Human nuclear RNAi-defective 2 (NRDE2) is an essential RNA splicing factor

Abstract

The accurate inheritance of genetic material is a basic necessity in all domains of life and an unexpectedly large number of RNA processing factors are required for mitotic progression and genome stability. NRDE2 (nuclear RNAi defective-2) is an evolutionarily conserved protein originally discovered for its role in nuclear RNA interference (RNAi) and heritable gene silencing in Caenorhabditis elegans (C. elegans). The function of the human NRDE2 gene remains poorly understood. Here we show that human NRDE2 is an essential protein required for suppressing intron retention in a subset of pre-mRNAs containing short, GC-rich introns with relatively weak 5 ′ ′ ′ ′ ′ and 3 ′ ′ ′ ′ ′ splice sites. NRDE2 preferentially interacts with components of the U5 small nuclear ribonucleoprotein (snRNP), the exon junction complex, and the RNA exosome. Interestingly, NRDE2-depleted cells exhibit greatly increased levels of genomic instability and DNA damage, as well as defects in centrosome maturation and mitotic progression. We identify the essential centriolar satellite protein, CEP131, as a direct NRDE2-regulated target. NRDE2 specifically binds to and promotes the efficient splicing of CEP131 pre-mRNA, and depleting NRDE2 dramatically reduces CEP131 protein expression, contributing to impaired recruitment of critical centrosomal proteins (e.g., γ-tubulin and Aurora Kinase A) to the spindle poles during mitosis. Our work establishes a conserved role for human NRDE2 in RNA splicing, characterizes the severe genomic instability phenotypes observed upon loss of NRDE2, and highlights the direct regulation of CEP131 splicing as one of multiple mechanisms through which such phenotypes might be explained.

The SON RNA splicing factor is required for intracellular trafficking structures that promote centriole assembly and ciliogenesis

“…We find that centriolar satellites have an intimate relationship to assembling centrioles, adding to the evidence that centriolar satellites contribute to centriole assembly (Hori et al, 2015). Interestingly, CEP131 has previously been identified as a target of the splicing factor NRDE2 (Jiao et al, 2019), suggesting regulation of CEP131 transcript formation has an important role in centriolar satellite formation and function. Splicing of PCNT pre-mRNA utilizes SON (Ahn et al, 2011).…”

Moonlighting in Mitosis: Analysis of the Mitotic Functions of Transcription and Splicing Factors

“…Reduction of the CEP131 level impairs recruitment of proteins such as AURKA, γ-tubulin, and CEP192 to the centrosomes, and leads to defective chromosome segregation. During mitosis, NRDE2 is diffuse in the cytoplasm and fails to accumulate in any mitotic structure [134].…”

Co-surveillance of ribosomal RNA by the exosome complex and nucleolar RNAi inC. elegans

“…7). Thus, our data suggest a mechanism for nucleolar RNAi: risiRNA-directed cotranscriptional silencing of RNAP I. NRDE-2 is a conserved protein, which is involved in processing of pre-mRNAs in mammalian cells [31–33]. It will be of interest to investigate whether risiRNAs and RNAP I are similarly linked in other metazoans [12].…”