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Promoter directionality is controlled by U1 snRNP and polyadenylation signals

Nature volume 499, pages 360–363 (2013)Cite this article

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Abstract

Transcription of the mammalian genome is pervasive, but productive transcription outside of protein-coding genes is limited by unknown mechanisms1. In particular, although RNA polymerase II (RNAPII) initiates divergently from most active gene promoters, productive elongation occurs primarily in the sense-coding direction2,3,4. Here we show in mouse embryonic stem cells that asymmetric sequence determinants flanking gene transcription start sites control promoter directionality by regulating promoter-proximal cleavage and polyadenylation. We find that upstream antisense RNAs are cleaved and polyadenylated at poly(A) sites (PASs) shortly after initiation. De novo motif analysis shows PAS signals and U1 small nuclear ribonucleoprotein (snRNP) recognition sites to be the most depleted and enriched sequences, respectively, in the sense direction relative to the upstream antisense direction. These U1 snRNP sites and PAS sites are progressively gained and lost, respectively, at the 5′ end of coding genes during vertebrate evolution. Functional disruption of U1 snRNP activity results in a dramatic increase in promoter-proximal cleavage events in the sense direction with slight increases in the antisense direction. These data suggest that a U1–PAS axis characterized by low U1 snRNP recognition and a high density of PASs in the upstream antisense region reinforces promoter directionality by promoting early termination in upstream antisense regions, whereas proximal sense PAS signals are suppressed by U1 snRNP. We propose that the U1–PAS axis limits pervasive transcription throughout the genome.

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Figure 1: Promoter-proximal PAS-dependent termination of uaRNA.
Figure 2: Asymmetric distribution of PAS and U1 signals flanking coding-gene TSS.
Figure 3: Promoter-proximal cleavage sites are altered upon functional U1 inhibition.
Figure 4: Evolutionary gain and loss of U1 and PAS sites.

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Gene Expression Omnibus

Data deposits

3′-end sequencing data is deposited in the Gene Expression Omnibus under accession number GSE46433.

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Acknowledgements

The authors acknowledge the service to the MIT community of the late Sean Collier. We would like to thank N. Spies for generously sharing his optimized 3′-end sequencing protocol, C. Lin for providing computational assistance, M. Lindstrom for assistance on constructing Supplementary Figure 11, and S. Chen, A. Chiu, M. Jangi, Q. Liu, J. Wilusz and J. Zamudio for reading of the manuscript. We also thank the Core Facility in the Swanson Biotechnology Center at the David H. Koch Institute for Integrative Cancer Research at MIT for their assistance with high-throughput sequencing. This work was supported by United States Public Health Service grants RO1-GM34277 and R01-CA133404 from the National Institutes of Health (P.A.S.), partially by Cancer Center Support (core) grant P30-CA14051 from the National Cancer Institute, and by a Public Health Service research grant (GM-085319) from the National Institute of General Medical Sciences (C.B.B.). X.W. is a Howard Hughes Medical Institute International Student Research fellow.

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Author notes

  1. Albert E. Almada and Xuebing Wu: These authors contributed equally to this work.

Authors and Affiliations

  1. David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Albert E. Almada, Xuebing Wu & Phillip A. Sharp

  2. Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Albert E. Almada, Andrea J. Kriz, Christopher B. Burge & Phillip A. Sharp

  3. Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Xuebing Wu & Christopher B. Burge

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Contributions

A.E.A., X.W. and P.A.S. conceived and designed the research. A.E.A. performed experiments. X.W. and A.J.K. performed computational analysis. A.E.A., X.W., C.B.B. and P.A.S. analysed the data and wrote the manuscript.

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Correspondence to Phillip A. Sharp.

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Almada, A., Wu, X., Kriz, A. et al. Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature 499, 360–363 (2013). https://doi.org/10.1038/nature12349

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