Database for mRNA half-life of 19,977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells
By Lioudmila V. Sharova, A. Sharov, Timur Nedorezov, Y. Piao, Nabeebi Shaik, M. Ko. DNA Research, 2008
600 citations recorded by the source corpus.
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 hrs and only <100 genes, including Prdm1, Myc, Gadd45g, Foxa2, Hes5, and Trib1, showed half-life less that 1 hr. 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 (ORF) length, and negative correlation with the presence of PUF-binding motifs and AU-rich elements (AREs) 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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/93b5fac726bda3e21e0eaa9747ac3781de6d8081
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Citations in the corpus
- Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. (2010, background): “The magnitude of the decrease observed ( 20%–40%) is consistent with the relatively short duration of inhibitor treatment relative to typical mRNA half-lives of 7 hr in mES cells (Sharova et al., 2009).”
- m6A RNA modification controls cell fate transition in mammalian embryonic stem cells (2014, methodology): “Mouse Pol II occupancy data, mRNA half life and Protein translation efficiency were obtained from (Ingolia et al., 2011; Rahl et al., 2010; Sharova et al., 2009).”