Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster

doi:10.1073/pnas.0509260103

Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster

*Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland;
^†Department of Biochemistry and
^¶Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305; and
^§Department of Genetics, University of Bayreuth, 95440 Bayreuth, Germany

Edited by Christine Guthrie, University of California, San Francisco, CA, and approved February 1, 2006 (received for review October 25, 2005)

Abstract

Genome-wide identification of RNAs associated with RNA-binding proteins is crucial for deciphering posttranscriptional regulatory systems. PUMILIO is a member of the evolutionary conserved Puf-family of RNA-binding proteins that repress gene expression posttranscriptionally. We generated transgenic flies expressing affinity-tagged PUMILIO under the control of an ovary-specific promoter, and we purified PUMILIO from whole adult flies and embryos and analyzed associated mRNAs by using DNA microarrays. Distinct sets comprising hundreds of mRNAs were associated with PUMILIO at the two developmental stages. Many of these mRNAs encode functionally related proteins, supporting a model for coordinated regulation of posttranscriptional modules by specific RNA-binding proteins. We identified a characteristic sequence motif in the 3′-untranslated regions of mRNAs associated with PUMILIO, and the sufficiency of this motif for interaction with PUMILIO was confirmed by RNA pull-down experiments with biotinylated synthetic RNAs. The RNA motif strikingly resembles the one previously identified for Puf3p, one of five Saccharomyces cerevisiae Puf proteins; however, proteins encoded by the associated mRNAs in yeast and Drosophila do not appear to be related. The results suggest extensive posttranscriptional regulation by PUMILIO and uncover evolutionary features of this conserved family of RNA-binding proteins.

Footnotes

^‡To whom correspondence may be addressed. E-mail: herschla{at}cmgm.stanford.edu, pbrown{at}cmgm.stanford.edu, or andre.gerber{at}pharma.ethz.ch
Author contributions: A.P.G., S.L., P.O.B., and D.H. designed research; A.P.G. and S.L. performed research; A.P.G., S.L., M.A.K., P.O.B., and D.H. contributed new reagents/analytic tools; A.P.G., S.L., and D.H. analyzed data; and A.P.G., S.L., M.A.K., P.O.B., and D.H. wrote the paper.
Conflict of interest statement: No conflicts declared.
This paper was submitted directly (Track II) to the PNAS office.
Data deposition: The microarray data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession nos. GSE3580 –GSE3582).
Abbreviations:

RBP,

RNA-binding protein;

PumHD,

Pum-homology domain;

NRE,

nanos-response element;

FDR,

false discovery rate;

GO,

gene ontology;

TAP,

tandem affinity purification
Freely available online through the PNAS open access option.