Evidence for transcript networks composed of chimeric RNAs in human cells
Authors
Djebali, SarahLagarde, Julien
Kapranov, Philipp
Lacroix, Vincent
Borel, Christelle
Mudge, Jonathan M.
Howald, Cedric
Foissac, Sylvain
Ucla, Catherine
Chrast, Jacqueline
Ribeca, Paolo
Marin, David
Murray, Ryan R.
Yang, Xinping
Ghamasari, Lila
Lin, Chenwei
Bell, Ian
Dumais, Erica
Drenkow, Jorg
Tress, Michael L.
Gelpi, Josep Lluis
Orozco, Modesto
Valencia, Alfonso
van Berkum, Nynke L.
Lajoie, Bryan R.
Vidal, Marc
Stamatoyannopoulos, John A.
Batut, Philippe
Dobin, Alex
Harrow, Jennifer
Hubbard, Tim
Dekker, Job
Frankish, Adam
Salehi-Ashtiani, Kourosh
Reymond, Alexandre
Antonarakis, Stylianos E.
Guigo, Roderic
Gingeras, Thomas R.
UMass Chan Affiliations
Department of Biochemistry and Molecular PharmacologyProgram in Systems Biology
Program in Gene Function and Expression
Document Type
Journal ArticlePublication Date
2012-01-04Keywords
AlgorithmsCells
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
Biochemistry, Biophysics, and Structural Biology
Genetics and Genomics
Systems Biology
Metadata
Show full item recordAbstract
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.Source
PLoS One. 2012;7(1):e28213. Link to article on publisher's siteDOI
10.1371/journal.pone.0028213Permanent Link to this Item
http://hdl.handle.net/20.500.14038/49928PubMed ID
22238572Related Resources
Link to Article in PubMedRights
Copyright: © 2012 Djebali et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
ae974a485f413a2113503eed53cd6c53
10.1371/journal.pone.0028213