Evidence for transcript networks composed of chimeric RNA's in human cells

Djebali, S., Lagarde, J., Kapranov, P., Lacroix, V., Borel, C., Mudge, J. M., Howald, C., Foissac, S., Ucla, C., Chrast, J., Ribeca, P., Martin, D., Murray, R. R., Yang, X., Ghamsari, L., Lin, C., Bell, I., Dumais, E., Drenkow, J., Tress, M. L., Gelpí, J. L., Orozco, M., Valencia, A., van Berkum, N. L., Lajoie, B. R., Vidal, M., Stamatoyannopoulos, J., Batut, P., Dobin, A., Harrow, J., Hubbard, T., Dekker, J., Frankish, A., Salehi-Ashtiani, K., Reymond, A., Antonarakis, S. E., Guigó, R., Gingeras, T. R. (January 2012) Evidence for transcript networks composed of chimeric RNA's in human cells. PLoS ONE, 7 (1). ISSN 19326203 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/22238572
DOI: 10.1371/journal.pone.0028213

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. © 2012 Djebali et al.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
bioinformatics > genomics and proteomics > annotation > gene expression profiling annotation
CSHL Authors:
Communities: CSHL Cancer Center Program > Gene Regulation and Cell Proliferation
CSHL Cancer Center Shared Resources > DNA Sequencing Service
CSHL labs > Gingeras lab
Watson School > Publications
CSHL Cancer Center Shared Resources > Functional Genomics and Genetics Service
Depositing User: CSHL Librarian
Date: January 2012
Date Deposited: 08 Mar 2012 14:16
Last Modified: 30 Oct 2015 16:21
PMCID: PMC3251577
Related URLs:
URI: http://repository.cshl.edu/id/eprint/25351

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