Chromatin accessibility and epigenetic modifications differ between frequently and infrequently rearranging VH genes

The molecular mechanisms that control the temporal and lineage-specific accessibility, as well as the rearrangement frequency of VH genes for VH-to-DJH recombination, are not fully understood. We previously found a positive correlation between the extent of histone acetylation and the differential rearrangement frequency of individual VH genes. Here, we demonstrated that poorly rearranging VH genes are more highly associated with histone H3 dimethylated at lysine 9, a marker of repressive chromatin, than frequently rearranging VH genes. We also observed a positive relationship between the differential binding of Pax5 to individual VHS107 genes and rearrangement frequency. Furthermore, we showed that accessibility of the regions flanking the Pax5 binding site and the recombination signal sequence (RSS) to restriction enzyme cleavage correspond with the differential rearrangement frequency of the VHS107 family members. In addition, we found that the CpG sites located in the coding regions of VH genes are methylated in general, while the extent of DNA methylation drops dramatically near the RSS. For the VHS107 family, one CpG site located 101 bp upstream of the RSS showed variable methylation that correlates with rearrangement frequency, and the methylation status of a CpG site located 34 bp downstream of the RSS could also favor the rearrangement of V1 over V11. These findings suggest that the extent of histone modifications, chromatin accessibility, DNA methylation, as well as the differential binding of Pax5 to VH coding regions, could all influence the rearrangement frequency of individual VH genes, although some of these mechanisms are not strictly B cell specific.