title: Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans.
abstract: We have recently shown that transcription initiation RNAs (tiRNAs) are derived from sequences immediately downstream of transcription start sites. Here, using cytoplasmic and nuclear small RNA high-throughput sequencing datasets, we report the identification of a second class of nuclear-specific approximately 17- to 18-nucleotide small RNAs whose 3' ends map precisely to the splice donor site of internal exons in animals. These splice-site RNAs (spliRNAs) are associated with highly expressed genes and show evidence of developmental stage- and region-specific expression. We also show that tiRNAs are localized to the nucleus, are enriched at chromatin marks associated with transcription initiation and possess a 3'-nucleotide bias. Additionally, we find that microRNA-offset RNAs (moRNAs), the miR-15/16 cluster previously linked to oncosuppression and most small nucleolar RNA (snoRNA)-derived small RNAs (sdRNAs) are enriched in the nucleus, whereas most miRNAs and two H/ACA sdRNAs are cytoplasmically enriched. We propose that nuclear-localized tiny RNAs are involved in the epigenetic regulation of gene expression.
authors.affiliation: Institute for Molecular Bioscience, School of Integrative Biology, University of Queensland, St. Lucia, Australia.
authors.forename: Ryan J
authors.initials: RJ
authors.lastname: Taft
authors.forename: Cas
authors.initials: C
authors.lastname: Simons
authors.forename: Satu
authors.initials: S
authors.lastname: Nahkuri
authors.forename: Harald
authors.initials: H
authors.lastname: Oey
authors.forename: Darren J
authors.initials: DJ
authors.lastname: Korbie
authors.forename: Timothy R
authors.initials: TR
authors.lastname: Mercer
authors.forename: Jeff
authors.initials: J
authors.lastname: Holst
authors.forename: William
authors.initials: W
authors.lastname: Ritchie
authors.forename: Justin J-L
authors.initials: JJ
authors.lastname: Wong
authors.forename: John E J
authors.initials: JE
authors.lastname: Rasko
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Rokhsar
authors.forename: Bernard M
authors.initials: BM
authors.lastname: Degnan
authors.forename: John S
authors.initials: JS
authors.lastname: Mattick
mesh_terms: D000818:Animals; D002460:Cell Line; D002467:Cell Nucleus / Q000235:genetics*; D002843:Chromatin / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000378:metabolism; D006098:Granulocytes / Q000378:metabolism; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D022821:RNA Splice Sites / Q000235:genetics*; D034443:RNA Transport / Q000235:genetics*; D020537:RNA, Small Nucleolar / Q000378:metabolism; D013347:Subcellular Fractions / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D035683:MicroRNAs; D022821:RNA Splice Sites; D020537:RNA, Small Nucleolar; D012313:RNA