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Author Notes:

Dimple Notani, dnotani@ncbs.res.in

The study was conceptualized and designed by Z.I., B.S., and D.N. Most experiments were performed by Z.I. with help from U.F. and K.W. B.S. performed NGS data analysis. A.P. performed NGS library preparation and sequencing. A.K.S. and R.S. assisted in data analysis. D.N., Z.I., B.S., and S.H. wrote the manuscript with input from J.T. All authors read and edited the manuscript.

We thank D.N. laboratory members, Ranveer Jayani and Amanjot Singh, for the discussions. We acknowledge support of the Department of Atomic Energy, Government of India, under project no. 12-R&D-TFR-5.04-0800 and intramural funds from National Center for Biological Sciences–Tata Institute of Fundamental Research (NCBS-TIFR) (to D.N.). D.N. is an EMBO Global Investigator. We also acknowledge the funding support from Wellcome-IA (IA/1/14/2/501539) and Department of Science and Technology core grant (CRG/2019/005714) to D.N. U.F. is supported by the Council of Scientific and Industrial Research (CSIR, Government of India) senior research fellowship. K.W. and A.K.S. are supported by the TIFR-NCBS graduate program. K.W. is also supported by the CSIR-SPM (Government of India) fellowship. The genome sequence described/used in this research was derived from a HeLa cell line. Henrietta Lacks, and the HeLa cell line that was established from her tumor cells without her knowledge or consent in 1951, have made significant contributions to scientific progress and advances in human health. We thank Henrietta Lacks, now deceased, and her surviving family members for their contributions to biomedical research. This study was reviewed by the National Institutes of Health HeLa Genome Data Access Working Group.

The authors declare no competing interests.

Subject:

Keywords:

  • Chromatin
  • CCCTC-Binding Factor
  • Binding Sites
  • Promoter Regions, Genetic
  • RNA
  • Enhancer Elements, Genetic

Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries

Journal Title:

Genome Research

Volume:

Volume 33, Number 1

Publisher:

, Pages 1-17

Type of Work:

Article | Final Publisher PDF

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.

Copyright information:

© 2023 Islam et al.; Published by Cold Spring Harbor Laboratory Press

This is an Open Access work distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (https://creativecommons.org/licenses/by-nc/4.0/).
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