Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human cartilage–hair hypoplasia

Abstract

Post-transcriptional processing of some long non-coding RNAs (lncRNAs) reveals that they are a source of miRNAs. We show that the 268-nt non-coding RNA component of mitochondrial RNA processing endoribonuclease, (RNase MRP), is the source of at least two short (∼20 nt) RNAs designated RMRP-S1 and RMRP-S2, which function as miRNAs. Point mutations in RNase MRP cause human cartilage-hair hypoplasia (CHH), and several disease-causing mutations map to RMRP-S1 and -S2. SHAPE chemical probing identified two alternative secondary structures altered by disease mutations. RMRP-S1 and -S2 are significantly reduced in two fibroblast cell lines and a B-cell line derived from CHH patients. Tests of gene regulatory activity of RMRP-S1 and -S2 identified over 900 genes that were significantly regulated, of which over 75% were down-regulated, and 90% contained target sites with seed complements of RMRP-S1 and -S2 predominantly in their 3' UTRs. Pathway analysis identified regulated genes that function in skeletal development, hair development and hematopoietic cell differentiation including PTCH2 and SOX4 among others, linked to major CHH phenotypes. Also, genes associated with alternative RNA splicing, cell proliferation and differentiation were highly targeted. Therefore, alterations RMRP-S1 and -S2, caused by point mutations in RMRP, are strongly implicated in the molecular mechanism of CHH.

Identification and Diagnostic Performance of a Small RNA within the PCA3 and BMCC1 Gene Locus That Potentially Targets mRNA

“…27). Recently, Rogler and colleagues reported that RNase MRP (a 268 bp noncoding RNA component of mitochondrial RNA processing endoribonuclease) was the source for two short (around 20 bp) RNAs important in the biology of cartilage-hair hypoplasia (13). As such, we hypothesized that one role for PCA3 could be as a source for short biologically active species.…”

“…The GENCODE consortium recently annotated 9,277 lncRNA genes, corresponding to 14,880 transcripts (11). In contrast with protein coding genes, lncRNAs typically have few gene exons, can be processed into active short species (12)(13)(14), and are not conserved from primitive species (15). As no functional role for PCA3 has been assigned to date, we wondered whether this ncRNA might encode an active shorter species.…”

Targeted CRISPR disruption reveals a role for RNase MRP RNA in human preribosomal RNA processing

“…S1F). While it is intriguing that an siRNA targeting the ncRNA subunit of RNase MRP would also target the messages for its protein subunits and that microRNAs (miRNAs) derived from the MRP RNA locus closely overlap the siRNA sequence examined here (Rogler et al 2014), this reagent's effect was too pleiotropic to examine MRP RNA-specific function and was not pursued further.…”

Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure

“…human disease phenotypes (Halvorsen et al 2010;Martin et al 2012;Jafarifar et al 2014;Rogler et al 2014;Kutchko et al 2015). However, it is likely that the vast majority of natural and somatic genetic variation is phenotypically benign.…”