Evidence for transcript networks composed of chimeric rnas in human cells

PLoS ONE

Volumn 7, Issue 1, 2012, Pages

  Djebali, Sarah ^a   Lagarde, Julien ^a   Kapranov, Philipp ^b,m   Lacroix, Vincent ^a,n   Borel, Christelle ^c   Mudge, Jonathan M ^d   Howald, Cédric ^e   Foissac, Sylvain ^a,b,o   Ucla, Catherine ^c   Chrast, Jacqueline ^e   Ribeca, Paolo ^a   Martin, David ^a   Murray, Ryan R ^f   Yang, Xinping ^f   Ghamsari, Lila ^f   Lin, Chenwei ^f   Bell, Ian ^b   Dumais, Erica ^b   Drenkow, Jorg ^g   Tress, Michael L ^h   Gelpí, Josep Lluís ⁱ   Orozco, Modesto ⁱ   Valencia, Alfonso ^h   van Berkum, Nynke L ^j   Lajoie, Bryan R ^j   Vidal, Marc ^f   Stamatoyannopoulos, John ^k   Batut, Philippe ^g   Dobin, Alex ^g   Harrow, Jennifer ^d   Hubbard, Tim ^d   Dekker, Job ^j   Frankish, Adam ^d   Salehi Ashtiani, Kourosh ^f,l   Reymond, Alexandre ^e   Antonarakis, Stylianos E ^c   Guigó, Roderic ^a   Gingeras, Thomas R ^b,g   more..

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b Thermo Fisher Scientific   (United States)

^c UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^e UNIVERSITY OF LAUSANNE   (Switzerland)

^f DANA FARBER CANCER INSTITUTE   (United States)

^g Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^h Centro Nacional de Investigaciones Oncológicas   (Spain)

ⁱ UNIVERSITY OF BARCELONA   (Spain)

^j UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^k UNIVERSITY OF WASHINGTON   (United States)

^l NEW YORK UNIVERSITY ABU DHABI   (United Arab Emirates)

^m Helicos BioSciences Corporation   (United States)

ⁿ UNIVERSITÉ LYON 1   (France)

^o Integromics   (Spain)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CHIMERIC RNA; RNA; UNCLASSIFIED DRUG; CHIMERIN; RNA ISOFORM; TRANSCRIPTOME;

AMINO ACID SEQUENCE; ARTICLE; CHROMOSOME 21; CHROMOSOME 22; CONTROLLED STUDY; EXON; GENE EXPRESSION REGULATION; GENE INTERACTION; GENE REGULATORY NETWORK; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; HUMAN TISSUE; MOLECULAR CLONING; MOLECULAR GENETICS; MOLECULAR PHYLOGENY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; TRANSCRIPTOMICS; ALGORITHM; BIOLOGICAL MODEL; CELLS; CHEMISTRY; CHROMOSOME 1; FEMALE; GENE EXPRESSION PROFILING; GENETICS; MALE; METABOLISM; METHODOLOGY; MICROARRAY ANALYSIS; NUCLEIC ACID AMPLIFICATION; PHYSIOLOGY; VALIDATION STUDY;

BACTERIA (MICROORGANISMS);

ALGORITHMS; CELLS; CHIMERIN PROTEINS; CHROMOSOMES, HUMAN, PAIR 1; FEMALE; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; MALE; MICROARRAY ANALYSIS; MODELS, BIOLOGICAL; NUCLEIC ACID AMPLIFICATION TECHNIQUES; RNA; RNA ISOFORMS; TRANSCRIPTION, GENETIC; TRANSCRIPTOME; VALIDATION STUDIES AS TOPIC;

EID: 84855396196     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028213     Document Type: Article

References (45)

