A global identification of PUM1 and PUM2 mRNA targets and their protein cofactors in human seminoma TCam-2 cells

The functions of human PUM1 and PUM2 are considered to be redundant given that both PUF1 and PUF2 recognize the same PBE motif UGUANAUA. However pools of mRNAs published so far for PUM1 and PUM2 do not overlap. Therefore we sought to investigate the issue of redundancy in human cells. The both PUM proteins are less conserved in the region that is outside the PUM domain. We sought that interactors could be different. We identified mRNA pools binding separately PUM1 and PUM2 by RIP-Seq approach, normalized them using the whole TCam-2 cells transcriptome and aligned them with mRNA pools activated or repressed as tested by siRNA PUM1 and PUM2 knockdown. PUM1 and PUM2-regulated RNAs were studied by RIP-Seq and siRNA-mediated PUM1 or PUM2 knockdown followed by RNA-Seq in TCam-2 cell line. RIP-Seq with non-immunized serum and TCam-2 transcriptome or control non-target siRNA were used as controls for RIP-Seq and RNA-Seq respectively. Each experiment was performed in 3 biological replicates.