Many RNAs associate with chromatin, either directly or indirectly. Several technologies for mapping regions where RNAs interact across the genome have been developed to investigate the function of these RNAs. Obtaining information on the proteins involved in these RNA–chromatin interactions is critical for further analysis. Here, we developed RADIP [RNA and DNA interacting complexes ligated and sequenced (RADICL-seq) with immunoprecipitation], a novel technology that combines RADICL-seq technology with chromatin immunoprecipitation to characterize RNA–chromatin interactions mediated by individual proteins. Building upon the foundational principles of RADICL-seq, RADIP extends its advantages by increasing genomic coverage and unique mapping rate efficiency compared to existing methods. To demonstrate its effectiveness, we applied an anti-H3K27me3 antibody to the RADIP technology and generated libraries from mouse embryonic stem cells (mESCs). We identified a multitude of RNAs, including RNAs from protein-coding genes and non-coding RNAs, that are associated with chromatin via H3K27me3 and that likely facilitate the spread of Polycomb repressive complexes over broad regions of the mammalian genome, thereby affecting gene expression, chromatin structures and pluripotency of mESCs. Our study demonstrates the applicability of RADIP to investigations of the functions of chromatin-associated RNAs.

中文翻译：

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RADIP 技术可全面识别 H3K27me3 相关 RNA-染色质相互作用


许多 RNA 直接或间接地与染色质相关。已经开发了几种用于绘制 RNA 在基因组中相互作用的区域的技术来研究这些 RNA 的功能。获取有关这些 RNA-染色质相互作用中涉及的蛋白质的信息对于进一步分析至关重要。在这里，我们开发了 RADIP [RNA 和 DNA 相互作用复合物连接和测序 （RADICL-seq） 与免疫沉淀]，这是一种将 RADICL-seq 技术与染色质免疫沉淀相结合的新技术，以表征由单个蛋白质介导的 RNA-染色质相互作用。RADIP 基于 RADICL-seq 的基本原理，与现有方法相比，RADIP 通过增加基因组覆盖率和独特的定位率效率来扩展其优势。为了证明其有效性，我们将抗 H3K27me3 抗体应用于 RADIP 技术，并从小鼠胚胎干细胞 （mESC） 生成文库。我们鉴定了多种 RNA，包括来自蛋白质编码基因和非编码 RNA 的 RNA，它们通过 H3K27me3 与染色质相关，并且可能促进多梳抑制复合物在哺乳动物基因组的广泛区域传播，从而影响基因表达、染色质结构和 mESC 的多能性。我们的研究表明 RADIP 适用于染色质相关 RNA 功能的研究。