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Evidence for transcript networks composed of chimeric RNAs in human cells.

TitleEvidence for transcript networks composed of chimeric RNAs in human cells.
Publication TypeJournal Article
Year of Publication2012
AuthorsDjebali-Quelen, S, Lagarde, J, Kapranov, P, Lacroix, V, Borel, C, Mudge, JM, Howald, C, Foissac, S, Ucla, C, Chrast, J, Ribeca, P, Martin, D, Murray, RR, Yang, X, Ghamsari, L, Lin, C, Bell, I, Dumais, E, Drenkow, J, Tress, ML, Gelpí, JLluís, Orozco, M, Valencia, A, van Berkum, NL, Lajoie, BR, Vidal, M, Stamatoyannopoulos, J, Batut, P, Dobin, A, Harrow, J, Hubbard, T, Dekker, J, Frankish, A, Salehi-Ashtiani, K, Reymond, A, Antonarakis, SE, Guigó, R, Gingeras, TR
JournalPLoS One
Volume7
Issue1
Paginatione28213
Date Published2012
ISSN1932-6203
KeywordsAlgorithms, 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
Abstract

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

DOI10.1371/journal.pone.0028213
Alternate JournalPLoS ONE
PubMed ID22238572
PubMed Central IDPMC3251577
Grant ListHG003143 / HG / NHGRI NIH HHS / United States
U01HG003150 / HG / NHGRI NIH HHS / United States
U01 HG003147 / HG / NHGRI NIH HHS / United States
R01 HG003143 / HG / NHGRI NIH HHS / United States
U54HG004557 / HG / NHGRI NIH HHS / United States
U54 HG004557 / HG / NHGRI NIH HHS / United States
U01HG003147 / HG / NHGRI NIH HHS / United States
U54 HG004592 / HG / NHGRI NIH HHS / United States
/ / Wellcome Trust / United Kingdom
U01 HG003150 / HG / NHGRI NIH HHS / United States