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

Abstract

The molecular mechanisms that control the temporal and lineage-specific accessibility, as well as the rearrangement frequency of V H genes for V H -to-DJ H recombination, are not fully understood. We previously found a positive correlation between the extent of histone acetylation and the differential rearrangement frequency of individual V H genes. Here, we demonstrated that poorly rearranging V H genes are more highly associated with histone H3 dimethylated at lysine 9, a marker of repressive chromatin, than frequently rearranging V H genes. We also observed a positive relationship between the differential binding of Pax5 to individual V H S107 genes and rearrangement frequency. Furthermore, we showed that accessibility of the regions flanking the Pax5 binding site and the RSS to restriction enzyme cleavage correspond with the differential rearrangement frequency of the V H S107 family members. In addition, we found that the CpG sites located in the coding regions of V H genes are methylated in general, while the extent of DNA methylation drops dramatically near the RSS. For the V H S107 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 V H coding regions, could all influence the rearrangement frequency of individual V H genes, although some of these mechanisms are not strictly B cell specific.

Determinants of public T cell responses

“…Apart from cis-elements in the immune receptor loci, including recombination signal sequence, enhancers and promoters [48,65], some trans-elements have been shown to play an important part in the regulation of V(D)J recombination [66][67][68]. Moreover, accumulating evidence has demonstrated the role of epigenetic factors in the regulation of V(D)J recombination, probably by altering the chromatin accessibility at the immune receptor loci [66,[69][70][71][72][73][74][75]. Future investigations into the upstream signals that regulate those known downstream regulators of V(D)J recombination should be able to provide insights into how the V(D)J recombination process can be manipulated.…”

Epigenetic and 3-dimensional regulation of V(D)J rearrangement of immunoglobulin genes

“…However, V11 and V13 rearrange at very different frequencies, yet they have identical RSS. Analysis of the acetylation status, however, showed a gradient of enrichment of H3Ac that mirrored the rearrangement frequency, and the reciprocal pattern was observed for the repressive modification H3K9me2 [23, 24]. Likewise, the extent of acetylation of 81X gene is much higher than that of the other V H 7183 genes, and it rearranges at a very high frequency [23].…”

Epigenetic aspects of lymphocyte antigen receptor gene rearrangement or ‘when stochasticity completes randomness’

“…Available immunoglobulin/TCR enhancer or promoter mouse mutants also provided invaluable sources of lymphoid cell nuclei for these studies. Overall, none too surprisingly, the immunoglobulin and TCR accessible loci were found to be enriched in epigenetic marks commonly associated with gene activation [including histone H3/H4 acetylation (H3ac; H4ac); di‐/tri‐methylation of Lys 4 of histone H3 (H3K4me2/me3)]; whereas the inaccessible loci were mostly decorated with epigenetic marks associated with gene silencing [including di‐/tri‐methylation of Lys 9 or Lys 27 of histone H3 (H3K9me2 and H3K27me3, respectively)] . Interestingly, hotspots of specific activating marks (H3K4me2/me3) or of marks differentially affected by enhancer mutations, for example, were identified, which may represent discrete domains perhaps important in, respectively, primary recruitment of the RAG nuclease, and the hierarchical establishment of locus‐specific, chromosomal accessibility …”