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Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans

Nature Structural & Molecular Biology volume 17, pages 1030–1034 (2010)Cite this article

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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 ∼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.

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Figure 1: Human THP-1 nuclear and cytoplasmic small-RNA library characteristics.
Figure 2: Features of nuclear-localized very small RNAs.
Figure 3: Splice-site RNAs are conserved across metazoa.
Figure 4: Mouse spliRNAs from primary granulocyte nuclei and embryonic stem cells.
Figure 5: moRNAs and a subset of miRNAs are enriched in the nucleus of human THP-1 cells.

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  • 21 July 2010

    In the version of this article initially published online, reference 26 was incorrectly cited and should be “Drinnenberg, I.A. et al. RNAi in budding yeast. Science 326, 544–550 (2009).” The error has been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

We thank GeneWorks for assistance modifying the Illumina protocol to facilitate detection of very small RNA species and for deep sequencing the THP-1 and primary mouse granulocyte nuclei small-RNA samples and M.E. Dinger for bioinformatic assistance with the analysis of wiggle format tracks. J.S.M. and R.J.T. are supported by a Federation Fellowship grant (FF0561986) and a Discovery Project grant (DP0988851) from the Australian Research Council. J.E.J.R. received project support from the Australian National Health and Medical Research Council (358300) and the Sydney Cancer Centre Foundation. J.E.J.R. and J.H. received project and equipment support from Cancer Institute NSW and NSW Cancer Council. J.E.J.R. and J.J.-L.W. received support from Cure The Future Foundation. W.R. received salary support from an Australian National Health and Medical Research Council Training Fellowship.

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Author notes

  1. Ryan J Taft and Cas Simons: These authors contributed equally to this work.

Authors and Affiliations

  1. Institute for Molecular Bioscience, University of Queensland, St. Lucia, Australia

    Ryan J Taft, Cas Simons, Satu Nahkuri, Harald Oey, Darren J Korbie, Timothy R Mercer & John S Mattick

  2. Queensland Facility for Advanced Bioinformatics, St. Lucia, Australia

    Cas Simons

  3. Gene & Stem Cell Therapy Program, Centenary Institute of Cancer Medicine and Cell Biology, Camperdown, Australia

    Jeff Holst, William Ritchie, Justin J-L Wong & John EJ Rasko

  4. Sydney Medical School, University of Sydney, Australia

    Jeff Holst, William Ritchie & John EJ Rasko

  5. Cell and Molecular Therapies, Sydney Cancer Centre, Royal Prince Alfred Hospital, Camperdown, Australia

    John EJ Rasko

  6. Department of Molecular and Cell Biology and Center for Integrative Genomics, University of California Berkeley, Berkeley, California, USA

    Daniel S Rokhsar

  7. School of Integrative Biology, University of Queensland, St. Lucia, Australia

    Bernard M Degnan

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Contributions

R.J.T. designed the THP-1 deep sequencing and bioinformatic experiments, led the analysis and wrote the manuscript; C.S. made the initial spliRNA observation, designed the bioinformatic analysis of spliRNAs with R.J.T. and helped to write the manuscript; S.N. performed the analysis of spliRNA expression with respect to exon position and exon and intron size and helped to write the manuscript. H.O. and D.J.K. isolated the THP-1 nuclear and cytoplasmic RNA and performed the northern blots, respectively; T.R.M. performed the initial GRO-seq analysis; J.H., W.R., J.J.-L.W. and J.E.J.R. isolated and sequenced the mouse primary granulocyte nuclei small RNAs; D.S.R. and B.M.D. provided A. queenslandica genome sequences; J.S.M. helped to design the study and wrote the manuscript.

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Correspondence to John S Mattick.

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Supplementary Figures 1–13, Supplementary Tables 1–7 and Supplementary Methods (PDF 7415 kb)

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Taft, R., Simons, C., Nahkuri, S. et al. Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nat Struct Mol Biol 17, 1030–1034 (2010). https://doi.org/10.1038/nsmb.1841

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