It is well established that histone modification play a major role in normal gene regulation and are often altered in carcinogenesis. However, the role of histone variant modification is less well studied. H2A.Z is an evolutionarily conserved H2A variant, implicated in the regulation of gene expression and its role in transcriptional deregulation in cancer also remains poorly understood. Recently however, we reported that acetylation of H2A.Z (acH2A.Z) is a key modification associated with gene activity in normal cells and epigenetic gene deregulation in tumourigenesis.
We now propose that acH2A.Z affects gene transcription by altering nucleosome occupancy at gene promoters and enhancers and this mechanism is used in cancer when cancer-related genes become deregulated.
Using epigenome-wide studies, including ChIP-seq and G-Nome-seq, we found first, that the acetylation of H2A.Z is found not only at active promoters but also at other genomic regulatory regions like active enhancers. Second we find that acH2A.Z occupancy is highly correlated with well positioned-nucleosomes suggesting that acetylation of H2A.Z-nucleosomes facilitates a rapid nucleosome eviction during transcriptional activation.
In addition, we have developed technique, which consists of performing next generation sequencing on bisulphite PCR amplicons to study in depth changes in nucleosome positioning in a representative example of a cancer-related gene. This analysis revealed a nucleosome shifting and ejection at the TSS of KLK2 gene in the cancer cell line (LNCaP) compare to the normal cell line (PrEC). We also showed a change in acH2A.Z at the TSS of KLK2 gene suggesting an association between acH2A.Z, well positioned nucleosomes and gene activation and confirming the genome-wide studies.
Our results demonstrate the importance of the acetylation of the histone variant H2A.Z in the establishment of active chromatin in a normal cell and that in cancer aberrant H2A.Z acetylation can lead to transcriptional deregulation through mechanisms that involve nucleosome positioning.