It is increasingly evident that various RNAs can bind chromatin to regulate gene expression and genome organization. Here we adapted a sequencing-based technique to profile RNA–chromatin interactions at a genome-wide scale in Arabidopsis seedlings. We identified more than 10,000 RNA–chromatin interactions mediated by protein-coding RNAs and non-coding RNAs. Cis and intra-chromosomal interactions are mainly mediated by protein-coding RNAs, whereas inter-chromosomal interactions are primarily mediated by non-coding RNAs. Many RNA–chromatin interactions tend to positively correlate with DNA–DNA interactions, suggesting their mutual influence and reinforcement. We further show that some RNA–chromatin interactions undergo alterations in response to biotic and abiotic stresses and that altered RNA–chromatin interactions form co-regulatory networks. Our study provides a global view on RNA–chromatin interactions in Arabidopsis and a rich resource for future investigations of regulatory roles of RNAs in gene expression and genome organization.

越来越明显的是，各种 RNA 可以结合染色质来调节基因表达和基因组组织。在这里，我们采用了一种基于测序的技术来分析拟南芥幼苗中全基因组范围内的 RNA-染色质相互作用。我们鉴定了 10,000 多种由蛋白质编码 RNA 和非编码 RNA 介导的 RNA-染色质相互作用。顺式染色体内相互作用主要由蛋白质编码 RNA 介导，而染色体间相互作用主要由非编码 RNA 介导。许多 RNA-染色质相互作用往往与 DNA-DNA 相互作用呈正相关，表明它们相互影响和强化。我们进一步表明，一些 RNA-染色质相互作用在对生物和非生物胁迫的反应中发生改变，并且改变的 RNA-染色质相互作用形成共同调节网络。我们的研究提供了拟南芥中 RNA-染色质相互作用的全局视图，并为未来研究 RNA 在基因表达和基因组组织中的调控作用提供了丰富的资源。