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Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes

Nature Structural & Molecular Biology volume 18, pages 1075–1082 (2011)Cite this article

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Abstract

Efforts to catalog eukaryotic transcripts have uncovered many small RNAs (sRNAs) derived from gene termini and splice sites. Their biogenesis pathways are largely unknown, but a mechanism based on backtracking of RNA polymerase II (RNAPII) has been suggested. By sequencing transcripts 12–100 nucleotides in length from cells depleted of major RNA degradation enzymes and RNAs associated with Argonaute (AGO1/2) effector proteins, we provide mechanistic models for sRNA production. We suggest that neither splice site–associated (SSa) nor transcription start site–associated (TSSa) RNAs arise from RNAPII backtracking. Instead, SSa RNAs are largely degradation products of splicing intermediates, whereas TSSa RNAs probably derive from nascent RNAs protected by stalled RNAPII against nucleolysis. We also reveal new AGO1/2-associated RNAs derived from 3′ ends of introns and from mRNA 3′ UTRs that appear to draw from noncanonical microRNA biogenesis pathways.

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Figure 1: The majority of gene-derived sRNAs are decay products.
Figure 2: sRNAs around splice sites.
Figure 3: sRNA density around TSSs is dependent on promoter type and sRNA length.
Figure 4: TSSa RNAs are likely produced by protection of nascent RNA by stalled RNAPII.
Figure 5: Human tailed mirtrons.
Figure 6: AGO1/2-associating sRNAs located in 3′ UTRs.

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Change history

  • 21 August 2011

    In the version of this article initially published online, in Figure 5a, the x-axis tick marks and labels were placed incorrectly; in Figure 5c, there were two extraneous tracks; and in Figure 5d, the y-axis label was missing, a stem in the RNA was incorrectly colored in gray (instead of red) and the sRNA tracks were incorrectly shifted to the left. These errors have been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

We thank A. Jacquier, A.H. Lund, K. Adelman and members of the T.H.J. and A.S. laboratories for stimulating discussions. The following colleagues are acknowledged for sharing antibodies: J. Lykke-Andersen (Division of Biology, University of California, San Diego), D.L. Black (Howard Hughes Medical Institute, Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles), G.J. Pruijn (Department of Biomolecular Chemistry, Nijmegen Center for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University) and K. Nishikura (The Wistar Institute). This work was supported by the Danish National Research Foundation, the Danish Cancer Society and the Lundbeck Foundation (to T.H.J.) and the EU 7th Framework Programme (FP7/2007–2013)/ERC grant agreement 204135, the Novo Nordisk Foundation, the Danish Cancer Society and the Lundbeck Foundation (to A.S.). E.V. was supported by the Danish Council for Independent Research. P.P. was the recipient of a research grant from the Lundbeck Foundation during part of this work. Work in the laboratory of G.M. was supported by the Bayerisches Staatsministerium für Wissenschaft, Forschung und Kunst (BayGene), the European Union (ERC grant 'sRNAs') and the Deutsche Forschungsgemeinschaft (DFG, Me 2064/2-2 and FOR855). Sequencing was carried out at the Beijing Genome Institute (BGI) in Shenzhen, China.

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  1. Eivind Valen, Pascal Preker and Peter Refsing Andersen: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biology and the Biotech Research and Innovation Centre (BRIC), The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark

    Eivind Valen, Xiaobei Zhao, Yun Chen & Albin Sandelin

  2. Department of Molecular Biology, Centre for mRNP Biogenesis and Metabolism, Aarhus University, Denmark

    Pascal Preker, Peter Refsing Andersen & Torben Heick Jensen

  3. Laboratory of RNA Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany

    Christine Ender & Gunter Meister

  4. Department of Biochemistry, University of Regensburg, Regensburg, Germany

    Anne Dueck & Gunter Meister

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  1. Eivind Valen
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Contributions

E.V., P.P., P.R.A., G.M., A.S. and T.H.J. designed the experiments. P.P., P.R.A., C.E. and A.D. conducted the experiments. E.V., X.Z., Y.C. and A.S. did the bioinformatics analyses. E.V., P.P., P.R.A., G.M., A.S. and T.H.J. evaluated the results. E.V., P.P., P.R.A., X.Z., Y.C., A.S. and T.H.J. produced the figures. E.V., P.P., P.R.A., A.S. and T.H.J. wrote the manuscript.

Corresponding authors

Correspondence to Albin Sandelin or Torben Heick Jensen.

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Valen, E., Preker, P., Andersen, P. et al. Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes. Nat Struct Mol Biol 18, 1075–1082 (2011). https://doi.org/10.1038/nsmb.2091

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