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Open Access Research article

Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes

Rintaro Saito18, Keisuke Kohno2, Yuki Okada13, Yuko Osada1, Koji Numata4, Chihiro Kohama5, Kazufumi Watanabe6, Hajime Nakaoka7, Naoyuki Yamamoto7, Akio Kanai138, Hiroshi Yasue9, Soichiro Murata2, Kuniya Abe45, Masaru Tomita138, Nobuhiro Ohkohchi102 and Hidenori Kiyosawa1145*

Author Affiliations

1 Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan

2 Department of Surgery, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Ibaraki 305-8575, Japan

3 Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-8520, Japan

4 Technology and Development Team for Mammalian Cellular Dynamics, BioResource Center (BRC), RIKEN Tsukuba Institute, Ibaraki 305-0074, Japan

5 Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-0006, 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 NEXT Co. Ltd. Maruito Kita 4-jyou Bldg., 4F, Kita 4-jyou Higashi 2-8-2, Tyuo-ku, Sapporo 060-0034, Japan

8 Faculty of Environment and Information Studies, Keio University, Fujisawa, 252-8520, Japan

9 National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan

10 Inquiries regarding clinical aspects of the samples should be addressed to N.O

11 Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan

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BMC Medical Genomics 2011, 4:42  doi:10.1186/1755-8794-4-42

Published: 16 May 2011

Abstract

Background

Recent studies have identified thousands of sense-antisense gene pairs across different genomes by computational mapping of cDNA sequences. These studies have shown that approximately 25% of all transcriptional units in the human and mouse genomes are involved in cis-sense-antisense pairs. However, the number of known sense-antisense pairs remains limited because currently available cDNA sequences represent only a fraction of the total number of transcripts comprising the transcriptome of each cell type.

Methods

To discover novel antisense transcripts encoded in the antisense strand of important genes, such as cancer-related genes, we conducted expression analyses of antisense transcripts using our custom microarray platform along with 2376 probes designed specifically to detect the potential antisense transcripts of 501 well-known genes suitable for cancer research.

Results

Using colon cancer tissue and normal tissue surrounding the cancer tissue obtained from 6 patients, we found that antisense transcripts without poly(A) tails are expressed from approximately 80% of these well-known genes. This observation is consistent with our previous finding that many antisense transcripts expressed in a cell are poly(A)-. We also identified 101 and 71 antisense probes displaying a high level of expression specifically in normal and cancer tissues respectively.

Conclusion

Our microarray analysis identified novel antisense transcripts with expression profiles specific to cancer tissue, some of which might play a role in the regulatory networks underlying oncogenesis and thus are potential targets for further experimental validation. Our microarray data are available at http://www.brc.riken.go.jp/ncrna2007/viewer-Saito-01/index.html webcite.