Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.
Tsinghua-Peking Center for Life Sciences, Beijing, China.
Nat Plants. 2021 Oct;7(10):1364-1378. doi: 10.1038/s41477-021-01004-x. Epub 2021 Oct 14.
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.
越来越多的证据表明，各种 RNA 可以与染色质结合，以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，在拟南芥幼苗中在全基因组范围内描绘 RNA-染色质相互作用。我们鉴定了由编码 RNA 和非编码 RNA 介导的超过 10000 个 RNA-染色质相互作用。顺式和染色体内相互作用主要由编码 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加强。我们进一步表明，一些 RNA-染色质相互作用会响应生物和非生物胁迫而发生改变，并且改变的 RNA-染色质相互作用形成共同调节网络。我们的研究提供了在拟南芥中 RNA-染色质相互作用的全局视图，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。
