Selective MicroRNA-Offset RNA Expression in Human Embryonic Stem Cells

Abstract

Small RNA molecules, including microRNAs (miRNAs), play critical roles in regulating pluripotency, proliferation and differentiation of embryonic stem cells. miRNA-offset RNAs (moRNAs) are similar in length to miRNAs, align to miRNA precursor (pre-miRNA) loci and are therefore believed to derive from processing of the pre-miRNA hairpin sequence. Recent next generation sequencing (NGS) studies have reported the presence of moRNAs in human neurons and cancer cells and in several tissues in mouse, including pluripotent stem cells. In order to gain additional knowledge about human moRNAs and their putative development-related expression, we applied NGS of small RNAs in human embryonic stem cells (hESCs) and fibroblasts. We found that certain moRNA isoforms are notably expressed in hESCs from loci coding for stem cell-selective or cancer-related miRNA clusters. In contrast, we observed only sparse moRNAs in fibroblasts. Consistent with earlier findings, most of the observed moRNAs derived from conserved loci and their expression did not appear to correlate with the expression of the adjacent miRNAs. We provide here the first report of moRNAs in hESCs, and their expression profile in comparison to fibroblasts. Moreover, we expand the repertoire of hESC miRNAs. These findings provide an expansion on the known repertoire of small non-coding RNA contents in hESCs.

MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data

“…To evaluate miR&moRe2 performance, we applied our method to three datasets from previous studies on human cell samples in which (i) moRNAs were detected, validated and studied (ASI dataset) [14], (ii) moRNAs were considered and explicitly mentioned (BUR dataset) [20], and (iii) sequences derived from miRNA precursor flanking regions were detected (MAV dataset) [29] (Table 1). Considering the datasets together,~8% of miRNA-expressing precursors expressed at least one moRNA.…”

“…Since their discovery, moRNAs have been detected in different organisms [3,[5][6][7][8][9][10], including humans [11][12][13][14][15][16][17]. MoRNAs are characterized by high sequence conservation [18] and have been Novel miRNAs are inferred from the known miRNA complementary sequence projected on the precursor, according to the secondary structure hairpin-like folding.…”

“…Results demonstrate that miR&moRe2 is a valid tool for a comprehensive study of small RNAs generated from microRNA precursors and could help to investigate their biogenesis and function. demonstrated to be functional RNAs [14], potentially having an miRNA-like regulative effect [5]. Moreover, it has been shown that moRNA expression can vary between different phenotypes in mammals [19] and is deregulated in human disease [15,17].…”

“…Although moRNA biogenesis has not yet been fully elucidated, it has been hypothesized that moRNAs may originate by alternative Drosha/DGCR8-mediated processing of the pre-miRNA hairpins [15,20]. Besides, moRNA expression can be independent from, or compete with, the adjacent miRNA [14,21].To detect moRNAs, most authors had to devise custom bioinformatics procedures that analyzed the sRNA-seq data left uncharacterized by the existing software tools. To date, no tool that explicitly characterizes moRNAs, miRNAs, and isomiRs from sRNA-seq data is publicly and freely available to the scientific community [2].…”

“…Although moRNA biogenesis has not yet been fully elucidated, it has been hypothesized that moRNAs may originate by alternative Drosha/DGCR8-mediated processing of the pre-miRNA hairpins [15,20]. Besides, moRNA expression can be independent from, or compete with, the adjacent miRNA [14,21].…”