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DNA Research Advance Access originally published online on July 8, 2008
DNA Research 2008 15(4):241-251; doi:10.1093/dnares/dsn015
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© The Author 2008. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Novel DNA Microarray System for Analysis of Nascent mRNAs

Masaya Ohtsu1, Mika Kawate1, Masashi Fukuoka1, Wataru Gunji2, Fumio Hanaoka3, Takahiko Utsugi2, Fumitoshi Onoda1 and Yasufumi Murakami1,2,*

1 Faculty of Industrial Science and Technology, Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan
2 Bio Matrix Research Inc., 105 Higashifukai, Nagareyama, Chiba 275-0101, Japan
3 Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-oka, Suita, Osaka 565-0871, Japan

Received 3 May 2008 ; accepted 11 June 2008.

Transcriptional activation and repression are a key step in the regulation of all cellular activities. The development of comprehensive analysis methods such as DNA microarray has advanced our understanding of the correlation between the regulation of transcription and that of cellular mechanisms. However, DNA microarray analysis based on steady-state mRNA (total mRNA) does not always correspond to transcriptional activation or repression. To comprehend these transcriptional regulations, the detection of nascent RNAs is more informative. Although the nuclear run-on assay can detect nascent RNAs, it has not been fully applied to DNA microarray analysis. In this study, we have developed a highly efficient method for isolating bromouridine-labeled nascent RNAs that can be successfully applied to DNA microarray analysis. This method can linearly amplify small amounts of mRNAs with little bias. Furthermore, we have applied this method to DNA microarray analysis from mouse G2-arrested cells and have identified several genes that exhibit novel expression profiles. This method will provide important information in the field of transcriptome analysis of various cellular processes.

* To whom correspondence should be addressed. Tel. +81 4-7124-1501 ext. 4408. Fax. +81 4-7122-1360. E-mail: yasufumi{at}rs.noda.tus.ac.jp

Edited by Kazuo Shinozaki


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