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Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

Nature Structural & Molecular Biology volume 20, pages 923–928 (2013)Cite this article

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Abstract

Active human promoters produce promoter-upstream transcripts (PROMPTs). Why these RNAs are coupled to decay, whereas their neighboring promoter-downstream mRNAs are not, is unknown. Here high-throughput sequencing demonstrates that PROMPTs generally initiate in the antisense direction closely upstream of the transcription start sites (TSSs) of their associated genes. PROMPT TSSs share features with mRNA-producing TSSs, including stalled RNA polymerase II (RNAPII) and the production of small TSS-associated RNAs. Notably, motif analyses around PROMPT 3′ ends reveal polyadenylation (pA)-like signals. Mutagenesis studies demonstrate that PROMPT pA signals are functional but linked to RNA degradation. Moreover, pA signals are under-represented in promoter-downstream versus promoter-upstream regions, thus allowing for more efficient RNAPII progress in the sense direction from gene promoters. We conclude that asymmetric sequence distribution around human gene promoters serves to provide a directional RNA output from an otherwise bidirectional transcription process.

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Figure 1: Exosome depletion reveals similar transcription profiles up- and downstream of promoters.
Figure 2: Exosome sensitivity is triggered by TSS-proximal pA sites.
Figure 3: Mutagenesis of PROMPT pA signals underscores their functionality.
Figure 4: Transcription declines more rapidly downstream of asPROMPT TSSs than mRNA TSSs.
Figure 5: Asymmetric sequence distribution around promoters ensures transcription directionality.

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Acknowledgements

We thank M. Schmid and S. Lykke-Andersen for comments on the manuscript as well as P. Carninci and H. Takahashi for help with the CAGE protocol and S. Wilkening with the 3′ tag protocol. This work was supported by the Danish National Research Foundation (grant DNRF58), the Villum Kann Foundation and the Danish Cancer Society (T.H.J.); the EU 7th Framework Programme (FP7/2007–2013)/European Research Council grant agreement 204135, the Novo Nordisk and Lundbeck Foundations (A. Sandelin); and University of Luxembourg—Institute for Systems Biology Program and the Deutsche Forschungsgemeinschaft (L.M.S.). A. Schein was supported as a recipient of a European Molecular Biology Organization postdoctoral grant.

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  1. Aleks Schein & Eivind Valen

    Present address: Present addresses: Omics Science Center, RIKEN Yokohama Institute, Yokohama City, Japan (A.S.), and Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA (E.V.).,

  2. Aino I Järvelin, Jette Bornholdt and Yun Chen: These authors contributed equally to this work.

Authors and Affiliations

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

    Evgenia Ntini, Aleks Schein, Peter R Andersen, Pia K Andersen, Pascal Preker & Torben Heick Jensen

  2. Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

    Aino I Järvelin, Vicent Pelechano & Lars M Steinmetz

  3. Department of Biology, Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark

    Jette Bornholdt, Yun Chen, Mette Boyd, Mette Jørgensen, Robin Andersson, Ilka Hoof, Eivind Valen, Xiaobei Zhao & Albin Sandelin

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Contributions

E.N., J.B., A. Sandelin and T.H.J. designed the experiments. E.N., J.B., M.B., A. Schein, P.R.A., P.K.A. and P.P. performed the experiments. A.I.J., Y.C., M.J., R.A., I.H., E.V., X.Z., J.B., V.P., L.M.S. and A. Sandelin did the bioinformatics analyses. E.N., A. Sandelin and T.H.J. wrote the manuscript. All authors have critically read and approved of the manuscript.

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Correspondence to Torben Heick Jensen.

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Ntini, E., Järvelin, A., Bornholdt, J. et al. Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality. Nat Struct Mol Biol 20, 923–928 (2013). https://doi.org/10.1038/nsmb.2640

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