CAPRIN1 links embryonic stem cell differentiation with RNA metabolism

Embryonic stem cells (ESCs) are self-renewing and pluripotent. In recent years, factors controlling pluripotency, mostly nuclear, have been identified. To reveal non-nuclear regulators of ESCs, we screened an endogenously-labelled fluorescent fusion-protein library in mouse ESCs. One of the more compelling hits was the cell cycle-associated protein, CAPRIN1. CAPRIN1, a Stress Granule (SG) component, exhibited a strikingly cyclical localization pattern in sync with mitosis, and localized to SGs, in response to stress. CAPRIN1 knockout had little effect in ESCs, but dramatically skewed differentiation and gene expression programs. RIP-seq and SLAM-seq revealed that CAPRIN1 associates with, and promotes the degradation of, thousands of RNA transcripts. CAPRIN1 interactome identified XRN2 as the likely ribonuclease. Upon early differentiation or stress, XRN2 colocalizes with CAPRIN1 inside SGs in a CAPRIN1-dependent manner. We propose that CAPRIN1 regulates an RNA degradation pathway operating during early ESC differentiation, eliminating undesired spuriously transcribed transcripts in ESCs. Overall design: 1. RIP-seq for CAPRIN1-pulldown followed by RNA-seq of Total RNA. 2. RNA-seq in WT and Caprin1-KO partially differentiated ESCs (4d RA) treated with a-amanitin for 0, 2, 4 and 8 hrs.