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.
%0 Journal Article
%1 Djebali2012
%A Djebali, Sarah
%A Lagarde, Julien
%A Kapranov, Philipp
%A Lacroix, Vincent
%A Borel, Christelle
%A Mudge, Jonathan M.
%A Howald, Cédric
%A Foissac, Sylvain
%A Ucla, Catherine
%A Chrast, Jacqueline
%A Ribeca, Paolo
%A Martin, David
%A Murray, Ryan R.
%A Yang, Xinping
%A Ghamsari, Lila
%A Lin, Chenwei
%A Bell, Ian
%A Dumais, Erica
%A Drenkow, Jorg
%A Tress, Michael L.
%A Gelpí, Josep Lluís
%A Orozco, Modesto
%A Valencia, Alfonso
%A van Berkum, Nynke L.
%A Lajoie, Bryan R.
%A Vidal, Marc
%A Stamatoyannopoulos, John
%A Batut, Philippe
%A Dobin, Alex
%A Harrow, Jennifer
%A Hubbard, Tim
%A Dekker, Job
%A Frankish, Adam
%A Salehi-Ashtiani, Kourosh
%A Reymond, Alexandre
%A Antonarakis, Stylianos E.
%A Guigó, Roderic
%A Gingeras, Thomas R.
%D 2012
%J PLoS One
%K rna highthroughput methods
%N 1
%P e28213
%R 10.1371/journal.pone.0028213
%T Evidence for transcript networks composed of chimeric RNAs in human cells.
%U http://dx.doi.org/10.1371/journal.pone.0028213
%V 7
%X 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.
@article{Djebali2012,
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.},
added-at = {2013-10-01T22:41:15.000+0200},
author = {Djebali, Sarah and Lagarde, Julien and Kapranov, Philipp and Lacroix, Vincent and Borel, Christelle and Mudge, Jonathan M. and Howald, Cédric and Foissac, Sylvain and Ucla, Catherine and Chrast, Jacqueline and Ribeca, Paolo and Martin, David and Murray, Ryan R. and Yang, Xinping and Ghamsari, Lila and Lin, Chenwei and Bell, Ian and Dumais, Erica and Drenkow, Jorg and Tress, Michael L. and Gelpí, Josep Lluís and Orozco, Modesto and Valencia, Alfonso and {van Berkum}, Nynke L. and Lajoie, Bryan R. and Vidal, Marc and Stamatoyannopoulos, John and Batut, Philippe and Dobin, Alex and Harrow, Jennifer and Hubbard, Tim and Dekker, Job and Frankish, Adam and Salehi-Ashtiani, Kourosh and Reymond, Alexandre and Antonarakis, Stylianos E. and Guigó, Roderic and Gingeras, Thomas R.},
biburl = {https://www.bibsonomy.org/bibtex/2d338eabdb2eedf74b468491027f57865/aorchid},
doi = {10.1371/journal.pone.0028213},
file = {:Laboratory/Genomics/PLoSONE.7.e28213.pdf:PDF},
groups = {public},
institution = {Bioinformatics and Genomics, Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.},
interhash = {9b4f2cb9433deb1ebc186ecca7f8feea},
intrahash = {d338eabdb2eedf74b468491027f57865},
journal = {PLoS One},
keywords = {rna highthroughput methods},
language = {eng},
medline-pst = {ppublish},
number = 1,
pages = {e28213},
pii = {PONE-D-11-12706},
pmid = {22238572},
timestamp = {2013-10-01T22:41:15.000+0200},
title = {Evidence for transcript networks composed of chimeric RNAs in human cells.},
url = {http://dx.doi.org/10.1371/journal.pone.0028213},
username = {aorchid},
volume = 7,
year = 2012
}