The SSUP-72/PINN-1 module is required for efficient 3’end processing and coordinates developmental gene expression during exit from diapause in C. elegans [RNAseq-SSUP72]

During the exit from the developmental diapause of Caenorhabditis elegans (C. elegans), a network of growth and developmental genes is activated. These genes are organized into operons, where transcriptional termination is uncoupled from mRNA 3’-end processing. Although the Pol II CTD-S2P mark deposited by CDK-12 is unnecessary during embryogenesis, it plays a critical role in the timely expression of most operonic genes by enhancing SL2 trans-splicing at position 2 and above. This process protects mRNA from degradation and prevents termination. Here, a genetic screen has identified the SSUP-72/PINN-1 module as an effective suppressor of CDK-12-induced defects. Our data show that the SSUP-72/PINN-1 module regulates intra-operon termination and affects 3’ pausing genome-wide, coordinating growth and developmental gene expression during post-embryonic development in C. elegans. SSUP-72[E22K] is a potent suppressor of the L1 arrest induced by the inhibition of CDK-12as. However, little is known about its cellular role. To investigate the implication of the SSUP-72/PINN-1 module in transcription, we conducted RNA-seq on various SSUP-72/PINN-1 mutants. Worms were L1 synchronized and fed for 4H (liquid culture) prior to RNA extraction.