染色质
表观遗传学
核糖核酸
计算生物学
H3K4me3
生物
芯片排序
非编码RNA
遗传学
DNA
染色质重塑
基因
发起人
基因表达
作者
Ligang Fan,Wei-Hsin Sun,Yingguo Lyu,Furong Ju,Wenju Sun,Yuhua Huang,Haiqian Ma,Shifei Yang,Xiaomin Zhou,Nan Wu,Wenkai Yi,Erfei Chen,Rodrigo Villaseñor,Tuncay Baubec,Jian Yan
出处
期刊:Science Advances
[American Association for the Advancement of Science (AAAS)]
日期:2024-07-31
卷期号:10 (31)
标识
DOI:10.1126/sciadv.adn1397
摘要
Chromatin marks are associated with transcriptional regulatory activities. However, very few lncRNAs have been characterized with the role in regulating epigenetic marks, largely due to the technical difficulty in identifying chromatin-associating RNA. Current methods are largely limited by the availability of ChIP-grade antibody and the crosslinking, which generates high noise. Here, we developed a method termed Chrom-seq to efficiently capture RNAs associated with various chromatin marks in living cells. Chrom-seq jointly applies highly specific chromatin mark reader with APEX2, which catalyzes the oxidation of biotin-aniline to label the adjacent RNAs for isolation by streptavidin-coated beads. Using the readers of mCBX7/dPC, mCBX1, and mTAF3, we detected RNA species significantly associated with H3K27me3, H3K9me3, and H3K4me3, respectively. We demonstrated that Chrom-seq outperformed other equivalent methods in terms of sensitivity, efficiency, and cost of practice. It provides an antibody-free approach to systematically map RNAs at chromatin marks with potential regulatory roles in epigenetic events.
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