Human Molecular Genetics Advance Access originally published online on February 18, 2008
Human Molecular Genetics 2008 17(11):1631-1640; doi:10.1093/hmg/ddn051
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Comparative expression analysis uncovers novel features of endogenous antisense transcription
1 Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan 2 Systems Biology Program, Graduate School of Media and Governance 3 Faculty of Environment and Information Studies, Keio University, Fujisawa 252-8520, Japan 4 Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-0006, Japan 5 Technology and Development Team for Mammalian Cellular Dynamics, BioResource Center (BRC), RIKEN Tsukuba Institute, Ibaraki 305-0074, Japan 6 Custom Biotechnology Service Group, Hokkaido System Science Co. Ltd, 2-1 Shinkawa Nishi 2-1, Kita-ku, Sapporo 001-0932, Japan 7 C’s Lab Co. Ltd, Maruito Sapporo Bldg, 7F, Kita 2 Nishi 1, Kita-ku, Sapporo 060-0002, Japan 8 Genostaff Inc., Kawauchi Bldg. 6F 1-4-4, Nezu, Bunkyo-Ku, Tokyo 113-0031, Japan
* To whom correspondence should be addressed. Tel/Fax: +81 466475099; Email: rsaito{at}sfc.keio.ac.jp (R.S.); Tel/Fax: +81 298369199; Email: kiyosawa{at}rtc.riken.jp (H.K.)
Received December 7, 2007; Accepted February 13, 2008
Increasing numbers of sense–antisense transcripts (SATs), which are transcribed from the same chromosomal location but in opposite directions, have been identified in various eukaryotic species, but the biological meanings of most SATs remain unclear. To improve understanding of natural sense–antisense transcription, we performed comparative expression profiling of SATs conserved among humans and mice. Using custom oligo-arrays loaded with probes that represented SATs with both protein-coding and non-protein-coding transcripts, we showed that 33% of the 291 conserved SATs displayed identical expression patterns in the two species. Among these SATs, expressional balance inversion of sense–antisense genes was mostly observed in testis at a tissue-specific manner. Northern analyses of the individual conserved SAT loci revealed that: (i) a smeary hybridization pattern was present in mice, but not in humans, and (2) small RNAs (about 60 to 80 nt) were detected from the exon-overlapping regions of SAT loci. In addition, further analyses showed marked alteration of sense–antisense expression balance throughout spermatogenesis in testis. These results suggest that conserved SAT loci are rich in potential regulatory roles that will help us understand this new class of transcripts underlying the mammalian genome.