Journal Article

Novel DNA Microarray System for Analysis of Nascent mRNAs

Masaya Ohtsu, Mika Kawate, Masashi Fukuoka, Wataru Gunji, Fumio Hanaoka, Takahiko Utsugi, Fumitoshi Onoda and Yasufumi Murakami

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 15, issue 4, pages 241-251
Published in print August 2008 | ISSN: 1340-2838
Published online July 2008 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsn015

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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.

Journal Article.  5920 words.  Illustrated.

Subjects: Genetics and Genomics

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