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Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster
André P. Gerber*,,,
Mark A. Krasnow,¶,
Patrick O. Brown,,¶, and
*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 publication October 25, 2005.
Genome-wide identification of RNAs associated with RNA-bindingproteins is crucial for deciphering posttranscriptional regulatorysystems. PUMILIO is a member of the evolutionary conserved Puf-familyof RNA-binding proteins that repress gene expression posttranscriptionally.We generated transgenic flies expressing affinity-tagged PUMILIOunder the control of an ovary-specific promoter, and we purifiedPUMILIO from whole adult flies and embryos and analyzed associatedmRNAs by using DNA microarrays. Distinct sets comprising hundredsof mRNAs were associated with PUMILIO at the two developmentalstages. Many of these mRNAs encode functionally related proteins,supporting a model for coordinated regulation of posttranscriptionalmodules by specific RNA-binding proteins. We identified a characteristicsequence motif in the 3'-untranslated regions of mRNAs associatedwith PUMILIO, and the sufficiency of this motif for interactionwith PUMILIO was confirmed by RNA pull-down experiments withbiotinylated synthetic RNAs. The RNA motif strikingly resemblesthe one previously identified for Puf3p, one of five Saccharomycescerevisiae Puf proteins; however, proteins encoded by the associatedmRNAs in yeast and Drosophila do not appear to be related. Theresults suggest extensive posttranscriptional regulation byPUMILIO and uncover evolutionary features of this conservedfamily of RNA-binding proteins.
Key Words: DNA microarray posttranscriptional gene regulation RNA-binding protein
Freely available online through the PNAS open access option.
Author contributions: A.P.G., S.L., P.O.B., and D.H. designedresearch; 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.