ChIP-on-chip examination of inducible genes in T cells

Specific chromatin characteristics, especially the modification status of the core histone proteins, are associated with different gene expression states. For example, active genes are marked by histone acetylation and methylation on specific lysine residues while inactive genes are marked by histones that are methylated on a different set of lysine residues and are not acetylated. There is growing interest in the chromatin characteristics of genes that respond to environmental or developmental signals with evidence that developmentally regulated genes may possess distinct chromatin marks. Using a T cell model, we examined the chromatin characteristics of inducible genes that respond to activation using ChIP-on-chip. We find that inducible genes, especially rapidly induced primary response genes, are more likely to display the chromatin characteristics of active genes, ie high levels of H3K9 acetylation. Consequently, only a small percentage of inducible genes display an increase in chromatin acetylation following activation. Our results provide evidence that inducible genes, especially rapidly induced genes, can be defined by their chromatin signature. Keywords: ChIP-chip Cells were stimulated for 0h, 0.5h or 4h. Extracts were immunoprecipitated with either, H3K9ac, H3 or no antibody and total genomic input DNA was also collected. H3K9acetylated ChIP samples were compared to either total input genomic DNA or pan histone 3 (H3) ChIP samples. Mock ChIP samples were compared to total input DNA. 2 biological replicates were used for all treatments except for non-stimulated EL4 cells where 3 replicates were used.