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Antisense transcripts are targets for activating small RNAs

Nature Structural & Molecular Biology volume 15, pages 842–848 (2008)Cite this article

Abstract

Agents that activate expression of specific genes to probe cellular pathways or alleviate disease would go beyond existing approaches for controlling gene expression. Duplex RNAs complementary to promoter regions can repress or activate gene expression. The mechanism of these promoter-directed antigene RNAs (agRNAs) has been obscure. Other work has revealed noncoding transcripts that overlap mRNAs. The function of these noncoding transcripts is also not understood. Here we link these two sets of enigmatic results. We find that antisense transcripts are the target for agRNAs that activate or repress expression of progesterone receptor (PR). agRNAs recruit Argonaute proteins to PR antisense transcripts and shift localization of the heterogeneous nuclear ribonucleoprotein-k, RNA polymerase II and heterochromatin protein 1γ. Our data demonstrate that antisense transcripts have a central role in recognition of the PR promoter by both activating and inhibitory agRNAs.

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Figure 1: Antisense transcription at the PR promoter.
Figure 2: Expression levels of antisense transcript AT2.
Figure 3: Gene activation by agRNAs was reversed by single-stranded oligonucleotides that target the antisense transcript.
Figure 4: Binding of biotinylated agRNAs to PR antisense transcript AT2.
Figure 5: Association of AGO proteins, hnRNP-K and HP1γ with PR antisense transcript AT2 examined by RIP.
Figure 6: Factors that associate with gene promoters during agRNA-mediated gene activation or silencing.

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Acknowledgements

This work was supported by grants from the US National Institutes of Health (NIGMS 60642, 77253 and 73042 to D.R.C. and EB 05556 to J.C.S.) and Robert A. Welch Foundation (I-1244). We thank Z. Mourelatos (University of Pennsylvania) for providing anti-AGO antibody and D. Shames for helpful discussions.

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Authors and Affiliations

  1. Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, 75390-9041, Texas, USA

    Jacob C Schwartz, Scott T Younger, Ngoc-Bich Nguyen, David R Corey & Bethany A Janowski

  2. Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, 75390-9041, Texas, USA

    Jacob C Schwartz, Scott T Younger, Ngoc-Bich Nguyen, David R Corey & Bethany A Janowski

  3. Department of Obstetrics and Gynaecology, and Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, N6A 5C1, Ontario, Canada

    Daniel B Hardy

  4. Isis Pharmaceutical, 1896 Rutherford Court, Carlsbad, 92008, California, USA

    Brett P Monia

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Contributions

J.C.S., S.T.Y., N.-B.N., D.B.H. and B.A.J. designed and performed experiments. B.P.M. synthesized single-stranded oligonucleotides for inhibiting expression of PR antisense transcript. D.R.C. and B.A.J. supervised experiments.

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Correspondence to David R Corey or Bethany A Janowski.

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Supplementary Figures 1–5 and Supplementary Tables 1–3 (PDF 318 kb)

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Schwartz, J., Younger, S., Nguyen, NB. et al. Antisense transcripts are targets for activating small RNAs. Nat Struct Mol Biol 15, 842–848 (2008). https://doi.org/10.1038/nsmb.1444

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