Nucleic Acids Research Advance Access originally published online on June 26, 2009
Nucleic Acids Research 2009 37(17):e115; doi:10.1093/nar/gkp542
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2009, Vol. 37, No. 17 e115
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Methods Online |
Conserved principles of mammalian transcriptional regulation revealed by RNA half-life
1Institute for Informatics, Ludwig-Maximilians-Universität München, Munich 80333 and 2Max von Pettenkofer-Institute, Ludwig-Maximilians-Universität München, Munich 80337, Germany
*To whom correspondence should be addressed. Tel: +49-89-2180-4056; Fax: +49-89-2180-4054; Email: caroline.friedel{at}bio.ifi.lmu.de Correspondence may also be addressed to Dr Lars Dölken. Tel: +49-89-5160-5290; Fax: +49-89-5160-5292; Email: doelken{at}mvp.uni-muenchen.de
Received May 13, 2009. Revised June 8, 2009. Accepted June 9, 2009.
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.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. Ruepp, B. Waegele, M. Lechner, B. Brauner, I. Dunger-Kaltenbach, G. Fobo, G. Frishman, C. Montrone, and H.-W. Mewes CORUM: the comprehensive resource of mammalian protein complexes--2009 Nucleic Acids Res., November 1, 2009; (2009) gkp914v1. [Abstract] [Full Text] [PDF]
|
|