Chromatin-Associated RNA Sequencing (ChAR-seq).
Chromatin-Associated RNA Sequencing (ChAR-seq).
复制标题
染色质相关 RNA 测序（ChAR-seq）。
DOI：
10.1002/cpmb.87
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发表时间：
2019-04
影响因子：
--
通讯作者：
Straight AF
中科院分区：
文献类型：
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作者：
Jukam D;Limouse C;Smith OK;Risca VI;Bell JC;Straight AF
RNA是染色质的基本组成部分。非编码RNA（ncRNA）可以与染色质结合，影响基因表达和染色质状态;许多也在远离其转录起点的地方起作用。然而，我们对大多数ncRNA的功能或作用位点几乎一无所知。目前鉴定RNA与基因组相互作用位点的方法仅限于一次研究单个RNA。在这里，我们描述了一种用于ChAR-seq的协议，这是一种识别所有染色质相关RNA并在全基因组范围内绘制其DNA接触图的策略。在ChAR-seq中，使用RNA和DNA与接头分子的邻近连接来构建嵌合RNA-DNA分子，该嵌合RNA-DNA分子被转化为DNA用于测序。在一次检测中，ChAR-seq可以发现不同RNA的从头染色质相互作用，包括新生转录物，剪接RNA和长非编码RNA（lncRNA）。由此产生的基因组结合RNA的“地图”应该为RNA生物学提供新的见解。
RNA is a fundamental component of chromatin. Noncoding RNAs (ncRNAs) can associate with chromatin to influence gene expression and chromatin state; many also act at long distances from their transcriptional origin. Yet we know almost nothing about the functions or sites of action for most ncRNAs. Current methods to identify sites of RNA interaction with the genome are limited to the study of a single RNA at a time. Here we describe a protocol for ChAR-seq, a strategy to identify all chromatin-associated RNAs and map their DNA contacts genome-wide. In ChAR-seq, proximity ligation of RNA and DNA to a linker molecule is used to construct a chimeric RNA-DNA molecule that is converted to DNA for sequencing. In a single assay, ChAR-seq can discover de novo chromatin interactions of distinct RNAs, including nascent transcripts, splicing RNAs, and long noncoding RNAs (lncRNAs). Resulting “maps” of genome-bound RNAs should provide new insights into RNA biology.