title: Evidence for transcript networks composed of chimeric RNAs in human cells.
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.
authors.affiliation: Bioinformatics and Genomics, Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
authors.forename: Sarah
authors.initials: S
authors.lastname: Djebali
authors.forename: Julien
authors.initials: J
authors.lastname: Lagarde
authors.forename: Philipp
authors.initials: P
authors.lastname: Kapranov
authors.forename: Vincent
authors.initials: V
authors.lastname: Lacroix
authors.forename: Christelle
authors.initials: C
authors.lastname: Borel
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Mudge
authors.forename: Cédric
authors.initials: C
authors.lastname: Howald
authors.forename: Sylvain
authors.initials: S
authors.lastname: Foissac
authors.forename: Catherine
authors.initials: C
authors.lastname: Ucla
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Chrast
authors.forename: Paolo
authors.initials: P
authors.lastname: Ribeca
authors.forename: David
authors.initials: D
authors.lastname: Martin
authors.forename: Ryan R
authors.initials: RR
authors.lastname: Murray
authors.forename: Xinping
authors.initials: X
authors.lastname: Yang
authors.forename: Lila
authors.initials: L
authors.lastname: Ghamsari
authors.forename: Chenwei
authors.initials: C
authors.lastname: Lin
authors.forename: Ian
authors.initials: I
authors.lastname: Bell
authors.forename: Erica
authors.initials: E
authors.lastname: Dumais
authors.forename: Jorg
authors.initials: J
authors.lastname: Drenkow
authors.forename: Michael L
authors.initials: ML
authors.lastname: Tress
authors.forename: Josep Lluís
authors.initials: JL
authors.lastname: Gelpí
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
authors.forename: Alfonso
authors.initials: A
authors.lastname: Valencia
authors.forename: Nynke L
authors.initials: NL
authors.lastname: van Berkum
authors.forename: Bryan R
authors.initials: BR
authors.lastname: Lajoie
authors.forename: Marc
authors.initials: M
authors.lastname: Vidal
authors.forename: John
authors.initials: J
authors.lastname: Stamatoyannopoulos
authors.forename: Philippe
authors.initials: P
authors.lastname: Batut
authors.forename: Alex
authors.initials: A
authors.lastname: Dobin
authors.forename: Jennifer
authors.initials: J
authors.lastname: Harrow
authors.forename: Tim
authors.initials: T
authors.lastname: Hubbard
authors.forename: Job
authors.initials: J
authors.lastname: Dekker
authors.forename: Adam
authors.initials: A
authors.lastname: Frankish
authors.forename: Kourosh
authors.initials: K
authors.lastname: Salehi-Ashtiani
authors.forename: Alexandre
authors.initials: A
authors.lastname: Reymond
authors.forename: Stylianos E
authors.initials: SE
authors.lastname: Antonarakis
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigó
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Gingeras
mesh_terms: D000465:Algorithms; D002477:Cells / Q000378:metabolism*; D020740:Chimerin Proteins / Q000737:chemistry / Q000235:genetics; D002878:Chromosomes, Human, Pair 1 / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks / Q000235:genetics / Q000502:physiology*; D006801:Humans; D008297:Male; D046228:Microarray Analysis / Q000379:methods; D008954:Models, Biological; D021141:Nucleic Acid Amplification Techniques / Q000379:methods; D012313:RNA / Q000235:genetics / Q000502:physiology*; D059368:RNA Isoforms / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic / Q000235:genetics; D059467:Transcriptome / Q000502:physiology*; D054928:Validation Studies as Topic
chemical_list: D020740:Chimerin Proteins; D059368:RNA Isoforms; D012313:RNA