National Center for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, Karnataka 560065, India.
Sastra Deemed University, Thanjavur, Tamil Nadu 613401, India.
Genome Res. 2023 Jan;33(1):1-17. doi: 10.1101/gr.276643.122. Epub 2023 Jan 17.
Vertebrate genomes are partitioned into chromatin domains or topologically associating domains (TADs), which are typically bound by head-to-head pairs of CTCF binding sites. Transcription at domain boundaries correlates with better insulation; however, it is not known whether the boundary transcripts themselves contribute to boundary function. Here we characterize boundary-associated RNAs genome-wide, focusing on the disease-relevant and TAD. Using CTCF site deletions and boundary-associated RNA knockdowns, we observe that boundary-associated RNAs facilitate recruitment and clustering of CTCF at TAD borders. The resulting CTCF enrichment enhances TAD insulation, enhancer-promoter interactions, and TAD gene expression. Importantly, knockdown of boundary-associated RNAs results in loss of boundary insulation function. Using enhancer deletions and CRISPRi of promoters, we show that active TAD enhancers, but not promoters, induce boundary-associated RNA transcription, thus defining a novel class of regulatory enhancer RNAs.
脊椎动物基因组被分割成染色质域或拓扑关联域（TAD），这些域通常由 CTCF 结合位点的对头对绑定。在域边界处的转录与更好的隔离相关联；然而，尚不清楚边界转录本本身是否有助于边界功能。在这里，我们在全基因组范围内对边界相关的 RNA 进行了表征，重点是疾病相关的和 TAD。使用 CTCF 位点缺失和边界相关的 RNA 敲低，我们观察到边界相关的 RNA 促进了 CTCF 在 TAD 边界的募集和聚类。由此产生的 CTCF 富集增强了 TAD 的隔离、增强子-启动子相互作用和 TAD 基因表达。重要的是，边界相关 RNA 的敲低导致边界隔离功能丧失。使用增强子缺失和启动子的 CRISPRi，我们表明活跃的 TAD 增强子，但不是启动子，诱导边界相关的 RNA 转录，从而定义了一类新的调控增强子 RNA。
