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Immunostaining of modified histones defines high-level features of the human metaphase epigenome

Edith Terrenoire12, Fiona McRonald13, John A Halsall1, Paula Page2, Robert S Illingworth45, A Malcolm R Taylor6, Val Davison2, Laura P O'Neill1 and Bryan M Turner1*

Author affiliations

1 Chromatin and Gene Expression Group, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK

2 West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Metchley Park Road, Edgbaston, Birmingham B15 2TG, UK

3 Current address: School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK

4 The Wellcome Trust Centre for Cell Biology, University of Edinburgh, The King's Buildings, Edinburgh EH9 3JR, UK

5 Current address: MRC Human Genetics Unit, Crewe Road, Edinburgh EH4 2XU, UK

6 School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK

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Citation and License

Genome Biology 2010, 11:R110  doi:10.1186/gb-2010-11-11-r110

Published: 15 November 2010

Abstract

Background

Immunolabeling of metaphase chromosome spreads can map components of the human epigenome at the single cell level. Previously, there has been no systematic attempt to explore the potential of this approach for epigenomic mapping and thereby to complement approaches based on chromatin immunoprecipitation (ChIP) and sequencing technologies.

Results

By immunostaining and immunofluorescence microscopy, we have defined the distribution of selected histone modifications across metaphase chromosomes from normal human lymphoblastoid cells and constructed immunostained karyotypes. Histone modifications H3K9ac, H3K27ac and H3K4me3 are all located in the same set of sharply defined immunofluorescent bands, corresponding to 10- to 50-Mb genomic segments. Primary fibroblasts gave broadly the same banding pattern. Bands co-localize with regions relatively rich in genes and CpG islands. Staining intensity usually correlates with gene/CpG island content, but occasional exceptions suggest that other factors, such as transcription or SINE density, also contribute. H3K27me3, a mark associated with gene silencing, defines a set of bands that only occasionally overlap with gene-rich regions. Comparison of metaphase bands with histone modification levels across the interphase genome (ENCODE, ChIP-seq) shows a close correspondence for H3K4me3 and H3K27ac, but major differences for H3K27me3.

Conclusions

At metaphase the human genome is packaged as chromatin in which combinations of histone modifications distinguish distinct regions along the euchromatic chromosome arms. These regions reflect the high-level interphase distributions of some histone modifications, and may be involved in heritability of epigenetic states, but we also find evidence for extensive remodeling of the epigenome at mitosis.