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

Autor:	Clarkson CT; School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK., Deeks EA; School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.; Biological Sciences BSc Program, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK., Samarista R; School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.; Wellcome Trust Vacation Student., Mamayusupova H; School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK., Zhurkin VB; Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA., Teif VB; School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2019 Dec 02; Vol. 47 (21), pp. 11181-11196.
DOI:	10.1093/nar/gkz908
Abstrakt:	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. (© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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