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Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast

Anagha Joshi, Yves Van de Peer UGent and Tom Michoel (2011) NUCLEIC ACIDS RESEARCH. 39(21). p.9108-9117
abstract
Post-transcriptional control of mRNA transcript processing by RNA binding proteins (RBPs) is an important step in the regulation of gene expression and protein production. The post-transcriptional regulatory network is similar in complexity to the transcriptional regulatory network and is thought to be organized in RNA regulons, coherent sets of functionally related mRNAs combinatorially regulated by common RBPs. We integrated genome-wide transcriptional and translational expression data in yeast with large-scale regulatory networks of transcription factor and RBP binding interactions to analyze the functional organization of post-transcriptional regulation and RNA regulons at a system level. We found that post-transcriptional feedback loops and mixed bifan motifs are overrepresented in the integrated regulatory network and control the coordinated translation of RNA regulons, manifested as clusters of functionally related mRNAs which are strongly coexpressed in the translatome data. These translatome clusters are more functionally coherent than transcriptome clusters and are expressed with higher mRNA and protein levels and less noise. Our results show how the post-transcriptional network is intertwined with the transcriptional network to regulate gene expression in a coordinated way and that the integration of heterogeneous genome-wide datasets allows to relate structure to function in regulatory networks at a system level.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
NOISE, GENOME-WIDE, SACCHAROMYCES-CEREVISIAE, GENE-EXPRESSION, BINDING PROTEINS, TRANSCRIPTOME, COORDINATION, FEEDBACK, MOTIFS
journal title
NUCLEIC ACIDS RESEARCH
Nucleic Acids Res.
volume
39
issue
21
pages
9108 - 9117
Web of Science type
Article
Web of Science id
000297375700012
JCR category
BIOCHEMISTRY & MOLECULAR BIOLOGY
JCR impact factor
8.026 (2011)
JCR rank
26/286 (2011)
JCR quartile
1 (2011)
ISSN
0305-1048
DOI
10.1093/nar/gkr661
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1986410
handle
http://hdl.handle.net/1854/LU-1986410
date created
2012-01-13 15:47:45
date last changed
2013-02-27 09:11:11
@article{1986410,
  abstract     = {Post-transcriptional control of mRNA transcript processing by RNA binding proteins (RBPs) is an important step in the regulation of gene expression and protein production. The post-transcriptional regulatory network is similar in complexity to the transcriptional regulatory network and is thought to be organized in RNA regulons, coherent sets of functionally related mRNAs combinatorially regulated by common RBPs. We integrated genome-wide transcriptional and translational expression data in yeast with large-scale regulatory networks of transcription factor and RBP binding interactions to analyze the functional organization of post-transcriptional regulation and RNA regulons at a system level. We found that post-transcriptional feedback loops and mixed bifan motifs are overrepresented in the integrated regulatory network and control the coordinated translation of RNA regulons, manifested as clusters of functionally related mRNAs which are strongly coexpressed in the translatome data. These translatome clusters are more functionally coherent than transcriptome clusters and are expressed with higher mRNA and protein levels and less noise. Our results show how the post-transcriptional network is intertwined with the transcriptional network to regulate gene expression in a coordinated way and that the integration of heterogeneous genome-wide datasets allows to relate structure to function in regulatory networks at a system level.},
  author       = {Joshi, Anagha and Van de Peer, Yves and Michoel, Tom},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {NOISE,GENOME-WIDE,SACCHAROMYCES-CEREVISIAE,GENE-EXPRESSION,BINDING PROTEINS,TRANSCRIPTOME,COORDINATION,FEEDBACK,MOTIFS},
  language     = {eng},
  number       = {21},
  pages        = {9108--9117},
  title        = {Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast},
  url          = {http://dx.doi.org/10.1093/nar/gkr661},
  volume       = {39},
  year         = {2011},
}

Chicago
Joshi, Anagha, Yves Van de Peer, and Tom Michoel. 2011. “Structural and Functional Organization of RNA Regulons in the Post-transcriptional Regulatory Network of Yeast.” Nucleic Acids Research 39 (21): 9108–9117.
APA
Joshi, Anagha, Van de Peer, Y., & Michoel, T. (2011). Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast. NUCLEIC ACIDS RESEARCH, 39(21), 9108–9117.
Vancouver
1.
Joshi A, Van de Peer Y, Michoel T. Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast. NUCLEIC ACIDS RESEARCH. 2011;39(21):9108–17.
MLA
Joshi, Anagha, Yves Van de Peer, and Tom Michoel. “Structural and Functional Organization of RNA Regulons in the Post-transcriptional Regulatory Network of Yeast.” NUCLEIC ACIDS RESEARCH 39.21 (2011): 9108–9117. Print.