Argonaute binding within human nuclear RNA and its impact on alternative splicing

YONGJUN CHU, SHINNICHI YOKOTA, JING LIU, AUDRIUS KILIKEVICIUS, KRYSTAL C. JOHNSON, DAVID R. COREY

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Mammalian RNA interference (RNAi) is often linked to the regulation of gene expression in the cytoplasm. Synthetic RNAs, however, can also act through the RNAi pathway to regulate transcription and splicing. While nuclear regulation by synthetic RNAs can be robust, a critical unanswered question is whether endogenous functions for nuclear RNAi exist in mammalian cells. Using enhanced crosslinking immunoprecipitation (eCLIP) in combination with RNA sequencing (RNA-seq) and multiple AGO knockout cell lines, we mapped AGO2 protein binding sites within nuclear RNA. The strongest AGO2 binding sites were mapped to micro RNAs (miRNAs). The most abundant miRNAs were distributed similarly between the cytoplasm and nucleus, providing no evidence for mechanisms that facilitate localization of miRNAs in one compartment versus the other. Beyond miRNAs, most statistically significant AGO2 binding was within introns. Splicing changes were confirmed by RT-PCR and recapitulated by synthetic miRNA mimics complementary to the sites of AGO2 binding. These data support the hypothesis that miRNAs can control gene splicing. While nuclear RNAi proteins have the potential to be natural regulatory mechanisms, careful study will be necessary to identify critical RNA drivers of normal physiology and disease.

Original languageEnglish (US)
Pages (from-to)991-1003
Number of pages13
JournalRNA
Volume27
Issue number9
DOIs
StatePublished - Sep 2021

Keywords

  • Argonaute
  • MiRNA
  • Micro RNA
  • RNA
  • RNA interference
  • RNAi

ASJC Scopus subject areas

  • Molecular Biology

Fingerprint

Dive into the research topics of 'Argonaute binding within human nuclear RNA and its impact on alternative splicing'. Together they form a unique fingerprint.

Cite this