Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins

• Published in: Nucleic acids research Vol. 38; no. 22; pp. 8039 - 8050
• Main Authors: Cridge, Andrew G, Castelli, Lydia M, Smirnova, Julia B, Selley, Julian N, Rowe, William, Hubbard, Simon J, McCarthy, John E G, Ashe, Mark P, Grant, Christopher M, Pavitt, Graham D
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.12.2010
• Subjects: Amino Acids - metabolism; Cyclins - genetics; Eukaryotic Initiation Factors - genetics; Eukaryotic Initiation Factors - physiology; Gene Deletion; Gene Expression Regulation, Fungal; Gene Regulation, Chromatin and Epigenetics; Nitrogen - metabolism; Oligonucleotide Array Sequence Analysis; Protein Biosynthesis; RNA, Messenger - metabolism; RNA-Binding Proteins - metabolism; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - growth & development; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - physiology; Transcription Factors - genetics; Transcription Factors - physiology; Transcription, Genetic
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkq686

eIF4E-binding proteins (4E-BPs) regulate translation of mRNAs in eukaryotes. However the extent to which specific mRNA targets are regulated by 4E-BPs remains unknown. We performed translational profiling by microarray analysis of polysome and monosome associated mRNAs in wild-type and mutant cells to identify mRNAs in yeast regulated by the 4E-BPs Caf20p and Eap1p; the first-global comparison of 4E-BP target mRNAs. We find that yeast 4E-BPs modulate the translation of >1000 genes. Most target mRNAs differ between the 4E-BPs revealing mRNA specificity for translational control by each 4E-BP. This is supported by observations that eap1Δ and caf20Δ cells have different nitrogen source utilization defects, implying different mRNA targets. To account for the mRNA specificity shown by each 4E-BP, we found correlations between our data sets and previously determined targets of yeast mRNA-binding proteins. We used affinity chromatography experiments to uncover specific RNA-stabilized complexes formed between Caf20p and Puf4p/Puf5p and between Eap1p and Puf1p/Puf2p. Thus the combined action of each 4E-BP with specific 3'-UTR-binding proteins mediates mRNA-specific translational control in yeast, showing that this form of translational control is more widely employed than previously thought.