Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells
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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.
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PPARγ-3'UTR contains several ARE1 and ARE4 sites and a potential miR-27a/b binding site.
“In silico analysis showed several ARE 1 (AUUUA) and ARE 4 (12-mer A/U, max.one mismatch) sites (33) as well as a potential miR-27a/b binding site.”
From MicroRNA-27b Contributes to Lipopolysaccharide-mediated Peroxisome Proliferator-activated Receptor γ (PPARγ) mRNA Destabilization (2010) · cites this paper as [33]
The Results and discussion section (Multivariate analysis of gene structural features; page unavailable) defines ARE1 as AUUUA and ARE4 as A/U 12-mers with no more than one mismatch. It does not report that several such sites occur in the PPARγ 3′-UTR. The miR-27a/b clause follows citation (33) and is not assessed as attributed to this source. (LLM, conf=0.84)
Experimental — accuracy not yet measuredThe gene ontology result matches earlier observations in mouse embryonic stem cells, supporting the validity of the experiment.
“This result is in agreement with that previously observed in mESCs 54,55 , thus suggesting the bona fide of the experiment.”
From Intragenic DNA methylation prevents spurious transcription initiation (2017) · cites this paper as [54]
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- Authors
- Sharova, L. V., Sharov, A. A., Nedorezov, T., Piao, Y., Shaik, N., & Ko, M. S. H.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Ko, M. S.H.
- Venue
- DNA Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-01-08
- Volume
- 16
- Issue
- 1
- Pages
- 45-58
- ISSN
- 1340-2838 (ISSN-L)
- 1756-1663
- PMC
- PMC2644350
- OpenAlex
- W2106014350
- Cited by
- 591
- References
- 57
- Citations by year
- 2026: 20 · 2025: 28 · 2024: 42 · 2023: 40 · 2022: 39 · 2021: 42 · 2020: 37 · 2019: 35 · 2018: 36 · 2017: 38 · 2016: 33 · 2015: 43 · 2014: 40 · 2013: 31 · 2012: 30
- FWCI
- 7.82
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- DNA Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute on Aging (Z01AG000656)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- mRNA half-life, mRNA stability, mouse embryonic stem cells, pluripotency, cell differentiation, gene expression regulation, exon-exon junctions, AU-rich elements, 3' untranslated region, CpG, 5' untranslated region, transcription factors, steady-state mRNA levels
- MeSH terms
- Animals, Cell Differentiation, Cells, Cultured, Half-Life, Humans, Mice, Inbred C57BL, Mice, Inbred Strains, RNA, Messenger, Oligonucleotide Array Sequence Analysis, 3' Untranslated Regions, Gene Expression Profiling, RNA Stability, Databases, Genetic, Pluripotent Stem Cells, Mice, Embryonic Stem Cells
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