1. Kaessmann H, (2010) Origins, evolution, and phenotypic impact of new genes. Genome Res 20: 1313-1326.
2. Wu X, Xiao H, (2009) Progress in the detection of human genome structural variations. Sci China C Life Sci 52: 560-567.
3. Li H, Wang J, Mor G, Sklar J, (2008) A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells. Science 321: 1357-1361.
4. Gingeras TR, (2009) Implications of chimaeric non-co-linear transcripts. Nature 461: 206-211.
5. Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, et al. (2007) Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res 17: 746-759.
6. Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, et al. (2008) Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods 5: 629-635.
7. Kapranov P, Drenkow J, Cheng J, Long J, Helt G, et al. (2005) Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res 15: 987-997.
8. Li X, Zhao L, Jiang H, Wang W, (2009) Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes. J Mol Evol 68: 56-65.
9. Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, et al. (2009) Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A 106: 12353-12358.
10. Parra G, Reymond A, Dabbouseh N, Dermitzakis ET, Castelo R, et al. (2006) Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res 16: 37-44.
11. Unneberg P, Claverie JM, (2007) Tentative mapping of transcription-induced interchromosomal interaction using chimeric EST and mRNA data. PLoS One 2: e254.
12. Houseley J, Tollervey D, (2010) Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro. PLoS One 5: e12271.
13. Bowman RR, Hu WS, Pathak VK, (1998) Relative rates of retroviral reverse transcriptase template switching during RNA- and DNA-dependent DNA synthesis. J Virol 72: 5198-5206.
14. Gilboa E, Mitra SW, Goff S, Baltimore D, (1979) A detailed model of reverse transcription and tests of crucial aspects. Cell 18: 93-100.
15. Temin HM, (1993) Retrovirus variation and reverse transcription: abnormal strand transfers result in retrovirus genetic variation. Proc Natl Acad Sci U S A 90: 6900-6903.
16. McManus CJ, Duff MO, Eipper-Mains J, Graveley BR, (2010) Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci U S A 107: 12975-12979.
17. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
18. Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, et al. (2006) GENCODE: producing a reference annotation for ENCODE. Genome Biol 7 (Suppl 1): 1-9 S4.
19. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639-1645.
20. Fullwood MJ, Wei CL, Liu ET, Ruan Y, (2009) Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res 19: 521-532.
21. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, et al. (2008) A large genome center's improvements to the Illumina sequencing system. Nat Methods 5: 1005-1010.
22. Cocquet J, Chong A, Zhang G, Veitia RA, (2006) Reverse transcriptase template switching and false alternative transcripts. Genomics 88: 127-131.
23. Qu Y, Boutjdir M, (2007) RNase protection assay for quantifying gene expression levels. Methods Mol Biol 366: 145-158.
24. Thorvaldsen JL, Bartolomei MS, (2001) Ribonuclease protection. Methods Mol Biol 181: 133-144.
25. Khanin R, Wit E, (2006) How scale-free are biological networks. J Comput Biol 13: 810-818.
26. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, et al. (2006) Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16: 1299-1309.
27. Ozsolak F, Platt AR, Jones DR, Reifenberger JG, Sass LE, et al. (2009) Direct RNA sequencing. Nature 461: 814-818.
28. Jackson DA, Hassan AB, Errington RJ, Cook PR, (1993) Visualization of focal sites of transcription within human nuclei. EMBO J 12: 1059-1065.
29. Pombo A, Cook PR, (1996) The localization of sites containing nascent RNA and splicing factors. Exp Cell Res 229: 201-203.
30. Akiva P, Toporik A, Edelheit S, Peretz Y, Diber A, et al. (2006) Transcription-mediated gene fusion in the human genome. Genome Res 16: 30-36.
31. Kannan K, Wang L, Wang J, Ittmann MM, Li W, et al. (2011) Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing. Proc Natl Acad Sci U S A 108: 9172-9177.
32. Roy SW, Irimia M, (2008) When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis. Bioessays 30: 601-605.
33. Collins JE, Goward ME, Cole CG, Smink LJ, Huckle EJ, et al. (2003) Reevaluating human gene annotation: a second-generation analysis of chromosome 22. Genome Res 13: 27-36.
34. Kent WJ, (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
35. Rozen S, Skaletsky H, (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
36. Salehi-Ashtiani K, Yang X, Derti A, Tian W, Hao T, et al. (2008) Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing. Nat Methods 5: 597-600.
37. Walhout AJ, Temple GF, Brasch MA, Hartley JL, Lorson MA, et al. (2000) GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol 328: 575-592.
38. Gordon D, Abajian C, Green P, (1998) Consed: a graphical tool for sequence finishing. Genome Res 8: 195-202.
39. Searle SM, Gilbert J, Iyer V, Clamp M, (2004) The otter annotation system. Genome Res 14: 963-970.
40. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
41. Sonnhammer EL, Wootton JC, (2001) Integrated graphical analysis of protein sequence features predicted from sequence composition. Proteins 45: 262-273.
42. Durbin R, Griffiths E, (2005) Acedb genome database. In: Interscience W, editors. Online Encyclopedia of genetics, genomics, proteomics and bioinformatics.
43. Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T, et al. (2008) The vertebrate genome annotation (Vega) database. Nucleic Acids Res 36: D753-760.
44. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, et al. (2011) STAR: mapping non-contiguous RNA-seq data. Submitted.
45. Krzywinski MI, Schein JE, Birol I, Connors J, Gascoyne R, et al. (2009) Circos: An information aesthetic for comparative genomics. Genome Res.