NRDE2 Interacts with an Early Transcription Elongation Complex and Widely Impacts Gene Expression

NRDE2 is a highly conserved protein that is implicated in post-transcriptional gene silencing in S. pombe and C. elegans while in mammals, it has been shown to modulate splicing. To determine whether NRDE2 may be implicated in other processes in humans, we performed tandem affinity purification followed by proteomic analysis of NRDE2 from nuclear extracts in HEK293T and HeLa cells. Our data show that, in addition to its well-characterized partner, MTR4 helicase (MTREX), as well as several splicing factors, NRDE2 also interacts with chromatin-associated factors involved in transcription, including the Polymerase-Associated Factor 1 (PAF1) complex and elongating forms of RNA polymerase II (RNAPII). To further investigate the function of NRDE2 in gene expression, we performed RNA-seq following its transient depletion. Differential expression analysis showed that loss of NRDE2 modulated the expression of thousands of genes. While effects on splicing, including intron retention, were detected, as described previously, our analysis revealed that the impact of NRDE2 on intron retention is more widespread than previously thought. Moreover, intron retention was also highly associated with down-regulation of mRNA expression. Taken together, these results suggest that NRDE2 associates with the transcription and splicing machineries and affects RNA processing.