Conserved principles of mammalian transcriptional regulation revealed by RNA half-life
Open Access
- 26 June 2009
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 37 (17), e115
- https://doi.org/10.1093/nar/gkp542
Abstract
RNA levels in a cell are regulated by the relative rates of RNA synthesis and decay. We recently developed a new approach for measuring both RNA synthesis and decay in a single experimental setting by biosynthetic labeling of newly transcribed RNA. Here, we show that this provides measurements of RNA half-lives from microarray data with a so far unreached accuracy. Based on such measurements of RNA half-lives for human B-cells and mouse fibroblasts, we identified conserved regulatory principles for a large number of biological processes. We show that different regulatory patterns between functionally similar proteins are characterized by differences in the half-life of the corresponding transcripts and can be identified by measuring RNA half-life. We identify more than 100 protein families which show such differential regulatory patterns in both species. Additionally, we provide strong evidence that the activity of protein complexes consisting of subunits with overall long transcript half-lives can be regulated by transcriptional regulation of individual key subunits with short-lived transcripts. Based on this observation, we predict more than 100 key regulatory subunits for human complexes of which 28% could be confirmed in mice (P < 10−9). Therefore, this atlas of transcript half-lives provides new fundamental insights into many cellular processes.Keywords
This publication has 46 references indexed in Scilit:
- TU-tagging: cell type–specific RNA isolation from intact complex tissuesNature Methods, 2009
- Ensembl 2009Nucleic Acids Research, 2008
- The BCL-2 protein family: opposing activities that mediate cell deathNature Reviews Molecular Cell Biology, 2008
- Genome-Wide Analysis of mRNA Decay Rates and Their Determinants inArabidopsis thalianaPlant Cell, 2007
- CORUM: the comprehensive resource of mammalian protein complexesNucleic Acids Research, 2007
- Microarray analysis of newly synthesized RNA in cells and animalsProceedings of the National Academy of Sciences of the United States of America, 2007
- The mouse genome database (MGD): new features facilitating a model systemNucleic Acids Research, 2006
- Activation of Bak, Bax, and BH3-only Proteins in the Apoptotic Response to DoxorubicinPublished by Elsevier BV ,2002
- Proapoptotic BAX and BAK: A Requisite Gateway to Mitochondrial Dysfunction and DeathScience, 2001
- HuR and mRNA stabilityCellular and Molecular Life Sciences, 2001