Analysis of neonatal brain lacking ATRX or MeCP2 reveals changes in nucleosome density, CTCF binding and chromatin looping

Kristin D Kernohan; Douglas Vernimmen; Gregory B Gloor; Nathalie G Bérubé

doi:10.1093/nar/gku564

Analysis of neonatal brain lacking ATRX or MeCP2 reveals changes in nucleosome density, CTCF binding and chromatin looping

Nucleic Acids Res. 2014 Jul;42(13):8356-68. doi: 10.1093/nar/gku564. Epub 2014 Jul 2.

Authors

Kristin D Kernohan¹, Douglas Vernimmen², Gregory B Gloor³, Nathalie G Bérubé⁴

Affiliations

¹ Department of Biochemistry, University of Western Ontario, London N6C 2V5, Canada Children's Health Research Institute, London, Canada.
² Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
³ Department of Biochemistry, University of Western Ontario, London N6C 2V5, Canada.
⁴ Department of Biochemistry, University of Western Ontario, London N6C 2V5, Canada Children's Health Research Institute, London, Canada Department of Paediatrics, University of Western Ontario, London N6C 2V5, Canada nberube@uwo.ca.

Abstract

ATRX and MeCP2 belong to an expanding group of chromatin-associated proteins implicated in human neurodevelopmental disorders, although their gene-regulatory activities are not fully resolved. Loss of ATRX prevents full repression of an imprinted gene network in the postnatal brain and in this study we address the mechanistic aspects of this regulation. We show that ATRX binds many imprinted domains individually but that transient co-localization between imprinted domains in the nuclei of neurons does not require ATRX. We demonstrate that MeCP2 is required for ATRX recruitment and that deficiency of either ATRX or MeCP2 causes decreased frequency of long-range chromatin interactions associated with altered nucleosome density at CTCF-binding sites and reduced CTCF occupancy. These findings indicate that MeCP2 and ATRX regulate gene expression at a subset of imprinted domains by maintaining a nucleosome configuration conducive to CTCF binding and to the maintenance of higher order chromatin structure.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Binding Sites
Brain / growth & development
Brain / metabolism*
CCCTC-Binding Factor
Calcium-Binding Proteins
Cell Nucleus / metabolism
Chromatin / chemistry*
DNA Helicases / genetics
DNA Helicases / metabolism
DNA Helicases / physiology*
Gene Deletion
Genomic Imprinting*
Insulin-Like Growth Factor II / genetics
Intercellular Signaling Peptides and Proteins / genetics
Methyl-CpG-Binding Protein 2 / genetics
Methyl-CpG-Binding Protein 2 / physiology*
Mice
Neurons / metabolism
Nuclear Proteins / genetics
Nuclear Proteins / metabolism
Nuclear Proteins / physiology*
Nucleosomes / metabolism*
RNA, Long Noncoding / genetics
Repressor Proteins / metabolism*
X-linked Nuclear Protein

Substances

CCCTC-Binding Factor
CTCF protein, human
Calcium-Binding Proteins
Chromatin
Ctcf protein, mouse
Dlk1 protein, mouse
H19 long non-coding RNA
Intercellular Signaling Peptides and Proteins
MEG3 non-coding RNA, mouse
Mecp2 protein, mouse
Methyl-CpG-Binding Protein 2
Nuclear Proteins
Nucleosomes
RNA, Long Noncoding
Repressor Proteins
Insulin-Like Growth Factor II
DNA Helicases
Atrx protein, mouse
X-linked Nuclear Protein

Associated data

GEO/GSE22162

Grants and funding

MOP93697/Canadian Institutes of Health Research/Canada