Evidence for transcript networks composed of chimeric RNAs in human cells

Djebali, Sarah; Lagarde, Julien; Kapranov, Philipp; Lacroix, Vincent; Borel, Christelle; Mudge, Jonathan M; Howald, Cédric; Foissac, Sylvain; Ucla, Catherine; Chrast, Jacqueline; Ribeca, Paolo; Martin, David; Murray, Ryan R; Yang, Xinping; Ghamsari, Lila; Lin, Chenwei; Bell, Ian; Dumais, Erica; Drenkow, Jorg; Tress, Michael L; Gelpí, Josep Lluís; Orozco, Modesto; Valencia, Alfonso; van Berkum, Nynke L; Lajoie, Bryan R; Vidal, Marc; Stamatoyannopoulos, John; Batut, Philippe; Dobin, Alex; Harrow, Jennifer; Hubbard, Tim; Dekker, Job; Frankish, Adam; Salehi-Ashtiani, Kourosh; Reymond, Alexandre; Antonarakis, Stylianos; Guigó, Roderic; Gingeras, Thomas R

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Title		Evidence for transcript networks composed of chimeric RNAs in human cells
Authors		Djebali, Sarah Lagarde, Julien Kapranov, Philipp Lacroix, Vincent Borel, Christelle Mudge, Jonathan M Howald, Cédric Foissac, Sylvain Ucla, Catherine Chrast, Jacqueline Ribeca, Paolo Martin, David Murray, Ryan R Yang, Xinping Ghamsari, Lila Lin, Chenwei Bell, Ian Dumais, Erica Drenkow, Jorg Tress, Michael L Gelpí, Josep Lluís Orozco, Modesto Valencia, Alfonso van Berkum, Nynke L Lajoie, Bryan R Vidal, Marc Stamatoyannopoulos, John Batut, Philippe Dobin, Alex Harrow, Jennifer Hubbard, Tim Dekker, Job Frankish, Adam Salehi-Ashtiani, Kourosh Reymond, Alexandre Antonarakis, Stylianos Guigó, Roderic Gingeras, Thomas R show all authors [1 - 38]
Published in		PLOS ONE. 2012, vol. 7, no. 1, p. e28213
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.
Keywords		Algorithms — Cells/metabolism — Chimerin Proteins/chemistry/genetics — Chromosomes, Human, Pair 1/genetics — Female — Gene Expression Profiling — Gene Regulatory Networks/genetics/physiology — Humans — Male — Microarray Analysis/methods — Models, Biological — Nucleic Acid Amplification Techniques/methods — RNA/genetics/physiology — RNA Isoforms/chemistry/genetics/metabolism — Transcription, Genetic/genetics — Transcriptome/physiology — Validation Studies as Topic
Identifiers		DOI: 10.1371/journal.pone.0028213 PMID: 22238572
Full text		Article (Published version) (1.7 MB) - Free access
Structures		Faculté de médecine / Section de médecine fondamentale / Département de médecine génétique et développement
Research group		Pathologie Moléculaire de la Trisomie 21 et le Génome Humain (248)
Citation (ISO format)		DJEBALI, Sarah et al. Evidence for transcript networks composed of chimeric RNAs in human cells. In: PLOS ONE, 2012, vol. 7, n° 1, p. e28213. https://archive-ouverte.unige.ch/unige:34649