E-MTAB-336 - ChIP-chip by array of human cells for whole genome profiling of 4 histone modifications
Released on 3 December 2010, last updated on 25 January 2012
Whole genome profiling of 4 histone modifications (H3K27me1, H3K27me3,H3K36me1 and H3K36me3) using ChIP-on-chip. It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II) occupancy show preferential association with exons ("exon-intron marking"), linking chromatin structure and function to co- transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing.
ChIP-chip by array, binding site identification, cell type comparison, co-expression, tiling path
Complex Exon-intron Marking By Histone Modifications is Not Determined Solely by Nucleosome Distribution. Pawandeep Dhami; Peter Saffrey; Alexander W Bruce; Shane C Dillon; Kelly Chiang; Nicolas Bonhoure; Christoph M Koch; Jackie Bye; Keith D James; Nicola S Foad; Peter Ellis; Nicholas A Watkins; Willem H Ouwehand; Cordelia Langford; Robert M Andrews; Ian Dunham; David Vetrie.