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Published November 1, 2016 | Published + Supplemental Material
Journal Article Open

RNA polymerase II senses obstruction in the DNA minor groove via a conserved sensor motif

Abstract

RNA polymerase II (pol II) encounters numerous barriers during transcription elongation, including DNA strand breaks, DNA lesions, and nucleosomes. Pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA with programmable sequence specificity and high affinity. Previous studies suggest that Py-Im polyamides can prevent transcription factor binding, as well as interfere with pol II transcription elongation. However, the mechanism of pol II inhibition by Py-Im polyamides is unclear. Here we investigate the mechanism of how these minor-groove binders affect pol II transcription elongation. In the presence of site-specifically bound Py-Im polyamides, we find that the pol II elongation complex becomes arrested immediately upstream of the targeted DNA sequence, and is not rescued by transcription factor IIS, which is in contrast to pol II blockage by a nucleosome barrier. Further analysis reveals that two conserved pol II residues in the Switch 1 region contribute to pol II stalling. Our study suggests this motif in pol II can sense the structural changes of the DNA minor groove and can be considered a "minor groove sensor." Prolonged interference of transcription elongation by sequence-specific minor groove binders may present opportunities to target transcription addiction for cancer therapy.

Additional Information

© 2016 National Academy of Sciences. Freely available online through the PNAS open access option. Contributed by Peter B. Dervan, September 12, 2016 (sent for review June 15, 2016; reviewed by Roger D. Kornberg and Jesper Svejstrup). Published online before print October 17, 2016, doi: 10.1073/pnas.1612745113 This work was supported in part by NIH Grants GM102362 (to D.W.) and GM27681 (to P.B.D.); D.G. and J.N.S. were supported in part by the Intramural Research Program of the NIH, National Cancer Institute, and the Center for Cancer Research; and A.A.H. was supported in part by a postdoctoral Fellowship F32CA173977 from the NIH. L.X. and W.W. contributed equally to this work. Author contributions: L.X., W.W., J.N.S., P.B.D., and D.W. designed research; L.X., W.W., D.G., and F.Y. performed research; A.A.H., T.R.W., B.C.L., J.H.S., and J.C. contributed new reagents/analytic tools; L.X., W.W., F.Y., J.N.S., P.B.D., and D.W. analyzed data; and L.X., W.W., F.Y., J.N.S., P.B.D., and D.W. wrote the paper. Reviewers: R.D.K., Stanford University School of Medicine; and J.S., The Francis Crick Institute. Conflict of interest statement: P.B.D. and F.Y. own shares in Gene Sciences, Inc., a biotechnology company that is developing therapeutics for prostate cancer. This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1612745113/-/DCSupplemental.

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Published - PNAS-2016-Xu-12426-31.pdf

Supplemental Material - pnas.201612745SI.pdf

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Created:
August 22, 2023
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October 23, 2023