Transcriptome-wide identification and target analysis of the Pumilio family of RNA binding proteins

In this study, we identified the transcriptome-wide direct RNA target sites of the entire family of Pumilio proteins in the budding yeast Saccharomyces cerevisiae by deep sequencing of RNA regions bound by each of six Pumilio proteins. As a family, the Pumilio proteins of yeast interact with over half of the entire transcriptome. Computational analysis of Pumilio target sites reveal striking differences in mRNA stability, gene set categories, and response to nutrient deprivation conditions based on features of Pumilio binding. Some of these features include variations in primary sequence motif and presence of predicted structured RNA hairpins. Puf6p also binds snoRNAs. Overall design: Sequencing of RNAs bound by Puf1/2/4/5/6.