Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans.
Nat Struct Mol Biol, 2010/8;17(8):1030-4.
Taft RJ[1], Simons C, Nahkuri S, Oey H, Korbie DJ, Mercer TR, Holst J, Ritchie W, Wong JJ, Rasko JE, Rokhsar DS, Degnan BM, Mattick JS
Affiliations
PMID: 20622877DOI: 10.1038/nsmb.1841
Impact factor: 18.361
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.
MeSH terms
Animals; Cell Line; Cell Nucleus; Chromatin; Embryonic Stem Cells; Granulocytes; Humans; Mice; MicroRNAs; RNA; RNA Splice Sites; RNA Transport; RNA, Small Nucleolar; Subcellular Fractions; Transcription Initiation Site; Transcription, Genetic
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