Human proteins that interact with RNA/DNA hybrids
- Isabel X. Wang1,2,
- Christopher Grunseich3,
- Jennifer Fox1,2,
- Joshua Burdick1,2,
- Zhengwei Zhu2,4,
- Niema Ravazian1,
- Markus Hafner5 and
- Vivian G. Cheung1,2,4
- 1Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA;
- 2Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA;
- 3Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland 20892, USA;
- 4Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48109, USA;
- 5Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland 20892, USA
Abstract
RNA/DNA hybrids form when RNA hybridizes with its template DNA generating a three-stranded structure known as the R-loop. Knowledge of how they form and resolve, as well as their functional roles, is limited. Here, by pull-down assays followed by mass spectrometry, we identified 803 proteins that bind to RNA/DNA hybrids. Because these proteins were identified using in vitro assays, we confirmed that they bind to R-loops in vivo. They include proteins that are involved in a variety of functions, including most steps of RNA processing. The proteins are enriched for K homology (KH) and helicase domains. Among them, more than 300 proteins preferred binding to hybrids than double-stranded DNA. These proteins serve as starting points for mechanistic studies to elucidate what RNA/DNA hybrids regulate and how they are regulated.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.237362.118.
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Freely available online through the Genome Research Open Access option.
- Received March 20, 2018.
- Accepted July 27, 2018.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
