Post-transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq

Abstract

There is a growing body of evidence about the presence and the activity of the miRISC in the nucleus of mammalian cells. Here, we show by quantitative proteomic analysis that Ago2 interacts with the nucleoplasmic protein Sfpq in an RNA-dependent fashion. By a combination of HITS-CLIP and transcriptomic analyses, we demonstrate that Sfpq directly controls the miRNA targeting of a subset of binding sites by local binding. Sfpq modulates miRNA targeting in both nucleoplasm and cytoplasm, indicating a nucleoplasmic commitment of Sfpq-target mRNAs that globally influences miRNA modes of action. Mechanistically, Sfpq binds to a sizeable set of long 3′UTRs forming aggregates to optimize miRNA positioning/recruitment at selected binding sites, including let-7a binding to Lin28A 3′UTR. Our results extend the miRNA-mediated post-transcriptional gene silencing into the nucleoplasm and indicate that an Sfpq-dependent strategy for controlling miRNA activity takes place in cells, contributing to the complexity of miRNA-dependent gene expression control.

The RNA–RNA base pairing potential of human Dicer and Ago2 proteins

“…PUM1, by binding to its target sites, has been shown to induce a local change in RNA structure, which, in consequence, exposes specific miRNA binding sequence within 3′-UTRs [41]. Sfpq, a functionally versatile DNA-and RNA-binding protein, preferentially binds to long 3′-UTRs harboring multiple copies of Sfpq-binding motifs and promotes, presumably by modulating the secondary structure of a miRNA target, optimal positioning of miRNA-loaded RISC [42]. Nevertheless, other RBPs, such as Deadend 1 [43,44], RNA-binding motif protein 38 [45] and coding region determinant-binding protein [46,47], may limit the accessibility of miRNA targets by competitive binding within mRNAs.…”

Transcriptional memory in skeletal muscle. Don't forget (to) exercise

“…However, there is accumulating evidence that some fraction of mammalian miRNAs may also execute important nuclear regulatory functions by controlling gene expression in the nucleus at both transcriptional and posttranscriptional levels, as well as by affecting alternative splice site selection (Roberts, 2014). In a set of elegant experiments, a significant fraction of miRNAs and several RISC components, including AGOs, have been identified to become located and functionally operative within the nucleus of human cells (Avivi et al, 2017; Bottini et al, 2017; Castanotto et al, 2018; Gagnon, Li, Chu, Janowski, & Corey, 2014; Ohrt et al, 2008; Sarshad et al, 2018; Weinmann et al, 2009). Nuclear localized miRNAs were found capable both to suppress and to stimulate transcriptional expression at distinct gene loci, involving direct and indirect interference pathways.…”

Silica nanoparticles inducing the apoptosis of spermatocyte cell through microRNA-450b-3p targeting MTCH2-mediating mitochondrial signaling pathway

“…We found that the combination of the mir-450b-3p and MTCH2 is 6mer and identi ed its binding region on the chromosome. Bottini et al veri ed the targeting relationship between the mir-450b-3p and MTCH2, through the Ago-CLIP experiment (21). To verify the relationship between the miR-450b-3p and MTCH2,we rstly examined the levels of miR-450b-3p and MTCH2 mRNA in testis by RT-PCR.…”