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Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells
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 obtaine...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2644350/ https://www.ncbi.nlm.nih.gov/pubmed/19001483 http://dx.doi.org/10.1093/dnares/dsn030 |
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author | Sharova, Lioudmila V. Sharov, Alexei A. Nedorezov, Timur Piao, Yulan Shaik, Nabeebi Ko, Minoru S.H. |
author_facet | Sharova, Lioudmila V. Sharov, Alexei A. Nedorezov, Timur Piao, Yulan Shaik, Nabeebi Ko, Minoru S.H. |
author_sort | Sharova, Lioudmila V. |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-2644350 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-26443502009-04-13 Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells Sharova, Lioudmila V. Sharov, Alexei A. Nedorezov, Timur Piao, Yulan Shaik, Nabeebi Ko, Minoru S.H. DNA Res Full Papers 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. Oxford University Press 2009-02 2008-11-11 /pmc/articles/PMC2644350/ /pubmed/19001483 http://dx.doi.org/10.1093/dnares/dsn030 Text en Published by Oxford University Press 2008 |
spellingShingle | Full Papers Sharova, Lioudmila V. Sharov, Alexei A. Nedorezov, Timur Piao, Yulan Shaik, Nabeebi Ko, Minoru S.H. Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells |
title | Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells |
title_full | Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells |
title_fullStr | Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells |
title_full_unstemmed | Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells |
title_short | Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells |
title_sort | database for mrna half-life of 19 977 genes obtained by dna microarray analysis of pluripotent and differentiating mouse embryonic stem cells |
topic | Full Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2644350/ https://www.ncbi.nlm.nih.gov/pubmed/19001483 http://dx.doi.org/10.1093/dnares/dsn030 |
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