Selective microRNA-Offset RNA expression in human embryonic stem cells.

Suvi Asikainen,Timo Tuuri,Jere Weltner,Liisa Heikkinen,Timo Otonkoski,Milla Mikkola,Riina Lampela,Juuso Juhila,Outi Hovatta,Frida Holm,Diego Balboa,Sanna Toivonen,Katherine Icay,Garry Wong,Ras Trokovic,Fabio Martelli

doi:10.1371/journal.pone.0116668

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.

Highlights

Human embryonic stem cells are pluripotent cells derived from the inner cell mass of blastocyst stage embryos, which can be indefinitely maintained in culture [1,2,3]
We found that certain miRNA-offset RNAs (moRNAs) isoforms are notably expressed in human embryonic stem cells (hESCs) from loci coding for stem cell-selective or cancer-related miRNA clusters
We report here that moRNAs are notably expressed in hESCs and show that hESC moRNAs with highest expression levels are represented by a common length isoform in distinct hESC lines

Summary

Introduction

Human embryonic stem cells (hESC) are pluripotent cells derived from the inner cell mass of blastocyst stage embryos, which can be indefinitely maintained in culture [1,2,3]. The pluripotency, proliferation, and differentiation of hESCs are influenced by transcription factors that mediate their actions in concert with miRNAs, small endogenous RNAs processed by RNAse III endonucleases Dicer and Drosha [4,5,6,7,8]. With the ability of a single miRNA to regulate. PLOS ONE | DOI:10.1371/journal.pone.0116668 March 30, 2015

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