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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Change history
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.
References
Ghildiyal, M. & Zamore, P.D. Small silencing RNAs: an expanding universe. Nat. Rev. Genet. 10, 94–108 (2009).
Malone, C.D. & Hannon, G. Small RNAs as guardians of the genome. Cell 136, 656–668 (2009).
ENCODE Transcriptome Project. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 457, 1028–1032 (2009).
Seila, A.C. et al. Divergent transcription from active promoters. Science 322, 1849–1851 (2008).
Taft, R.J. et al. Tiny RNAs associated with transcription start sites in animals. Nat. Genet. 41, 572–578 (2009).
Taft, R.J., Kaplan, C.D., Simons, C. & Mattick, J.S. Evolution, biogenesis and function of promoter-associated RNAs. Cell Cycle 8, 2332–2338 (2009).
Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).
Wang, Z. et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 40, 897–903 (2008).
Babiarz, J.E., Ruby, J.G., Wang, Y., Bartel, D.P. & Blelloch, R. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev. 22, 2773–2785 (2008).
Chung, W.J., Okamura, K., Martin, R. & Lai, E.C. Endogenous RNA interference provides a somatic defense against Drosophila transposons. Curr. Biol. 18, 795–802 (2008).
Batista, P.J. et al. PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol. Cell 31, 67–78 (2008).
Grimson, A. et al. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455, 1193–1197 (2008).
Core, L.J., Waterfall, J.J. & Lis, J.T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845–1848 (2008).
Andersson, R., Enroth, S., Rada-Iglesias, A., Wadelius, C. & Komorowski, J. Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res. 19, 1732–1741 (2009).
Nahkuri, S., Taft, R.J. & Mattick, J.S. Nucleosomes are preferentially positioned at exons in somatic and sperm cells. Cell Cycle 8, 3420–3424 (2009).
Schwartz, S., Meshorer, E. & Ast, G. Chromatin organization marks exon-intron structure. Nat. Struct. Mol. Biol. 16, 990–995 (2009).
Tilgner, H. et al. Nucleosome positioning as a determinant of exon recognition. Nat. Struct. Mol. Biol. 16, 996–1001 (2009).
Kolasinska-Zwierz, P. et al. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat. Genet. 41, 376–381 (2009).
Shi, W., Hendrix, D., Levine, M. & Haley, B. A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate. Nat. Struct. Mol. Biol. 16, 183–189 (2009).
Langenberger, D. et al. Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics 25, 2298–2301 (2009).
Aqeilan, R.I., Calin, G.A. & Croce, C.M. miR-15a and miR-16–1 in cancer: discovery, function and future perspectives. Cell Death Differ. 17, 215–220 (2010).
Taft, R.J. et al. Small RNAs derived from snoRNAs. RNA 15, 1233–1240 (2009).
Ender, C. et al. A human snoRNA with microRNA-like functions. Mol. Cell 32, 519–528 (2008).
Saraiya, A.A. & Wang, C.C. snoRNA, a novel precursor of microRNA in Giardia lamblia. PLoS Pathog. 4, e1000224 (2008).
Scott, M.S., Avolio, F., Ono, M., Lamond, A.I. & Barton, G.J. Human miRNA precursors with box H/ACA snoRNA features. PLOS Comput. Biol. 5, e1000507 (2009).
Drinnenberg, I.A. et al. RNAi in budding yeast. Science 326, 544–550 (2009).
Suzuki, H. et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat. Genet. 41, 553–562 (2009).
Hwang, H.W., Wentzel, E.A. & Mendell, J.T. A hexanucleotide element directs microRNA nuclear import. Science 315, 97–100 (2007).
Holst, J. et al. Generation of T-cell receptor retrogenic mice. Nat. Protoc. 1, 406–417 (2006).
Guibal, F.C. et al. Identification of a myeloid committed progenitor as the cancer-initiating cell in acute promyelocytic leukemia. Blood 114, 5415–5425 (2009).
Kuhn, R.M. et al. The UCSC Genome Browser database: update 2009. Nucleic Acids Res. 37, D755–D761 (2009).
Byrne, K.P. & Wolfe, K.H. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15, 1456–1461 (2005).
Poole, R.L. The TAIR database. Methods Mol. Biol. 406, 179–212 (2007).
Mavrich, T.N. et al. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res. 18, 1073–1083 (2008).
Lin, H., Zhang, Z., Zhang, M., Ma, B. & Li, M. ZOOM! Zillions of oligos mapped. Bioinformatics 24, 2431–2437 (2008).
Schmid, C.D. & Bucher, P. ChIP-Seq data reveal nucleosome architecture of human promoters. Cell 131, 831–832 author reply 832–833 (2007).
Arbeitman, M.N. et al. Gene expression during the life cycle of Drosophila melanogaster. Science 297, 2270–2275 (2002).
Griffiths-Jones, S., Saini, H.K., van Dongen, S. & Enright, A.J. miRBase: tools for microRNA genomics. Nucleic Acids Res. 36, D154–D158 (2008).
Pall, G.S., Codony-Servat, C., Byrne, J., Ritchie, L. & Hamilton, A. Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot. Nucleic Acids Res. 35, e60 (2007).
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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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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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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DOI: https://doi.org/10.1038/nsmb.1841
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