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    Evidence for transcript networks composed of chimeric RNAs in human cells

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    Authors
    Djebali, Sarah
    Lagarde, 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.
    Show allShow less
    UMass Chan Affiliations
    Department of Biochemistry and Molecular Pharmacology
    Program in Systems Biology
    Program in Gene Function and Expression
    Document Type
    Journal Article
    Publication Date
    2012-01-04
    Keywords
    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
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    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.
    Source
    PLoS One. 2012;7(1):e28213. Link to article on publisher's site

    DOI
    10.1371/journal.pone.0028213
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/49928
    PubMed ID
    22238572
    Related Resources
    Link to Article in PubMed
    Rights

    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.

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    10.1371/journal.pone.0028213
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