title: Expression of distinct RNAs from 3' untranslated regions.
abstract: The 3' untranslated regions (3'UTRs) of eukaryotic genes regulate mRNA stability, localization and translation. Here, we present evidence that large numbers of 3'UTRs in human, mouse and fly are also expressed separately from the associated protein-coding sequences to which they are normally linked, likely by post-transcriptional cleavage. Analysis of CAGE (capped analysis of gene expression), SAGE (serial analysis of gene expression) and cDNA libraries, as well as microarray expression profiles, demonstrate that the independent expression of 3'UTRs is a regulated and conserved genome-wide phenomenon. We characterize the expression of several 3'UTR-derived RNAs (uaRNAs) in detail in mouse embryos, showing by in situ hybridization that these transcripts are expressed in a cell- and subcellular-specific manner. Our results suggest that 3'UTR sequences can function not only in cis to regulate protein expression, but also intrinsically and independently in trans, likely as noncoding RNAs, a conclusion supported by a number of previous genetic studies. Our findings suggest novel functions for 3'UTRs, as well as caution in the use of 3'UTR sequence probes to analyze gene expression.
authors.affiliation: Institute for Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
authors.forename: Tim R
authors.initials: TR
authors.lastname: Mercer
authors.forename: Dagmar
authors.initials: D
authors.lastname: Wilhelm
authors.forename: Marcel E
authors.initials: ME
authors.lastname: Dinger
authors.forename: Giulia
authors.initials: G
authors.lastname: Soldà
authors.forename: Darren J
authors.initials: DJ
authors.lastname: Korbie
authors.forename: Evgeny A
authors.initials: EA
authors.lastname: Glazov
authors.forename: Vy
authors.initials: V
authors.lastname: Truong
authors.forename: Maren
authors.initials: M
authors.lastname: Schwenke
authors.forename: Cas
authors.initials: C
authors.lastname: Simons
authors.forename: Klaus I
authors.initials: KI
authors.lastname: Matthaei
authors.forename: Robert
authors.initials: R
authors.lastname: Saint
authors.forename: Peter
authors.initials: P
authors.lastname: Koopman
authors.forename: John S
authors.initials: JS
authors.lastname: Mattick
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D004331:Drosophila melanogaster / Q000235:genetics / Q000378:metabolism; D047108:Embryonic Development / Q000235:genetics; D005091:Exons; D020869:Gene Expression Profiling; D006801:Humans; D051379:Mice; D012323:RNA Processing, Post-Transcriptional; D022661:RNA, Untranslated / Q000378:metabolism*
chemical_list: D020413:3' Untranslated Regions; D022661:RNA, Untranslated