Sarah Djebali, Universitat Pompeu Fabra
Julien Lagarde, Universitat Pompeu Fabra
Philipp Kapranov, Affymetrix
Vincent Lacroix, Universitat Pompeu Fabra
Christelle Borel, University Hospitals of Geneva
Jonathan M. Mudge, Wellcome Trust Sanger Institute
Cedric Howald, University of Lausanne
Sylvain Foissac, Universitat Pompeu Fabra
Catherine Ucla, University of Geneva Medical School
Jacqueline Chrast, University of Lausanne
Paolo Ribeca, Universitat Pompeu Fabra
David Marin, Universitat Pompeu Fabra
Ryan R. Murray, Harvard Medical School
Xinping Yang, Harvard Medical School
Lila Ghamasari, Harvard Medical School
Chenwei Lin, Harvard Medical School
Ian Bell, Affymetrix Inc.
Erica Dumais, Affymetrix Inc.
Jorg Drenkow, Cold Spring Harbor Laboratory
Michael L. Tress, Spanish National Cancer Research Centre
Josep Lluis Gelpi, Universitat de Barcelona
Modesto Orozco, Universitat de Barcelona
Alfonso Valencia, Spanish National Cancer Research Centre
Nynke L. van Berkum, University of Massachusetts Medical School
Bryan R. Lajoie, University of Massachusetts Medical School
Marc Vidal, Dana-Farber Cancer Institute
John A. Stamatoyannopoulos, University of Washington
Philippe Batut, Cold Spring Harbor Laboratory
Alex Dobin, Cold Spring Harbor Laboratory
Jennifer Harrow, Wellcome Trust Sanger Institute
Tim Hubbard, Wellcome Trust Sanger Institute
Job Dekker, University of Massachusetts Medical SchoolFollow
Adam Frankish, Wellcome Trust Sanger Institute
Kourosh Salehi-Ashtiani, Harvard Medical School
Alexandre Reymond, University of Lausanne
Stylianos E. Antonarakis, University of Geneva Medical School
Roderic Guigo, Universitat Pompeu Fabra
Thomas R. Gingeras, Affymetrix

UMMS Affiliation

Program in Gene Function and Expression; Program in Systems Biology; Department of Biochemistry and Molecular Pharmacology

Publication Date


Document Type



Algorithms; 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


Biochemistry, Biophysics, and Structural Biology | Genetics and Genomics | Systems Biology


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.

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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.

DOI of Published Version



PLoS One. 2012;7(1):e28213. Link to article on publisher's site

Journal/Book/Conference Title

PloS one

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