The chromatin state and transcription level of a chromosomal region has been found to be related to modifications of histones [1
] as well as DNA [3
]. The fundamental structural unit of chromatin is the nucleosome, which is formed by wrapping DNA around a histone octamer consisting of two copies each of four core histone proteins (H2A, H2B, H3, and H4). The tails of these histones can be modified in a variety of ways that relate to chromatin condensation and gene expression[2
]. Different histone residues can be methylated, acetylated, phosphorylated or ubiquitinated to either directly change the chromatin structure or allow for the binding of specific transcription factors [5
The acetylation and methylation states of various lysine residues have been extensively investigated. Due to the reactive nature of the amine group on the side chain of lysine, it can be acetylated or mono-, di- or tri- methylated. Enrichment for acetylated histones has been found to correlate with euchromatic and gene-coding regions [6
]. In contrast, certain methylations are associated with activation and others with repression. The most extensively characterized activating methylation is H3K4[8
], while the H3K9 [11
] and H3K27 [14
] methylations are thought to lead to repression and inactivation. Recently, though, mono-methylations of H3K27 and H3K9 have been found to be enriched in active genes [17
Using antibodies with specificity for a particular methylation state, cells have been profiled separately for mono-, di-, and tri- methylation of the same residue. These comparisons were originally performed using mass-spectroscopy and comparisons of staining patterns[18
]. Since these studies relied on comparisons of staining patterns, they were only able to produce low-resolution results that could not be linked to sequence positions. More recently, the ChIP-chip [21
] and ChIP-seq [17
] techniques have been utilized for high-resolution sequence level profiling of histone modifications in mammalian genomes[22
]. These techniques utilize chromatin immunoprecipitation coupled with either tiling microarray hybridization or high-throughput sequencing to determine the genomic locations of a particular modification. It is now possible to obtain resolution on the level of individual nucleosomes. Because histone modifications act on individual nucleosome and there may be modification differences between adjacent nucleosomes, this level of resolution is highly informative.
The most comprehensive profiling of histone modifications has been performed in CD4+
]. The genome-wide locations at a single nucleosome level resolution of 38 different histone methylations and acetylations were profiled, including different levels of methylation of the same residue. In these studies, the modification profiles surrounding the promoters of genes with different levels of expression were examined. Basic comparisons between the different modifications were performed in the region surrounding annotated genes, but here we are reporting the results of an extension of our initial studies [17
] to non-genic regions of the human genome.
In particular, we wanted to investigate histone modifications in three important largely non-coding regions of the genome: pericentromeres, subtelomeres, and gene deserts. These regions are mostly non-coding, but little work has been performed to characterize and differentiate them with regard to histone modifications. Using the identified genome-wide locations for histone methylations and acetylations in CD4+ T cells, we have identified the modifications that are strongly enriched in pericentromeres, subtelomeres, and intergenic regions (we have excluded all known genes in those regions). We have also used consensus repeat sequences to analyze histone modifications present in the unassembled portions of telomeres and centromeres.