RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions (CAGE)

Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodeling. To investigate the function of such RNAs,, methods to massively map the genomic interacting sites of multiple transcripts have been developed. However they present still some limitations. Here, we introduce RNA and DNA interacting complexes ligated and sequenced (RADICL-seq), a novel technology that maps genome-wide RNA-chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation based methodology that reduces the bias for nascent transcription, increases genomic coverage and unique mapping rate efficiency compared to existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type-specific RNA-chromatin interactions, and emphasizes the role of transcription in the establishment of chromatin structure. Overall design: Identification of genome-wide RNA-chromatin interactions in 2 cell types

哺乳动物基因组编码数万种非编码RNA（noncoding RNAs）。绝大多数非编码转录本呈现核定位特征，且已有多项研究证实其在基因表达调控与染色质重塑过程中发挥重要作用。为探究此类RNA的功能，科研人员已开发出可大规模绘制多种转录本基因组互作位点的技术，但这类技术仍存在一定局限。本研究介绍一种名为RNA与DNA互作复合物连接测序（RNA and DNA interacting complexes ligated and sequenced，缩写RADICL-seq）的新型技术，该技术可在完整细胞核中绘制全基因组范围的RNA-染色质互作图谱。相较于现有技术，基于邻近连接原理的RADICL-seq可降低新生转录带来的实验偏好性，同时提升基因组覆盖度与唯一比对效率。RADICL-seq可识别不同类别转录本的独特基因组占据模式，以及细胞类型特异性的RNA-染色质互作关系，并强调了转录过程在染色质结构构建中的关键作用。实验整体设计：在两种细胞类型中鉴定全基因组范围的RNA-染色质互作。