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DNA Research Advance Access originally published online on November 11, 2008
DNA Research 2009 16(1):45-58; doi:10.1093/dnares/dsn030
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Published by Oxford University Press 2008
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

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

Lioudmila V. Sharova {dagger}, Alexei A. Sharov {dagger}, Timur Nedorezov, Yulan Piao, Nabeebi Shaik and Minoru S.H. Ko*

Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, NIH, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA

Received 17 July 2008 ; accepted 21 October 2008.

Degradation of mRNA is one of the key processes that control the steady-state level of gene expression. However, the rate of mRNA decay for the majority of genes is not known. We successfully obtained the rate of mRNA decay for 19 977 non-redundant genes by microarray analysis of RNA samples obtained from mouse embryonic stem (ES) cells. Median estimated half-life was 7.1 h and only <100 genes, including Prdm1, Myc, Gadd45 g, Foxa2, Hes5 and Trib1, showed half-life less than 1 h. In general, mRNA species with short half-life were enriched among genes with regulatory functions (transcription factors), whereas mRNA species with long half-life were enriched among genes related to metabolism and structure (extracellular matrix, cytoskeleton). The stability of mRNAs correlated more significantly with the structural features of genes than the function of genes: mRNA stability showed the most significant positive correlation with the number of exon junctions per open reading frame length, and negative correlation with the presence of PUF-binding motifs and AU-rich elements in 3'-untranslated region (UTR) and CpG di-nucleotides in the 5'-UTR. The mRNA decay rates presented in this report are the largest data set for mammals and the first for ES cells.

Key words: mRNA decay; mRNA degradation; microarray; transcript; exon junction; AU-rich elements (ARE); embryonic stem cells; leukemia inhibitory factor (LIF); retinoic acid (RA); cell differentiation; mouse strain

* To whom correspondence should be addressed. Tel. +1 410-558-8359. Fax. +1 410-558-8331. E-mail: KoM{at}grc.nia.nih.gov

{dagger} The first two authors contributed equally to this work.


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