Evidence for transcript networks composed of chimeric rnas in human cells

Sarah Djebali, Julien Lagarde, Philipp Kapranov, Vincent Lacroix, Christelle Borel, Jonathan M. Mudge, Cédric Howald, Sylvain Foissac, Catherine Ucla, Jacqueline Chrast, Paolo Ribeca, David Martin, Ryan R. Murray, Xinping Yang, Lila Ghamsari, Chenwei Lin, Ian Bell, Erica Dumais, Jorg Drenkow, Michael L. Tress & 18 others Josep Lluís Gelpí, Modesto Orozco, Alfonso Valencia, Nynke L. van Berkum, Bryan R. Lajoie, Marc Vidal, John Stamatoyannopoulos, Philippe Batut, Alex Dobin, Jennifer Harrow, Tim Hubbard, Job Dekker, Adam Frankish, Kourosh Salehi-Ashtiani, Alexandre Reymond, Stylianos E. Antonarakis, Roderic Guigó, Thomas R. Gingeras

    Research output: Contribution to journalArticle

    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.

    Original languageEnglish (US)
    Article numbere28213
    JournalPLoS One
    Volume7
    Issue number1
    DOIs
    StatePublished - Jan 4 2012

    Fingerprint

    Genes
    Cells
    RNA
    genes
    cells
    Chromosomes, Human, 21-22 and Y
    Bacterial Genes
    Chromosome Mapping
    Transcriptome
    Exons
    Yeasts
    transcriptome
    Chromosomes
    Gene Expression
    exons
    Yeast
    yeasts
    chromosomes
    genomics
    gene expression

    ASJC Scopus subject areas

    • Biochemistry, Genetics and Molecular Biology(all)
    • Agricultural and Biological Sciences(all)

    Cite this

    Djebali, S., Lagarde, J., Kapranov, P., Lacroix, V., Borel, C., Mudge, J. M., ... Gingeras, T. R. (2012). Evidence for transcript networks composed of chimeric rnas in human cells. PLoS One, 7(1), [e28213]. https://doi.org/10.1371/journal.pone.0028213

    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 E.; Guigó, Roderic; Gingeras, Thomas R.

    In: PLoS One, Vol. 7, No. 1, e28213, 04.01.2012.

    Research output: Contribution to journalArticle

    Djebali, S, Lagarde, J, Kapranov, P, Lacroix, V, Borel, C, Mudge, JM, Howald, C, Foissac, S, Ucla, C, Chrast, J, Ribeca, P, Martin, D, Murray, RR, Yang, X, Ghamsari, L, Lin, C, Bell, I, Dumais, E, Drenkow, J, Tress, ML, Gelpí, JL, Orozco, M, Valencia, A, van Berkum, NL, Lajoie, BR, Vidal, M, Stamatoyannopoulos, J, Batut, P, Dobin, A, Harrow, J, Hubbard, T, Dekker, J, Frankish, A, Salehi-Ashtiani, K, Reymond, A, Antonarakis, SE, Guigó, R & Gingeras, TR 2012, 'Evidence for transcript networks composed of chimeric rnas in human cells', PLoS One, vol. 7, no. 1, e28213. https://doi.org/10.1371/journal.pone.0028213
    Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM et al. Evidence for transcript networks composed of chimeric rnas in human cells. PLoS One. 2012 Jan 4;7(1). e28213. https://doi.org/10.1371/journal.pone.0028213
    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 E. ; Guigó, Roderic ; Gingeras, Thomas R. / Evidence for transcript networks composed of chimeric rnas in human cells. In: PLoS One. 2012 ; Vol. 7, No. 1.
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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.",
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    AU - Kapranov, Philipp

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    AU - Borel, Christelle

    AU - Mudge, Jonathan M.

    AU - Howald, Cédric

    AU - Foissac, Sylvain

    AU - Ucla, Catherine

    AU - Chrast, Jacqueline

    AU - Ribeca, Paolo

    AU - Martin, David

    AU - Murray, Ryan R.

    AU - Yang, Xinping

    AU - Ghamsari, Lila

    AU - Lin, Chenwei

    AU - Bell, Ian

    AU - Dumais, Erica

    AU - Drenkow, Jorg

    AU - Tress, Michael L.

    AU - Gelpí, Josep Lluís

    AU - Orozco, Modesto

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    AU - van Berkum, Nynke L.

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    AU - Batut, Philippe

    AU - Dobin, Alex

    AU - Harrow, Jennifer

    AU - Hubbard, Tim

    AU - Dekker, Job

    AU - Frankish, Adam

    AU - Salehi-Ashtiani, Kourosh

    AU - Reymond, Alexandre

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    AU - Guigó, Roderic

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