title: Immunostaining of modified histones defines high-level features of the human metaphase epigenome.
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.
authors.affiliation: Chromatin and Gene Expression Group, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
authors.forename: Edith
authors.initials: E
authors.lastname: Terrenoire
authors.forename: Fiona
authors.initials: F
authors.lastname: McRonald
authors.forename: John A
authors.initials: JA
authors.lastname: Halsall
authors.forename: Paula
authors.initials: P
authors.lastname: Page
authors.forename: Robert S
authors.initials: RS
authors.lastname: Illingworth
authors.forename: A Malcolm R
authors.initials: AM
authors.lastname: Taylor
authors.forename: Val
authors.initials: V
authors.lastname: Davison
authors.forename: Laura P
authors.initials: LP
authors.lastname: O'Neill
authors.forename: Bryan M
authors.initials: BM
authors.lastname: Turner
mesh_terms: D002460:Cell Line; D002843:Chromatin / Q000737:chemistry; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D018899:CpG Islands; D044127:Epigenesis, Genetic; D057890:Epigenomics; D005260:Female; D020868:Gene Silencing; D015894:Genome, Human; D006657:Histones / Q000737:chemistry*; D006801:Humans; D007621:Karyotyping; D008297:Male; D008677:Metaphase / Q000235:genetics*; D046228:Microarray Analysis; D008938:Mitosis; D011499:Protein Processing, Post-Translational
chemical_list: D002843:Chromatin; D006657:Histones