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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 392.
Published online Aug 22, 2009. doi:  10.1186/1471-2164-10-392
PMCID: PMC2741491
Identification of novel endogenous antisense transcripts by DNA microarray analysis targeting complementary strand of annotated genes
Koji Numata,1 Yuko Osada,2 Yuki Okada,2 Rintaro Saito,2,3 Noriko Hiraiwa,4 Hajime Nakaoka,5 Naoyuki Yamamoto,5 Kazufumi Watanabe,6 Kazue Okubo,7 Chihiro Kohama,8 Akio Kanai,2,3 Kuniya Abe,1,8 and Hidenori Kiyosawacorresponding author1,8,9
1Technology and Development Team for Mammalian Cellular Dynamics, BioResource Center (BRC), RIKEN Tsukuba Institute, Ibaraki 305-0074, Japan
2Institute for Advanced Biosciences, Keio University, Yamagata 997-0017, Japan
3Department of Environmental Information, Keio University, Fujisawa 252-8520, Japan
4Experimental Animal Division, BioResource Center (BRC), RIKEN Tsukuba Institute, Ibaraki 305-0074, Japan
5C's Lab Co Ltd Maruito Sapporo Bldg, 7F Kita 2 Nishi 1, Kita-ku, Sapporo 060-0002, Japan
6Custom Biotechnology Service Group, Hokkaido System Science Co Ltd, 2-1 Shinkawa Nishi 2-1, Kita-ku, Sapporo 001-0932, Japan
7Genostaff Inc., Kawauchi Bldg 6F 1-4-4, Nezu, Bunkyo-Ku, Tokyo 113-0031, Japan
8Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-0006, Japan
9Technology and Development Team for BioSignal Program, BioResource Center (BRC), RIKEN Tsukuba Institute, Ibaraki 305-0074, Japan
corresponding authorCorresponding author.
Koji Numata: koji.numata/at/gmail.com; Yuko Osada: yuko.osada/at/gmail.com; Yuki Okada: okayan/at/gmail.com; Rintaro Saito: rsaito/at/sfc.keio.ac.jp; Noriko Hiraiwa: hiraiwa/at/rtc.riken.jp; Hajime Nakaoka: nakaoka/at/cslab.co.jp; Naoyuki Yamamoto: yamamoto/at/cslab.co.jp; Kazufumi Watanabe: watanabe/at/hssnet.co.jp; Kazue Okubo: okuboka/at/genostaff.com; Chihiro Kohama: s0921075/at/u.tsukuba.ac.jp; Akio Kanai: akio/at/sfc.keio.ac.jp; Kuniya Abe: abe/at/rtc.riken.jp; Hidenori Kiyosawa: kiyosawa/at/rtc.riken.jp
Received February 27, 2009; Accepted August 22, 2009.
Abstract
Background
Recent transcriptomic analyses in mammals have uncovered the widespread occurrence of endogenous antisense transcripts, termed natural antisense transcripts (NATs). NATs are transcribed from the opposite strand of the gene locus and are thought to control sense gene expression, but the mechanism of such regulation is as yet unknown. Although several thousand potential sense-antisense pairs have been identified in mammals, examples of functionally characterized NATs remain limited. To identify NAT candidates suitable for further functional analyses, we performed DNA microarray-based NAT screening using mouse adult normal tissues and mammary tumors to target not only the sense orientation but also the complementary strand of the annotated genes.
Results
First, we designed microarray probes to target the complementary strand of genes for which an antisense counterpart had been identified only in human public cDNA sources, but not in the mouse. We observed a prominent expression signal from 66.1% of 635 target genes, and 58 genes of these showed tissue-specific expression. Expression analyses of selected examples (Acaa1b and Aard) confirmed their dynamic transcription in vivo. Although interspecies conservation of NAT expression was previously investigated by the presence of cDNA sources in both species, our results suggest that there are more examples of human-mouse conserved NATs that could not be identified by cDNA sources. We also designed probes to target the complementary strand of well-characterized genes, including oncogenes, and compared the expression of these genes between mammary cancerous tissues and non-pathological tissues. We found that antisense expression of 95 genes of 404 well-annotated genes was markedly altered in tumor tissue compared with that in normal tissue and that 19 of these genes also exhibited changes in sense gene expression. These results highlight the importance of NAT expression in the regulation of cellular events and in pathological conditions.
Conclusion
Our microarray platform targeting the complementary strand of annotated genes successfully identified novel NATs that could not be identified by publically available cDNA data, and as such could not be detected by the usual "sense-targeting" microarray approach. Differentially expressed NATs monitored by this platform may provide candidates for investigations of gene function. An advantage of our microarray platform is that it can be applied to any genes and target samples of interest.
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