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PMID: 18959479 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system.

PLoS biology ·Vol. 6 ·No. 10 ·2008-10-28 ·Pages e255

Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO

Abstract

RNA-binding proteins (RBPs) have roles in the regulation of many post-transcriptional steps in gene expression, but relatively few RBPs have been systematically studied. We searched for the RNA targets of 40 proteins in the yeast Saccharomyces cerevisiae: a selective sample of the approximately 600 annotated and predicted RBPs, as well as several proteins not annotated as RBPs. At least 33 of these 40 proteins, including three of the four proteins that were not previously known or predicted to be RBPs, were reproducibly associated with specific sets of a few to several hundred RNAs. Remarkably, many of the RBPs we studied bound mRNAs whose protein products share identifiable functional or cytotopic features. We identified specific sequences or predicted structures significantly enriched in target mRNAs of 16 RBPs. These potential RNA-recognition elements were diverse in sequence, structure, and location: some were found predominantly in 3'-untranslated regions, others in 5'-untranslated regions, some in coding sequences, and many in two or more of these features. Although this study only examined a small fraction of the universe of yeast RBPs, 70% of the mRNA transcriptome had significant associations with at least one of these RBPs, and on average, each distinct yeast mRNA interacted with three of the RBPs, suggesting the potential for a rich, multidimensional network of regulation. These results strongly suggest that combinatorial binding of RBPs to specific recognition elements in mRNAs is a pervasive mechanism for multi-dimensional regulation of their post-transcriptional fate.

MeSH Terms
Databases, Protein Oligonucleotide Array Sequence Analysis Protein Binding Protein Interaction Domains and Motifs RNA, Messenger/metabolism RNA-Binding Proteins/chemistry,genetics,metabolism Saccharomyces cerevisiae Proteins/chemistry,genetics,metabolism Signal Transduction Untranslated Regions/genetics,metabolism
Chemicals
RNA, Messenger RNA-Binding Proteins Saccharomyces cerevisiae Proteins Untranslated Regions
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Hogan Daniel J
Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America.
Riordan Daniel P
Gerber André P
Herschlag Daniel
Brown Patrick O
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Article Info
Journal
PLoS biology
Abbr.
PLoS Biol
ISSN
1545-7885
DOI
10.1371/journal.pbio.0060255
Published
2008-10-28
Pages
e255
Language
English
Region
United States
NLM ID
101183755
PMCID
PMC2573929
Subset
IM
Grants
NCI NIH HHS · R01 CA077097 · United States
NHGRI NIH HHS · T32HG00044 · United States
NCI NIH HHS · R01 CA77097-08 · United States
Howard Hughes Medical Institute · United States
NHGRI NIH HHS · T32 HG000044 · United States
External Links
PubMed source DOI: 10.1371/journal.pbio.0060255 PMC Full Text View journal details
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