Sci. USA 103 (2006) 13415-13420
60. Lau N.C., Seto A.G., Kim J., Kuramochi-Miyagawa S., Nakano T., Bartel D.P., and Kingston R.E. Characterization of the piRNA complex from rat testes. Science 313 (2006) 363-367
61. Ambros V., and Chen X. The regulation of genes and genomes by small RNAs. Development 134 (2007) 1635-1641
62. Ambros V. The functions of animal microRNAs. Nature 431 (2004) 350-355
63. Kloosterman W.P., and Plasterk R.H. The diverse functions of microRNAs in animal development and disease. Dev. Cell 11 (2006) 441-450
64. Berezikov E., van Tetering G., Verheul M., van de Belt J., van Laake L., Vos J., Verloop R., van de Wetering M., Guryev V., Takada S., et al. Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res. 16 (2006) 1289-1298
65. Berezikov E., Cuppen E., and Plasterk R.H. Approaches to microRNA discovery. Nat. Genet. 38 Suppl (2006) S2-S7
66. Miranda K.C., Huynh T., Tay Y., Ang Y.S., Tam W.L., Thomson A.M., Lim B., and Rigoutsos I. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126 (2006) 1203-1217
67. Pang K.C., Frith M.C., and Mattick J.S. Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet. 22 (2006) 1-5
68. Siepel A., Bejerano G., Pedersen J.S., Hinrichs A.S., Hou M., Rosenbloom K., Clawson H., Spieth J., Hillier L.W., Richards S., et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15 (2005) 1034-1050