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Transcriptional regulation by small RNAs at sequences downstream from 3′ gene termini

Nature Chemical Biology volume 6, pages 621–629 (2010)Cite this article

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Abstract

Transcriptome studies reveal many noncoding transcripts overlapping 3′ gene termini. The function of these transcripts is unknown. Here we have characterized transcription at the progesterone receptor (PR) locus and identified noncoding transcripts that overlap the 3′ end of the gene. Small RNAs complementary to sequences beyond the 3′ terminus of PR mRNA modulated expression of PR, recruited argonaute 2 to a 3′ noncoding transcript, altered occupancy of RNA polymerase II, induced chromatin changes at the PR promoter and affected responses to physiological stimuli. We found that the promoter and 3′ terminal regions of the PR locus are in close proximity, providing a potential mechanism for RNA-mediated control of transcription over long genomic distances. These results extend the potential for small RNAs to regulate transcription to target sequences beyond the 3′ termini of mRNA.

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Figure 1: Characterization of PR mRNA and PR 3′ noncoding transcript.
Figure 2: Inhibition of PR expression in T47D cells by agRNAs complementary to sequences downstream from the terminus of PR mRNA.
Figure 3: Enhanced PR expression in MCF7 cells by an RNA complementary to a sequence downstream from the terminus of the PR 3′ UTR.
Figure 4: Effect of combining physiological stimuli with agRNAs.
Figure 5: Effect of 3′ or 5′ agRNAs on recruitment of AGO2 protein to the 3′ or 5′ noncoding transcripts at the PR locus.
Figure 6: 3C analysis of the PR locus.
Figure 7: Model for modulation of transcription by 3′ agRNAs.

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Acknowledgements

This work was supported by grants from the US National Institutes of Health (NIGMS GM77253 to D.R.C., GM85080 to B.A.J. and NIBIB EB 05556 to J.C.S.) and the Robert A. Welch Foundation (I-1244 to D.R.C.). B.A.J. was also supported by the High Impact/High Risk Grants Program, UT Southwestern Medical Center, and an Institutional Research Grant from the American Cancer Society (IRG-02-196-04). We gratefully acknowledge Z. Mourelatos (Univ. Pennsylvania) for providing anti-argonaute antibody. We thank A. Bhat for technical assistance and J. Watts for comments on the manuscript.

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Authors and Affiliations

  1. Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA

    Xuan Yue, Jacob C Schwartz, Yongjun Chu, Scott T Younger, Keith T Gagnon, Bethany A Janowski & David R Corey

  2. Alnylam Pharmaceuticals, Cambridge, Massachusetts, USA

    Sayda Elbashir

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All authors designed experiments and analyzed data. All authors except D.R.C. performed experiments. D.R.C. wrote the manuscript. The authors recognize that the contributions of J.C.S. and Y.C. would have been sufficient to merit separate publications.

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Correspondence to Bethany A Janowski or David R Corey.

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Yue, X., Schwartz, J., Chu, Y. et al. Transcriptional regulation by small RNAs at sequences downstream from 3′ gene termini. Nat Chem Biol 6, 621–629 (2010). https://doi.org/10.1038/nchembio.400

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