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Primary microRNA transcripts are processed co-transcriptionally

Nature Structural & Molecular Biology volume 15, pages 902–909 (2008)Cite this article

Abstract

microRNAs (miRNAs) are generated from long primary (pri-) RNA polymerase II (Pol II)–derived transcripts by two RNase III processing reactions: Drosha cleavage of nuclear pri-miRNAs and Dicer cleavage of cytoplasmic pre-miRNAs. Here we show that Drosha cleavage occurs during transcription acting on both independently transcribed and intron-encoded miRNAs. We also show that both 5′-3′ and 3′-5′ exonucleases associate with the sites where co-transcriptional Drosha cleavage occurs, promoting intron degradation before splicing. We finally demonstrate that miRNAs can also derive from 3` flanking transcripts of Pol II genes. Our results demonstrate that multiple miRNA-containing transcripts are co-transcriptionally cleaved during their synthesis and suggest that exonucleolytic degradation from Drosha cleavage sites in pre-mRNAs may influence the splicing and maturation of numerous mRNAs.

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Figure 1: Chromatin association of the Microprocessor complex.
Figure 2: Specificity of the Drosha–miRNA chromatin interaction.
Figure 3: miRNA maturation from the second intron and 3′ flanking region of the β-globin gene in HeLa cells.
Figure 4: Co-transcriptional processing of pre-miRNAs from the β-globin gene intron 2.
Figure 5: Exonuclease activities are associated with chromatin of intronic pre-miRNAs.

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Acknowledgements

We are grateful to D. Cacchiarelli for the bioinformatics analysis and to M. Dye and S. West for helpful advice and discussion and for sharing unpublished data. M.M. was supported by an EMBO Long term fellowship. This work was partly supported by the 6th Framework Programme of the European Commission, SIROCCO and RIGHT Integrated Projects (LSHG-CT-2006-037900 and LSHB-CT-2004 005276) and Centro di Eccellenza BEMM to I.B. and by the ESF project “NuRNASu” to I.B. and N.J.P. The Proudfoot laboratory is supported by a Wellcome Trust Programme Grant.

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Author notes

  1. Monica Ballarino and Natalia Gromak: These authors contributed equally to this work.

Authors and Affiliations

  1. Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK

    Mariangela Morlando, Natalia Gromak & Nick J Proudfoot

  2. Department of Genetics and Molecular Biology and IBPM, Institute Pasteur Cenci-Bolognetti, “La Sapienza”, University of Rome, Piazzale Aldo Moro 5, Rome, 00185, Italy

    Mariangela Morlando, Monica Ballarino, Francesca Pagano & Irene Bozzoni

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  1. Mariangela Morlando
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Contributions

M.M. performed the experimental work except that M.B. carried out experiments on intergenic miRNA host genes together with F.P., and N.G. carried out experiments on exonuclease involvement. M.M., I.B., N.G. and N.J.P. wrote the paper. All authors read and agree with the paper's contents.

Note: Supplementary information is available on the Nature Structural & Molecular Biology website.

Corresponding author

Correspondence to Nick J Proudfoot.

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Morlando, M., Ballarino, M., Gromak, N. et al. Primary microRNA transcripts are processed co-transcriptionally. Nat Struct Mol Biol 15, 902–909 (2008). https://doi.org/10.1038/nsmb.1475

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