%0 Journal Article
%T Determination of enriched histone modifications in non-genic portions of the human genome
%A Jeffrey A Rosenfeld
%A Zhibin Wang
%A Dustin E Schones
%A Keji Zhao
%A Rob DeSalle
%A Michael Q Zhang
%J BMC Genomics
%D 2009
%I BioMed Central
%R 10.1186/1471-2164-10-143
%X We have extended the analysis of histone modifications to gene deserts, pericentromeres and subtelomeres. Using data from human CD4+ T cells, we have found that each of these non-genic regions has a particular profile of histone modifications that distinguish it from the other non-coding regions. Different methylation states of H4K20, H3K9 and H3K27 were found to be enriched in each region relative to the other regions. These findings indicate that non-genic regions of the genome are variable with respect to histone modification patterns, rather than being monolithic. We furthermore used consensus sequences for unassembled centromeres and telomeres to identify the significant histone modifications in these regions. Finally, we compared the modification patterns in non-genic regions to those at silent genes and genes with higher levels of expression. For all tested methylations with the exception of H3K27me3, the enrichment level of each modification state for silent genes is between that of non-genic regions and expressed genes. For H3K27me3, the highest levels are found in silent genes.In addition to the histone modification pattern difference between euchromatin and heterochromatin regions, as is illustrated by the enrichment of H3K9me2/3 in non-genic regions while H3K9me1 is enriched at active genes; the chromatin modifications within non-genic (heterochromatin-like) regions (e.g. subtelomeres, pericentromeres and gene deserts) are also quite different.The chromatin state and transcription level of a chromosomal region has been found to be related to modifications of histones [1,2] as well as DNA [3,4]. 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
%U http://www.biomedcentral.com/1471-2164/10/143