@article{Islam01012023,
author = {Islam, Zubairul and Saravanan, Bharath and Walavalkar, Kaivalya and Farooq, Umer and Singh, Anurag Kumar and Radhakrishnan, Sabarinathan and Thakur, Jitendra and Pandit, Awadhesh and Henikoff, Steven and Notani, Dimple}, 
title = {Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries},
volume = {33}, 
number = {1}, 
pages = {1-17}, 
year = {2023}, 
doi = {10.1101/gr.276643.122}, 
abstract ={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 INK4a/ARF and MYC 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.}, 
URL = {http://genome.cshlp.org/content/33/1/1.abstract}, 
eprint = {http://genome.cshlp.org/content/33/1/1.full.pdf+html}, 
journal = {Genome Research} 
}