The organization of histone H3 modifications as revealed by a panel of specific monoclonal antibodies

Histone modifications play critical roles in the epigenetic regulation of gene expression and in the maintenance of genome integrity. Acetylation and methylation of histone H3 are particularly important in gene activation and silencing. We generated and characterized a panel of mouse monoclonal antibodies that specifically recognize different modifications on K4, K9, and K27 residues on histone H3. By using these antibodies for chromatin immunoprecipitation and immunoblotting, we analyzed the relationship between different modifications in nearby nucleosomes in human cells. Within a few nucleosome neighbors, trimethyl-K4 was associated with acetyl-K27, rather than with dimethyl-K4 and acetyl-K9, consistent with their co-localization on active promoters. Furthermore, simultaneous immunofluorescence using directly-labeled antibodies revealed that di- and tri-methylation on K4 was diminished during replicative senescence. These highly-reliable and fully-characterized monoclonal antibodies may facilitate future epigenomic studies on healthy and diseased cells.