Outward-oriented sites within clustered CTCF boundaries are key for intra-TAD chromatin interactions and gene regulation

Nat Commun. 2023 Dec 7;14(1):8101. doi: 10.1038/s41467-023-43849-0.

Abstract

CTCF plays an important role in 3D genome organization by adjusting the strength of chromatin insulation at TAD boundaries, where clustered CBS (CTCF-binding site) elements are often arranged in a tandem array with a complex divergent or convergent orientation. Here, using Pcdh and HOXD loci as a paradigm, we look into the clustered CTCF TAD boundaries and find that, counterintuitively, outward-oriented CBS elements are crucial for inward enhancer-promoter interactions as well as for gene regulation. Specifically, by combinatorial deletions of a series of putative enhancer elements in mice in vivo or CBS elements in cultured cells in vitro, in conjunction with chromosome conformation capture and RNA-seq analyses, we show that deletions of outward-oriented CBS elements weaken the strength of long-distance intra-TAD promoter-enhancer interactions and enhancer activation of target genes. Our data highlight the crucial role of outward-oriented CBS elements within the clustered CTCF TAD boundaries in developmental gene regulation and have interesting implications on the organization principles of clustered CTCF sites within TAD boundaries.

MeSH terms

  • Animals
  • Binding Sites
  • CCCTC-Binding Factor / genetics
  • CCCTC-Binding Factor / metabolism
  • Chromatin*
  • Enhancer Elements, Genetic* / genetics
  • Gene Expression Regulation
  • Mice
  • Promoter Regions, Genetic

Substances

  • Chromatin
  • CCCTC-Binding Factor