Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
WLA Laboratories, Shanghai 201203, China.
Genes Dev. 2021 Oct 1;35(19-20):1383-1394. doi: 10.1101/gad.348621.121. Epub 2021 Sep 16.
Enhancers generate bidirectional noncoding enhancer RNAs (eRNAs) that may regulate gene expression. At present, the eRNA function remains enigmatic. Here, we report a 5' capped antisense eRNA ( eRNA associated with R-loop formation) that is transcribed from the protocadherin () enhancer region. Through loss- and gain-of-function experiments with CRISPR/Cas9 DNA fragment editing, CRISPRi, and CRISPRa, as well as locked nucleic acid strategies, in conjunction with ChIRP, MeDIP, DRIP, QHR-4C, and HiChIP experiments, we found that regulates gene expression by forming local RNA-DNA duplexes (R-loops) in situ within the enhancer region to promote long-distance chromatin interactions between distal enhancers and target promoters. In particular, increased levels of eRNA via perturbing transcription elongation factor lead to strengthened local three-dimensional chromatin organization within the superTAD. These findings have important implications regarding molecular mechanisms by which the enhancer regulates stochastic promoter choice in single cells in the brain.
增强子产生双向非编码增强子 RNA（eRNA），可能调节基因表达。目前，eRNA 的功能仍然是个谜。在这里，我们报告了一个 5' 加帽的反义 eRNA（与 R 环形成相关的 eRNA），它是从原钙粘蛋白（）增强子区域转录而来的。通过使用 CRISPR/Cas9 DNA 片段编辑、CRISPRi 和 CRISPRa 以及锁核酸策略，结合 ChIRP、MeDIP、DRIP、QHR-4C 和 HiChIP 实验，我们发现通过在增强子区域内原位形成局部 RNA-DNA 双链体（R 环），调节基因表达，从而促进远端增强子和靶启动子之间的长距离染色质相互作用。特别是，通过干扰转录延伸因子，增加 eRNA 的水平，导致在超级 TAD 内增强局部三维染色质组织。这些发现对于增强子调节单个脑细胞中随机启动子选择的分子机制具有重要意义。
