BACKGROUND: Histone post-translational modifications (PTMs) constitute a branch 
of epigenetic mechanisms that can control the expression of eukaryotic genes in 
a heritable manner. Recent studies have identified several PTM-binding proteins 
containing diverse specialized domains whose recognition of specific PTM sites 
leads to gene activation or repression. Here, we present a high-throughput 
proteogenomic platform designed to characterize the nucleosomal make-up of 
chromatin enriched with a set of histone PTM binding proteins known as histone 
PTM readers. We support our findings with gene expression data correlating to 
PTM distribution.
RESULTS: We isolated human mononucleosomes bound by the bromodomain-containing 
proteins Brd2, Brd3 and Brd4, and by the chromodomain-containing heterochromatin 
proteins HP1β and HP1α. Histone PTMs were quantified by mass spectrometry 
(ChIP-qMS), and their associated DNAs were mapped using deep sequencing. Our 
results reveal that Brd- and HP1-bound nucleosomes are enriched in histone PTMs 
consistent with actively transcribed euchromatin and silent heterochromatin, 
respectively. Data collected using RNA-Seq show that Brd-bound sites correlate 
with highly expressed genes. In particular, Brd3 and Brd4 are most enriched on 
nucleosomes located within HOX gene clusters, whose expression is reduced upon 
Brd4 depletion by short hairpin RNA.
CONCLUSIONS: Proteogenomic mapping of histone PTM readers, alongside the 
characterization of their local chromatin environments and transcriptional 
information, should prove useful for determining how histone PTMs are bound by 
these readers and how they contribute to distinct transcriptional states.