CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length

Christopher T Clarkson, Emma A Deeks, Ralph Samarista, Hulkar Mamayusupova, Victor B Zhurkin, Vladimir B Teif

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32 Citations (Scopus)
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The CCCTC-binding factor (CTCF) organises the genome in 3D through DNA loops and in 1D by setting boundaries isolating different chromatin states, but these processes are not well understood. Here we investigate chromatin boundaries in mouse embryonic stem cells, defined by the regions with decreased Nucleosome Repeat Length (NRL) for ∼20 nucleosomes near CTCF sites, affecting up to 10% of the genome. We found that the nucleosome-depleted region (NDR) near CTCF is asymmetrically located >40 nucleotides 5'-upstream from the centre of CTCF motif. The strength of CTCF binding to DNA and the presence of cohesin is correlated with the decrease of NRL near CTCF, and anti-correlated with the level of asymmetry of the nucleosome array. Individual chromatin remodellers have different contributions, with Snf2h having the strongest effect on the NRL decrease near CTCF and Chd4 playing a major role in the symmetry breaking. Upon differentiation, a subset of preserved, common CTCF sites maintains asymmetric nucleosome pattern and small NRL. The sites which lost CTCF upon differentiation are characterized by nucleosome rearrangement 3'-downstream, with unchanged NDR 5'-upstream of CTCF motifs. Boundaries of topologically associated chromatin domains frequently contain several inward-oriented CTCF motifs whose effects, described above, add up synergistically.

Original languageEnglish
Pages (from-to)11181-11196
Number of pages16
JournalNucleic Acids Research
Issue number21
Early online date30 Oct 2019
Publication statusPublished - 02 Dec 2019
Externally publishedYes

Bibliographical note

© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.


  • Animals
  • Base Sequence
  • Binding Sites
  • CCCTC-Binding Factor/physiology
  • Cell Differentiation/genetics
  • Chromatin/chemistry
  • Chromatin Assembly and Disassembly/physiology
  • Humans
  • Mice
  • Mouse Embryonic Stem Cells/metabolism
  • Nucleic Acid Conformation
  • Nucleosomes/metabolism
  • Protein Binding


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