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

TL;DR

NRDE2 interacts with transcription and splicing complexes in human cells and affects gene expression on a large scale.

Contribution

NRDE2's interaction with transcription elongation complexes and its broader impact on RNA processing are newly identified.

Findings

NRDE2 interacts with chromatin-associated transcription factors like the PAF1 complex and elongating RNA polymerase II.

Depletion of NRDE2 leads to widespread changes in gene expression and increased intron retention.

Intron retention caused by NRDE2 loss is often linked to reduced mRNA levels.

Abstract

NRDE2 is a highly conserved protein implicated in post-transcriptional gene silencing in Schizosaccharomyces pombe and Caenorhabditis elegans and has been shown to modulate splicing in mammals. To explore whether NRDE2 participates in additional processes in human cells, we performed tandem affinity purification followed by proteomic analysis of NRDE2 from nuclear extracts of HEK293T and HeLa cells. Our analysis confirmed the interaction of NRDE2 with its well-characterized partner, the MTR4 helicase (MTREX), as well as with multiple splicing factors. Notably, we also identified interactions with chromatin-associated proteins involved in transcription, including the Polymerase-Associated Factor 1 (PAF1) complex and elongating forms of RNA polymerase II (RNAPII). To further investigate NRDE2 function, we conducted RNA-seq following its transient depletion. Differential expression analysis revealed that loss of NRDE2 alters the expression of thousands of genes. Consistent with earlier reports, we observed splicing defects, particularly intron retention; however, our results indicate that the impact of NRDE2 on intron retention is more extensive than previously recognized. Moreover, intron retention was frequently associated with reduced mRNA expression. Together, these findings suggest that NRDE2 associates with both transcriptional and splicing machineries and plays a broader role in RNA processing than previously appreciated.

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