title: 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.
authors.affiliation: Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17177, Stockholm, Sweden; Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland.
authors.forename: Suvi
authors.initials: S
authors.lastname: Asikainen
authors.affiliation: A.I. Virtanen Institute, University of Eastern Finland, 70211, Kuopio, Finland; Department of Biological and Environmental Science, University of Jyvaskyla, 40014, Jyvaskyla, Finland.
authors.forename: Liisa
authors.initials: L
authors.lastname: Heikkinen
authors.affiliation: Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland.
authors.forename: Juuso
authors.initials: J
authors.lastname: Juhila
authors.affiliation: Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17177, Stockholm, Sweden.
authors.forename: Frida
authors.initials: F
authors.lastname: Holm
authors.affiliation: Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland.
authors.forename: Jere
authors.initials: J
authors.lastname: Weltner
authors.affiliation: Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland.
authors.forename: Ras
authors.initials: R
authors.lastname: Trokovic
authors.affiliation: Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland.
authors.forename: Milla
authors.initials: M
authors.lastname: Mikkola
authors.affiliation: Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland.
authors.forename: Sanna
authors.initials: S
authors.lastname: Toivonen
authors.affiliation: Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland.
authors.forename: Diego
authors.initials: D
authors.lastname: Balboa
authors.affiliation: Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17177, Stockholm, Sweden.
authors.forename: Riina
authors.initials: R
authors.lastname: Lampela
authors.affiliation: Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland.
authors.forename: Katherine
authors.initials: K
authors.lastname: Icay
authors.affiliation: Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland.
authors.forename: Timo
authors.initials: T
authors.lastname: Tuuri
authors.affiliation: Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, 00014, Helsinki, Finland; Children's Hospital, Helsinki University Central Hospital, 00029, Helsinki, Finland.
authors.forename: Timo
authors.initials: T
authors.lastname: Otonkoski
authors.affiliation: A.I. Virtanen Institute, University of Eastern Finland, 70211, Kuopio, Finland; Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R., China.
authors.forename: Garry
authors.initials: G
authors.lastname: Wong
authors.affiliation: Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17177, Stockholm, Sweden.
authors.forename: Outi
authors.initials: O
authors.lastname: Hovatta
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002460:Cell Line; D019295:Computational Biology; D015870:Gene Expression; D020869:Gene Expression Profiling; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D000066449:Human Embryonic Stem Cells / Q000378:metabolism*; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D035683:MicroRNAs; D058727:RNA, Small Untranslated
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