Evidence for transcript networks composed of chimeric RNAs in human cells
Mudge, Jonathan M.
Murray, Ryan R.
Tress, Michael L.
Gelpi, Josep Lluis
van Berkum, Nynke L.
Lajoie, Bryan R.
Stamatoyannopoulos, John A.
Antonarakis, Stylianos E.
Gingeras, Thomas R.
UMass Chan AffiliationsDepartment of Biochemistry and Molecular Pharmacology
Program in Systems Biology
Program in Gene Function and Expression
Chromosomes, Human, Pair 1
Gene Expression Profiling
Gene Regulatory Networks
Nucleic Acid Amplification Techniques
Validation Studies as Topic
Biochemistry, Biophysics, and Structural Biology
Genetics and Genomics
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AbstractThe 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.
SourcePLoS One. 2012;7(1):e28213. Link to article on publisher's site
Permanent Link to this Itemhttp://hdl.handle.net/20.500.14038/49928
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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.