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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Evidence for transcript networks composed of chimeric rnas in human cells
PLoS ONE, Volume 7, No. 1, Article e28213, Year 2012
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Description
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. © 2012 Djebali et al.
Authors & Co-Authors
Djebali, Sarah
Spain, Barcelona
Universitat Pompeu Fabra Barcelona
Lagarde, Julien
Spain, Barcelona
Universitat Pompeu Fabra Barcelona
Kapranov, Philipp
United States, Waltham
Thermo Fisher Scientific Inc.
United States, Cambridge
Helicos Biosciences Corporation
Lacroix, Vincent
Spain, Barcelona
Universitat Pompeu Fabra Barcelona
France, Villeurbanne
Université Claude Bernard Lyon 1
Borel, Christelle
Switzerland, Geneva
Université de Genève Faculté de Médecine
Mudge, Jonathan M.
United Kingdom, Hinxton
Wellcome Sanger Institute
Howald, Cédric
Switzerland, Lausanne
Université de Lausanne Unil
Foissac, Sylvain
Spain, Barcelona
Universitat Pompeu Fabra Barcelona
United States, Waltham
Thermo Fisher Scientific Inc.
Spain, Madrid
Integromics
Ucla, Catherine
Switzerland, Geneva
Université de Genève Faculté de Médecine
Chrast, Jacqueline
Switzerland, Lausanne
Université de Lausanne Unil
Ribeca, Paolo
Spain, Barcelona
Universitat Pompeu Fabra Barcelona
Martin, David Michael Alan
Spain, Barcelona
Universitat Pompeu Fabra Barcelona
Murray, Ryan R.
United States, Boston
Dana-farber Cancer Institute
Yang, Xinping
United States, Boston
Dana-farber Cancer Institute
Ghamsari, Lila
United States, Boston
Dana-farber Cancer Institute
Lin, Chenwei
United States, Boston
Dana-farber Cancer Institute
Bell, Ian
United States, Waltham
Thermo Fisher Scientific Inc.
Dumais, Erica
United States, Waltham
Thermo Fisher Scientific Inc.
Drenkow, Jorg
United States, Cold Spring Harbor
Cold Spring Harbor Laboratory
Tress, Michael L.
Spain, Madrid
Centro Nacional de Investigaciones Oncológicas
Gelpí, Josep Lluís
Spain, Barcelona
Universitat de Barcelona
Orozco, Modesto
Spain, Barcelona
Universitat de Barcelona
Valencia, Alfonso
Spain, Madrid
Centro Nacional de Investigaciones Oncológicas
van Berkum, Nynke L.
United States, Worcester
University of Massachusetts Chan Medical School
Lajoie, Bryan R.
United States, Worcester
University of Massachusetts Chan Medical School
Vidal, Marc
United States, Boston
Dana-farber Cancer Institute
Stamatoyannopoulos, John A.
United States, Seattle
University of Washington
Batut, Philippe
United States, Cold Spring Harbor
Cold Spring Harbor Laboratory
Dobin, Alex
United States, Cold Spring Harbor
Cold Spring Harbor Laboratory
Harrow, Jennifer L.
United Kingdom, Hinxton
Wellcome Sanger Institute
Hubbard, Tim J.P.
United Kingdom, Hinxton
Wellcome Sanger Institute
Dekker, Job
United States, Worcester
University of Massachusetts Chan Medical School
Frankish, Adam
United Kingdom, Hinxton
Wellcome Sanger Institute
Salehi-Ashtiani, Kourosh
United States, Boston
Dana-farber Cancer Institute
United Arab Emirates, Abu Dhabi
Nyu Abu Dhabi
Reymond, Alexandre
Switzerland, Lausanne
Université de Lausanne Unil
Antonarakis, Stylianos E.
Switzerland, Geneva
Université de Genève Faculté de Médecine
Guigó, Roderic
Spain, Barcelona
Universitat Pompeu Fabra Barcelona
Gingeras, Thomas R.
United States, Waltham
Thermo Fisher Scientific Inc.
United States, Cold Spring Harbor
Cold Spring Harbor Laboratory
Statistics
Citations: 233
Authors: 38
Affiliations: 15
Identifiers
Doi:
10.1371/journal.pone.0028213
e-ISSN:
19326203
Research Areas
Genetics And Genomics