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dc.contributor.authorDjebali, Sarah
dc.contributor.authorLagarde, Julien
dc.contributor.authorKapranov, Philipp
dc.contributor.authorLacroix, Vincent
dc.contributor.authorBorel, Christelle
dc.contributor.authorMudge, Jonathan M.
dc.contributor.authorHowald, Cedric
dc.contributor.authorFoissac, Sylvain
dc.contributor.authorUcla, Catherine
dc.contributor.authorChrast, Jacqueline
dc.contributor.authorRibeca, Paolo
dc.contributor.authorMarin, David
dc.contributor.authorMurray, Ryan R.
dc.contributor.authorYang, Xinping
dc.contributor.authorGhamasari, Lila
dc.contributor.authorLin, Chenwei
dc.contributor.authorBell, Ian
dc.contributor.authorDumais, Erica
dc.contributor.authorDrenkow, Jorg
dc.contributor.authorTress, Michael L.
dc.contributor.authorGelpi, Josep Lluis
dc.contributor.authorOrozco, Modesto
dc.contributor.authorValencia, Alfonso
dc.contributor.authorvan Berkum, Nynke L.
dc.contributor.authorLajoie, Bryan R.
dc.contributor.authorVidal, Marc
dc.contributor.authorStamatoyannopoulos, John A.
dc.contributor.authorBatut, Philippe
dc.contributor.authorDobin, Alex
dc.contributor.authorHarrow, Jennifer
dc.contributor.authorHubbard, Tim
dc.contributor.authorDekker, Job
dc.contributor.authorFrankish, Adam
dc.contributor.authorSalehi-Ashtiani, Kourosh
dc.contributor.authorReymond, Alexandre
dc.contributor.authorAntonarakis, Stylianos E.
dc.contributor.authorGuigo, Roderic
dc.contributor.authorGingeras, Thomas R.
dc.date2022-08-11T08:11:00.000
dc.date.accessioned2022-08-23T17:27:44Z
dc.date.available2022-08-23T17:27:44Z
dc.date.issued2012-01-04
dc.date.submitted2012-08-10
dc.identifier.citationPLoS One. 2012;7(1):e28213. <a href="http://dx.doi.org/10.1371/journal.pone.0028213" target="_blank">Link to article on publisher's site</a></p>
dc.identifier.issn1932-6203 (Linking)
dc.identifier.doi10.1371/journal.pone.0028213
dc.identifier.pmid22238572
dc.identifier.urihttp://hdl.handle.net/20.500.14038/49928
dc.description.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.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=22238572&dopt=Abstract">Link to Article in PubMed</a>
dc.rights<p>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.</p>
dc.subjectAlgorithms
dc.subjectCells
dc.subjectChimerin Proteins
dc.subjectChromosomes, Human, Pair 1
dc.subjectFemale
dc.subjectGene Expression Profiling
dc.subjectGene Regulatory Networks
dc.subjectHumans
dc.subjectMale
dc.subjectMicroarray Analysis
dc.subjectModels, Biological
dc.subjectNucleic Acid Amplification Techniques
dc.subjectRNA
dc.subjectRNA Isoforms
dc.subjectTranscription, Genetic
dc.subjectTranscriptome
dc.subjectValidation Studies as Topic
dc.subjectBiochemistry, Biophysics, and Structural Biology
dc.subjectGenetics and Genomics
dc.subjectSystems Biology
dc.titleEvidence for transcript networks composed of chimeric RNAs in human cells
dc.typeJournal Article
dc.source.journaltitlePloS one
dc.source.volume7
dc.source.issue1
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=1004&amp;context=sysbio_pubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/sysbio_pubs/5
dc.identifier.contextkey3201822
refterms.dateFOA2022-08-23T17:27:44Z
html.description.abstract<p>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.</p>
dc.identifier.submissionpathsysbio_pubs/5
dc.contributor.departmentDepartment of Biochemistry and Molecular Pharmacology
dc.contributor.departmentProgram in Systems Biology
dc.contributor.departmentProgram in Gene Function and Expression
dc.source.pagese28213


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