Pseudo-messenger RNA: Phantoms of the transcriptome

Frith, Martin C., Wilming, Laurens G., Forrest, Alistair, Kawaji, Hideya, Tan, Sin Lam, Wahlestedt, Claes, Bajic, Vladimir B., Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, Bailey, Timothy L. and Huminiecki, Lukasz (2006) Pseudo-messenger RNA: Phantoms of the transcriptome. PLOS Genetics, 2 4: 504-514. doi:10.1371/journal.pgen.0020023

Author Frith, Martin C.
Wilming, Laurens G.
Forrest, Alistair
Kawaji, Hideya
Tan, Sin Lam
Wahlestedt, Claes
Bajic, Vladimir B.
Kai, Chikatoshi
Kawai, Jun
Carninci, Piero
Hayashizaki, Yoshihide
Bailey, Timothy L.
Huminiecki, Lukasz
Title Pseudo-messenger RNA: Phantoms of the transcriptome
Journal name PLOS Genetics   Check publisher's open access policy
ISSN 1553-7390
Publication date 2006
Sub-type Article (original research)
DOI 10.1371/journal.pgen.0020023
Open Access Status DOI
Volume 2
Issue 4
Start page 504
End page 514
Total pages 11
Place of publication San Francisco
Publisher Public Library Science
Collection year 2006
Language eng
Subject C1
270201 Gene Expression
780105 Biological sciences
Abstract The mammalian transcriptome harbours shadowy entities that resist classification and analysis. In analogy with pseudogenes, we define pseudo-messenger RNA to be RNA molecules that resemble protein- coding mRNA, but cannot encode full-length proteins owing to disruptions of the reading frame. Using a rigorous computational pipeline, which rules out sequencing errors, we identify 10,679 pseudo - messenger RNAs ( approximately half of which are transposonassociated) among the 102,801 FANTOM3 mouse cDNAs: just over 10% of the FANTOM3 transcriptome. These comprise not only transcribed pseudogenes, but also disrupted splice variants of otherwise protein- coding genes. Some may encode truncated proteins, only a minority of which appear subject to nonsense- mediated decay. The presence of an excess of transcripts whose only disruptions are opal stop codons suggests that there are more selenoproteins than currently estimated. We also describe compensatory frameshifts, where a segment of the gene has changed frame but remains translatable. In summary, we survey a large class of non- standard but potentially functional transcripts that are likely to encode genetic information and effect biological processes in novel ways. Many of these transcripts do not correspond cleanly to any identifiable object in the genome, implying fundamental limits to the goal of annotating all functional elements at the genome sequence level.
Keyword Genetics & Heredity
Homologous Coding Gene
Genomic Noise
Q-Index Code C1

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Created: Wed, 15 Aug 2007, 09:08:00 EST