Principles of mRNA control by human Pumilio proteins elucidated from global transcriptome stability, in vitro affinity profiling, and integrative data analysis

ABSTRACT: The human members of the PUF family of proteins, PUM1 and PUM2, are RNA-binding proteins that post-transcriptionally regulate gene expression through binding to a PUM recognition element (PRE) in the 3′ UTR of target mRNAs, promoting RNA decay. Recent RNA-seq experiments in PUM1/2 knockdown conditions have identified hundreds of known and new human PUM targets through measurement of changes in steady state RNA levels. However, steady-state RNA levels do not allow for measurement of changes in RNA stability between conditions and do not allow for the differentiation between the contributions of changes in transcription rates and changes in RNA decay. Here, we identify hundreds of human PUM1/2 targets that have changes in RNA stability following PUM1/2 knockdown. We separate the contributions of changes in transcription rate and RNA stability and find that human PUM proteins almost exclusively modulate RNA abundance through changing RNA stability and not transcription. In addition, we find that the sequence preferences for all possible 8mers are largely similar between PUM1 and PUM2, suggesting that PUM1 and PUM2 recognize similar targets. We identify an ideal PRE “rulebook” by determining key contextual features around PREs, including local AU content, location of a PRE within a 3′ UTR, clustering of PREs, and number of miRNA sites near a PRE, that help differentiate functional PREs from non-functional ones as measured by our decay dataset. Consistent with previously identified functional roles of mammalian PUMs, we find that human PUM1 and PUM2 modulate the decay of genes related to signaling cascades and neuronal function. Finally, we train machine learning models to predict functional regulation of RNA targets by the human PUM proteins and find that contextual features around PREs contribute meaningful information to our models.

ORGANISM(S): Homo sapiens

PROVIDER: GSE145237 | GEO | 2020/08/05

REPOSITORIES: GEO