Human proteins that interact with RNA/DNA hybrids

作者：Isabel Xiaorong Wang, Christopher Grunseich, Jennifer E. Fox, Joshua T. Burdick, Zhengwei Zhu, Niema Ravazian, Markus Hafner, Vivian G. Cheung · 发表于：Genome Research · 年份：2018 · DOI：10.1101/gr.237362.118 · 被引用次数：227 · 研究领域：RNA Research and Splicing、RNA and protein synthesis mechanisms、Genomics and Chromatin Dynamics

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.