Regulatory Mechanisms and RNA Targets of Human Pumilio Proteins.

Abstract

Gene expression requires balance between synthesis and decay of mRNAs. Aberrant expression of genes results in disease. PUF proteins are a family of eukaryotic RNA binding regulators characterized by a conserved RNA binding domain that binds 8-12 nucleotide sequence elements, called PREs, in target mRNAs. PUFs are thought to regulate processes including cell proliferation and memory formation. In model organisms, PUFs block translation and enhance deadenylation and mRNA decay. Humans have two PUFs: PUM1 and PUM2. Despite a substantial foundation of knowledge about PUFs in model organisms, the RNA targets of PUMs and mechanisms by which they repress remain unclear. I will present evidence herein that PUM1 and PUM2 are regulators in human cells. PUM1 and PUM2, which exhibit identical RNA binding specificities, employ a conserved mechanism of repression via direct recruitment of the CCR4-NOT deadenylase complex, causing translational inhibition and accelerated mRNA decay. PUMs also repress a non-adenylated mRNA; therefore, PUMs utilize a second, deadenylation-independent repression mechanism. RNAs regulated upon PUM knockdown in human cells were identified in this study and compared with RNAs in the genome that contain at least one PRE and previously classified, bound PUM mRNA targets to yield a dataset of 487 direct PUM targets. Direct PUM target mRNAs encode proteins involved in cancers, signaling, development, and neurological functions. This study demonstrates direct, potent PUM repression in human cells, illuminates mechanisms by which they enact repression, and identifies 487 direct RNA targets of PUM regulation; together revealing PUM regulated pathways in human cell networks.