PUF partner interactions at a conserved interface shape the RNA binding landscape and cell fate

Protein-RNA regulatory networks underpin much of biology. C. elegans FBF-2, a PUF RNA-binding protein, binds over 1000 RNAs to govern stem cells and differentiation. FBF-2 interacts with multiple protein partners via a key tyrosine, Y479. Here we investigate the in vivo significance of partnerships using a Y479A mutant. Y479A occupancy increases or decreases at specific sites across the transcriptome, varying with the RNA, and shifts from 3’UTRs to other regions. Germline development also changes in a very specific fashion: Y479A abolishes one FBF-2 function – the sperm to oocyte cell fate switch. Y479A changes to regulation of one mRNA, gld-1, are critical to this fate change, though other network changes are also important. FBF-2 switches from repression to activation of gld-1 RNA, likely by distinct FBF-2 partnerships. The role of partnerships in governing RNA regulatory networks will extend broadly, including for human health and disease, as protein partnerships pervade RNA control. Enhanced crosslinking and immunoprecipitation (eCLIP) followed by sequencing was used to determine the occupancy of wild-type FBF-2 and FBF-2(Y479A) on RNA targets in the germline of C. elegans. 4 biological replicates of each genotype were obtained (IP samples) as well as their corresponding size-matched input control (SMI).