Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

作者: Sarah Djebali , Julien Lagarde , Philipp Kapranov , Vincent Lacroix , Christelle Borel

DOI: 10.1371/JOURNAL.PONE.0028213

关键词:

摘要: The classic organization of a gene structure has followed the Jacob and Monod bacterial model proposed more than 50 years ago. Since then, empirical determinations complexity transcriptomes found in yeast to human blurred definition physical boundaries genes. Using multiple analysis approaches we have characterized individual mapping on chromosomes 21 22. Analyses locations 5' 3' transcriptional termini 492 protein coding genes revealed that for 85% these extend beyond current annotated termini, most often connecting with exons transcripts from other well biological evolutionary importance chimeric is underscored by (1) non-random interconnections involved, (2) greater phylogenetic depth involved many interactions, (3) coordination expression connected (4) close vivo three dimensional proximity genomic regions being transcribed contributing parts RNAs. nature connection suggest should not be studied isolation, but together, as an RNA network.

参考文章(44)
Yongxia Qu, Mohamed Boutjdir, RNase protection assay for quantifying gene expression levels. Methods of Molecular Biology. ,vol. 366, pp. 145- 158 ,(2007) , 10.1007/978-1-59745-030-0_8
Steve Rozen, Helen Skaletsky, Primer3 on the WWW for general users and for biologist programmers. Methods of Molecular Biology. ,vol. 132, pp. 365- 386 ,(2000) , 10.1385/1-59259-192-2:365
D.A. Jackson, A.B. Hassan, R.J. Errington, P.R. Cook, Visualization of focal sites of transcription within human nuclei The EMBO Journal. ,vol. 12, pp. 1059- 1065 ,(1993) , 10.1002/J.1460-2075.1993.TB05747.X
Albertha J.M. Walhout, Gary F. Temple, Michael A. Brasch, James L. Hartley, Monique A. Lorson, Sander van den Heuvel, Marc Vidal, GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods in Enzymology. ,vol. 328, pp. 575- 592 ,(2000) , 10.1016/S0076-6879(00)28419-X
Richard Durbin, Edward Griffiths, Acedb genome database Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. ,(2005) , 10.1002/047001153X.G409305
Fatih Ozsolak, Adam R. Platt, Dan R. Jones, Jeffrey G. Reifenberger, Lauryn E. Sass, Peter McInerney, John F. Thompson, Jayson Bowers, Mirna Jarosz, Patrice M. Milos, Direct RNA sequencing Nature. ,vol. 461, pp. 814- 818 ,(2009) , 10.1038/NATURE08390
K. Kannan, L. Wang, J. Wang, M. M. Ittmann, W. Li, L. Yen, Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing Proceedings of the National Academy of Sciences of the United States of America. ,vol. 108, pp. 9172- 9177 ,(2011) , 10.1073/PNAS.1100489108
Eli Gilboa, Sudha W. Mitra, Stephen Goff, David Baltimore, A Detailed Model of Reverse Transcription and Tests of Crucial Aspects Cell. ,vol. 18, pp. 93- 100 ,(1979) , 10.1016/0092-8674(79)90357-X
L. G. Wilming, J. G. R. Gilbert, K. Howe, S. Trevanion, T. Hubbard, J. L. Harrow, The vertebrate genome annotation (Vega) database Nucleic Acids Research. ,vol. 36, pp. 459- 465 ,(2004) , 10.1093/NAR/GKM987
Thomas R. Gingeras, Implications of chimaeric non-co-linear transcripts Nature. ,vol. 461, pp. 206- 211 ,(2009) , 10.1038/NATURE08452