Variant U1 snRNAs are implicated in human pluripotent stem cell maintenance and neuromuscular disease

Abstract

The U1 small nuclear (sn)RNA (U1) is a multifunctional ncRNA, known for its pivotal role in pre-mRNA splicing and regulation of RNA 3′ end processing events. We recently demonstrated that a new class of human U1-like snRNAs, the variant (v)U1 snRNAs (vU1s), also participate in pre-mRNA processing events. In this study, we show that several human vU1 genes are specifically upregulated in stem cells and participate in the regulation of cell fate decisions. Significantly, ectopic expression of vU1 genes in human skin fibroblasts leads to increases in levels of key pluripotent stem cell mRNA markers, including NANOG and SOX2. These results reveal an important role for vU1s in the control of key regulatory networks orchestrating the transitions between stem cell maintenance and differentiation. Moreover, vU1 expression varies inversely with U1 expression during differentiation and cell re-programming and this pattern of expression is specifically de-regulated in iPSC-derived motor neurons from Spinal Muscular Atrophy (SMA) type 1 patient's. Accordingly, we suggest that an imbalance in the vU1/U1 ratio, rather than an overall reduction in Uridyl-rich (U)-snRNAs, may contribute to the specific neuromuscular disease phenotype associated with SMA.

Transcriptional analysis supports the expression of human snRNA variants and reveals U2 snRNA homeostasis by an abundant U2 variant

“…In a mouse model of spinal muscular atrophy caused by decreased levels of SMN, a snRNP assembly factor, snRNA levels change in a tissue-specific manner (Zhang et al, 2008). Human iPS cells from spinal muscular atrophy (SMA) patients displayed dysregulation in the ratio of variant U1 to canonical U1 snRNAs (Vazquez-Arango et al, 2016). Our model suggests these findings could be due tissue-specific expression of variant snRNAs and their sensitivity to modulation in snRNP assembly factors.…”

“…The compensatory increase in canonical U2-1 upon U2-2 knockout might have been predicted when considering that introducing human U1 to mouse cells did not increase overall U1 levels (Mangin et al, 1985), and in differentiating cells canonical and variant U1 snRNAs are inversely expressed (Vazquez-Arango et al, 2016). It has also been observed that variant U1 sequences are able to bind multiple components of U1 snRNP but are out-competed by the canonical U1 snRNA (Somarelli et al, 2014).…”

“…Although the snRNA sequences are greatly divergent, the minor spliceosome could be considered an example of low abundance snRNA variants affecting the splicing of specific introns. Recent knock down of a variant U1, RNVU1-8 expressed in HeLa cells, altered levels of specific transcripts, whereas its ectopic expression in human skin fibroblasts led to an increase in two critical stem cell markers, Nanog and SOX2 (O'Reilly et al, 2013;Vazquez-Arango et al, 2016). Despite being proposed at the time of the discovery of snRNA variants, such investigation into mechanisms through which variant snRNAs might regulate alternative splicing has been limited.…”

Cutting a Long Intron Short: Recursive Splicing and Its Implications

“…We have also come to find out that the human genome encodes a large number of “variant” U1 snRNAs (Kyriakopoulou et al, 2006; O'Reilly et al, 2013). Their expression is markedly higher in primary, embryonic, and pluripotent cells (O'Reilly et al, 2013; Kelly et al, 2015; Vazquez-Arango et al, 2016) and they are able to form proper RNPs in vitro (Somarelli et al, 2014). In endothelial cells, the repertoire of expressed variant U1, together with the minor spliceosome (Turunen et al, 2013), would suffice for the recognition of the vast majority of all non-canonical RS donor dinucleotides recorded (Kelly et al, 2015).…”

A guide to naming human non‐coding RNA genes

“…The snRNA vU1.8, encoded by RNVU1‐8 , has been shown to be capable of processing the 3′ end of pre‐mRNAs expressed from a subset of target genes (O'Reilly et al , ). Moreover, snRNAs encoded by RNVU1‐3 , RNVU1‐8 and RNVU1‐20 are implicated in stem cell maintenance and neuromuscular disease (Vazquez‐Arango et al , ).…”