Human Pumilio proteins, PUM1 and PUM2, are sequence specific RNA-binding proteins that regulate protein expression. We used RNA-seq, rigorous statistical testing and an experimentally derived fold change cut-off to identify nearly 1000 target RNAs––including mRNAs and non-coding RNAs––that are functionally regulated by PUMs. Bioinformatic analysis defined a PUM Response Element (PRE) that was significantly enriched in transcripts that increased in abundance and matches the PUM RNA-binding consensus. We created a computational model that incorporates PRE position and frequency within an RNA relative to the magnitude of regulation. The model reveals significant correlation of PUM regulation with PREs in 3 untranslated regions (UTRs), coding sequences and noncoding RNAs, but not 5 UTRs. To define direct, high confidence PUM targets, we cross-referenced PUM-regulated RNAs with all PRE-containing RNAs and experimentally defined PUM-bound RNAs. The results define nearly 300 direct targets that include both PUM-repressed and, surprisingly, PUM-activated target RNAs. Annotation enrichment analysis reveal that PUMs regulate genes from multiple signaling pathways and developmental and neurological processes. Moreover, PUM target mRNAs impinge on human disease genes linked to cancer, neurological disorders and cardiovascular disease. These discoveries pave the way for determining how the PUM-dependent regulatory network impacts biological functions and disease states.
Bibliographical noteFunding Information:
American Cancer Society Research Scholar Grant [RSG-13–080-01-RMC to A.C.G.]; National Institute of General Medical Sciences, National Institutes of Health [R01GM105707 to A.C.G., R00GM097033 to P.L.F.]; University of Michigan Center for Genetics and Genomics Pilot Feasibility Grant (to A.C.G., T.L.S.); Promega Corporation; Michigan Predoctoral Training Program in Cellular Biotechnology through NIH National Research Service Award [5T32GM008353 to J.A.B.]. Funding for open access charge: Institutional Funds from the University of Minnesota. Conflict of interest statement. None declared.