Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq

RNA

Volumn 16, Issue 8, 2010, Pages 1610-1622

  Xu, Guorong ^a   Fewell, Claire ^b   Taylor, Christopher ^a,c   Deng, Nan ^a   Hedges, Dale ^d   Wang, Xia ^b   Zhang, Kun ^e   Lacey, Michelle ^b   Zhang, Haitao ^b   Yin, Qinyan ^b   Cameron, Jennifer ^b   Lin, Zhen ^b   Zhu, Dongxiao ^a,c   Flemington, Erik K ^b  

^a USA   (United States)

^b TULANE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c CHILDREN S HOSPITAL   (United States)

^d UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^e UNIVERSITY OF NEW ORLEANS   (United States)

Author keywords

Illumina; MicroRNA; MIR155; Next generation sequencing; RNA seq

Indexed keywords

MICRORNA; MICRORNA 155; TRANSCRIPTOME; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; PRIORITY JOURNAL; RNA SEQUENCE; RNA TRANSCRIPTION;

BASE SEQUENCE; CELLS; GENE EXPRESSION PROFILING; HUMANS; MICRORNAS; RESEARCH; RNA;

EID: 77955102632     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2194910     Document Type: Article

References (40)

1. Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noch E, Yendamuri S, Shimizu M, Rattan S, Bullrich F, Negrini M, et al. 2004. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci 101: 2999-3004.
2. Cameron JE, Yin Q, Fewell C, Lacey M, McBride J, Wang X, Lin Z, Schaefer BC, Flemington EK. 2008. Epstein-Barr virus latent membrane protein 1 induces cellular MicroRNA miR-146a, a modulator of lymphocyte signaling pathways. J Virol 82: 1946-1958. (Pubitemid 351206940)
3. Chi SW, Zang JB, Mele A, Darnell RB. 2009. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460: 479-486.
4. Clurman BE, Hayward WS. 1989. Multiple proto-oncogene activations in avian leukosis virus-induced lymphomas: Evidence for stage-specific events. Mol Cell Biol 9: 2657-2664.
5. Costinean S, Zanesi N, Pekarsky Y, Tili E, Volinia S, Heerema N, Croce CM. 2006. Pre-B cell proliferation and lymphoblastic leukemia/high-grade lymphoma in Eμ-miR155 transgenic mice. Proc Natl Acad Sci 103: 7024-7029.
6. Dabney AR, Storey JD. 2007. Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships. Genome Biol 8: R44. doi: 10.1186/gb-2007-8-3-r44.
7. Eis PS, Tam W, Sun L, Chadburn A, Li Z, Gomez MF, Lund E, Dahlberg JE. 2005. Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proc Natl Acad Sci 102: 3627-3632.
8. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al. 2004. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol 5: R80. doi: 10.1186/gb-2004-5-10-r80.
9. Gottwein E, Mukherjee N, Sachse C, Frenzel C, Majoros WH, Chi JT, Braich R, Manoharan M, Soutschek J, Ohler U, et al. 2007. A viral microRNA functions as an orthologue of cellular miR-155. Nature 450: 1096-1099.
10. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. 2007. MicroRNA targeting specificity in mammals: Determinants beyond seed pairing. Mol Cell 27: 91-105. (Pubitemid 46991392)
11. Hammell M. 2010. Computational methods to identify miRNA targets. Semin Cell Dev Biol doi: 10.1016/j.semcdb.2010.01.004.
12. Iorio MV, Ferracin M, Liu CG, Veronese A, Spizzo R, Sabbioni S, Magri E, Pedriali M, Fabbri M, Campiglio M, et al. 2005. MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65: 7065-7070.
13. Jiang H, Wong WH. 2008. SeqMap: Mapping massive amount of oligonucleotides to the genome. Bioinformatics 24: 2395-2396.
14. Jiang J, Lee EJ, Schmittgen TD. 2006. Increased expression of micro-RNA-155 in Epstein-Barr virus transformed lymphoblastoid cell lines. Genes Chromosomes Cancer 45: 103-106. (Pubitemid 46930866)
15. Kluiver J, Poppema S, de Jong D, Blokzijl T, Harms G, Jacobs S, Kroesen BJ, van den Berg A. 2005. BIC and miR-155 are highly expressed in Hodgkin, primary mediastinal and diffuse large B cell lymphomas. J Pathol 207: 243-249. (Pubitemid 41404155)
16. Kluiver J, Haralambieva E, de Jong D, Blokzijl T, Jacobs S, Kroesen BJ, Poppema S, van den Berg A. 2006. Lack of BIC and microRNA miR-155 expression in primary cases of Burkitt lymphoma. Genes Chromosomes Cancer 45: 147-153. (Pubitemid 43191021)
17. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
18. Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. 2010a. RNA-seq gene expression estimation with read mapping uncertainty. Bioinformatics 26: 493-500.
19. Li L, Xu J, Yang D, Tan X, Wang H. 2010b. Computational approaches for microRNA studies: A review. Mamm Genome 21: 1-12.
20. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, et al. 2005. MicroRNA expression profiles classify human cancers. Nature 435: 834-838.
21. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. 2008. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509-1517.
22. Mayr C, Bartel DP. 2009. Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138: 673-684.
23. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods 5: 621-628. (Pubitemid 351911867)
24. O'Connell RM, Taganov KD, Boldin MP, Cheng G, Baltimore D. 2007. MicroRNA-155 is induced during the macrophage inflammatory response. Proc Natl Acad Sci 104: 1604-1609.
25. O'Connell RM, Rao DS, Chaudhuri AA, Boldin MP, Taganov KD, Nicoll J, Paquette RL, Baltimore D. 2008. Sustained expression of microRNA-155 in hematopoietic stem cells causes a myeloproliferative disorder. J Exp Med 205: 585-594. (Pubitemid 351439306)
26. The R Development Core Team. 2008. R: A language and environment for statistical computing. R Foundation for Statistical Computing. http://cran.r-project.org/doc/manuals/refman.pdf.
27. Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, et al. 2010.The UCSC Genome Browser database: Update. Nucleic Acids Res 38:D613-619.
28. Rodriguez A, Vigorito E, Clare S, Warren MV, Couttet P, Soond DR, van Dongen S, Grocock RJ, Das PP, Miska EA, et al. 2007. Requirement of bic/microRNA-155 for normal immune function. Science 316: 608-611.
29. Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB. 2008. Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science 320: 1643-1647. (Pubitemid 351931255)
30. Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. 2008. Widespread changes in protein synthesis induced by microRNAs. Nature 455: 58-63.
31. Skalsky RL, Samols MA, Plaisance KB, Boss IW, Riva A, Lopez MC, Baker HV, Renne R. 2007. Kaposi's sarcoma-associated herpesvirus encodes an ortholog of miR-155. J Virol 81: 12836-12845. (Pubitemid 350156921)
32. Smyth GK. 2005. Limma: Linear models for microarray data. In Bioinformatics and computational biology solutions using R and Bioconductor (ed. R Gentleman et al.), pp 397-420. Springer, New York.
33. Storey JD, Tibshirani R. 2003. Statistical significance for genomewide studies. Proc Natl Acad Sci 100: 9440-9445.
34. Tam W, Ben-Yehuda D, Hayward WS. 1997. bic, a novel gene activated by proviral insertions in avian leukosis virus-induced lymphomas, is likely to function through its noncoding RNA. Mol Cell Biol 17: 1490-1502. (Pubitemid 27097379)
35. Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: Discovering splice junctions with RNA-seq. Bioinformatics 25: 1105-1111.
36. Tusher VG, Tibshirani R, Chu G. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci 98: 5116-5121.
37. Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, Petrocca F, Visone R, Iorio M, Roldo C, Ferracin M, et al. 2006. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci 103: 2257-2261.
38. Yin Q, McBride J, Fewell C, Lacey M, Wang X, Lin Z, Cameron J, Flemington EK. 2008. MicroRNA-155 is an Epstein-Barr virus-induced gene that modulates Epstein-Barr virus-regulated gene expression pathways. J Virol 82: 5295-5306.
39. Yin Q, Wang X, Fewell C, Cameron J, Zhu H, Baddoo M, Lin Z, Flemington EK. 2010. MiR-155 inhibits bone morphogenetic protein (BMP) signaling and BMP mediated Epstein-Barr virus reactivation. J Virol 84: 6318-6327.
40. Zhang L, Huang J, Yang N, Greshock J, Megraw MS, Giannakakis A, Liang S, Naylor TL, Barchetti A, Ward MR, et al. 2006. microRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci 103: 9136-9141.