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Bioinformatics Advance Access originally published online on November 30, 2007
Bioinformatics 2008 24(3):303-308; doi:10.1093/bioinformatics/btm589
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates

Shuji Fujita and Hideo Iba *

Division of Host-Parasite Interaction, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku Tokyo, 108-8639, Japan

*To whom correspondence should be addressed.


  Abstract

Motivation: Just as transcription factors, miRNA genes modulate global patterns of gene expression during differentiation, metabolic activation, stimulus response and also carcinogenesis. However, little is currently known how the miRNA gene expression itself is regulated owing to lack of basic information of their gene structure. Global prediction of promoter regions of miRNA genes would allow us to explore the mechanisms underlying gene-regulatory mechanisms involving these miRNAs.

Results: We speculate that if specific miRNA molecules are involved in evolutionarily conserved regulatory systems in vertebrates, this would entail a high level of conservation of the promoter of miRNA gene as well as the miRNA molecule. By our current screening of putative promoter regions of miRNA genes (miPPRs) on this base, we identified 59 miPPRs that would direct production of 79 miRNAs. We present both biochemical and bioinformatical verifications of these putative promoters.

Contact: iba{at}ims.u-tokyo.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Limsoon Wong

Received on October 2, 2007; revised on November 7, 2007; accepted on November 23, 2007

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