title: Functionality of intergenic transcription: an evolutionary comparison.
abstract: Although a large proportion of human transcription occurs outside the boundaries of known genes, the functional significance of this transcription remains unknown. We have compared the expression patterns of known genes as well as intergenic transcripts within the ENCODE regions between humans and chimpanzees in brain, heart, testis, and lymphoblastoid cell lines. We find that intergenic transcripts show patterns of tissue-specific conservation of their expression, which are comparable to exonic transcripts of known genes. This suggests that intergenic transcripts are subject to functional constraints that restrict their rate of evolutionary change as well as putative positive selection to an extent comparable to that of classical protein-coding genes. In brain and testis, we find that part of this intergenic transcription is caused by widespread use of alternative promoters. Further, we find that about half of the expression differences between humans and chimpanzees are due to intergenic transcripts.
authors.affiliation: Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. khaitovich@eva.mpg.de
authors.forename: Philipp
authors.initials: P
authors.lastname: Khaitovich
authors.forename: Janet
authors.initials: J
authors.lastname: Kelso
authors.forename: Henriette
authors.initials: H
authors.lastname: Franz
authors.forename: Johann
authors.initials: J
authors.lastname: Visagie
authors.forename: Thomas
authors.initials: T
authors.lastname: Giger
authors.forename: Sabrina
authors.initials: S
authors.lastname: Joerchel
authors.forename: Ekkehard
authors.initials: E
authors.lastname: Petzold
authors.forename: Richard E
authors.initials: RE
authors.lastname: Green
authors.forename: Michael
authors.initials: M
authors.lastname: Lachmann
authors.forename: Svante
authors.initials: S
authors.lastname: Pääbo
mesh_terms: D000818:Animals; D015342:DNA Probes / Q000378:metabolism; D021901:DNA, Intergenic / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics; D014644:Genetic Variation; D006801:Humans; D007438:Introns / Q000235:genetics; D002679:Pan troglodytes / Q000235:genetics*; D050436:Regulatory Elements, Transcriptional / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D015342:DNA Probes; D021901:DNA, Intergenic