Disclosing hidden transcripts: Mouse natural sense–antisense transcripts tend to be poly(A) negative and nuclear localized
- 1 Technology and Development Team for Mammalian Cellular Dynamics, BioResource Center (BRC), RIKEN Tsukuba Institute, Tsukuba, Ibaraki, Japan 305-0074
- 2 BioResource Information Division, BioResource Center (BRC), RIKEN Tsukuba Institute, Tsukuba, Ibaraki, Japan 305-0074
- 3 Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan 305-0006
- 4 Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan 230-0045
- 5 Genome Science Laboratory, RIKEN, Wako, Saitama, Japan 351-0198
- 6 Division of Genomic Information Resource Exploration, Science of Biological Supramolecular Systems, Yokohama City University, Graduate School of Integrated Science, Tsurumi-ku, Yokohama, Japan 230-0045
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.
Footnotes
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[Supplemental material is available online at www.genome.org. The expression data from this study have been submitted to Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) under accession no. GSE2185.]
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Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3155905. Article published online before print in March 2005.
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↵7 Corresponding author. E-mail abe{at}rtc.riken.jp; fax 81-29-836-9199.
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- Accepted January 26, 2005.
- Received August 18, 2004.
- Cold Spring Harbor Laboratory Press
