Disclosing hidden transcripts: Mouse natural sense–antisense transcripts tend to be poly(A) negative and nuclear localized

Abstract

Genome-wide in silico analysis identified thousands of natural sense–antisense transcript (SAT) pairs in the mouse transcriptome. We investigated their expression using strand-specific oligo-microarray that distinguishes expression of sense and antisense RNA from 1947 SAT pairs. The majority of the predicted SATs are expressed at various steady-state levels in various tissues, and cluster analysis of the array data demonstrated that the ratio of sense and antisense expression for some of the SATs fluctuated markedly among these tissues, while the rest was unchanged. Surprisingly, further analyses indicated that vast amounts of multiple-sized transcripts are expressed from the SAT loci, which tended to be poly(A) negative, and nuclear localized. The tendency that the SATs are often not polyadenylated is conserved, even in the randomly chosen SAT genes in the plant Arabidopsis thaliana. Such common characteristics imply general roles of the SATs in regulation of gene expression.

Eukaryotic regulatory RNAs: an answer to the ‘genome complexity’ conundrum

“…Recent genome-wide analyses suggest that as much as 15%-25% of human genes might be involved in antisense transcription (http://www.narna.ncl.ac.uk). Similar analyses in other organisms including mouse have revealed a large number of NATs (Kiyosawa et al 2003(Kiyosawa et al , 2005Lavorgna et al 2004;Katayama et al 2005). NATs are RNAs containing sequences that are complementary to other endogenous RNAs.…”

Plant SET domain-containing proteins: Structure, function and regulation

“…In Arabidopsis, the ratio of expression of the sense (S) to the antisense (AS) transcripts fluctuates markedly among different tissues during development [146]. In addition, sense-antisense transcripts (SAT) tend to be poly(A)-negative and nuclear localized in Arabidopsis, as in mouse [147].…”

Expression Profile and Localization of Mouse Calcitonin (CT) Sense/Antisense Transcripts in Pre- and Postnatal Tissue Development

“…Currently, many genes have been reported to produce sense and antisense transcripts in the mouse genome [7] and been listed in various databases (Ensemble Genome Brower, http://www.ensemble.org; FANTOM3, http:// f a n t o m 3 . g s c .…”

“…As supporting evidence for additional functions, the CT expression levels have been shown to be related with tumorigenicity of prostate cancer [15] and to be increased in the pregnant rat uterus during implantation [4]. Furthermore, treatment with antisense olignucleotide of CT mRNA severely impairs embryo implantation [18].In the past several years, the number of sense and antisense pair transcripts reported has sharply increased [7]. Due to the increase in the number of these studies, researchers have initiated investigations of not only of the localization of antisense transcripts but also of regulation of sense transcripts with their antisense transcripts in order to more fully understand the molecular interaction occurring in individual loci, cells and tissues.…”

“…In the past several years, the number of sense and antisense pair transcripts reported has sharply increased [7]. Due to the increase in the number of these studies, researchers have initiated investigations of not only of the localization of antisense transcripts but also of regulation of sense transcripts with their antisense transcripts in order to more fully understand the molecular interaction occurring in individual loci, cells and tissues.…”