RT Journal
A1 Islam, Zubairul
A1 Saravanan, Bharath
A1 Walavalkar, Kaivalya
A1 Farooq, Umer
A1 Singh, Anurag Kumar
A1 Radhakrishnan, Sabarinathan
A1 Thakur, Jitendra
A1 Pandit, Awadhesh
A1 Henikoff, Steven
A1 Notani, Dimple
T1 Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries
JF Genome Research 
JO Genome Research 
YR 2023 
FD January 01 
VO 33 
IS 1 
SP 1 
OP 17 
DO 10.1101/gr.276643.122 
UL http://genome.cshlp.org/content/33/1/1.abstract 
AB 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.