Cancer is a disease consisting of both genetic and epigenetic changes. While increasing evidence demonstrates that tumour progression entails chromatin-mediated changes such as DNA methylation, the role of histone variants in cancer initiation and progression currently remains unclear. Here, we report that the histone variant macroH2A (mH2A) suppresses tumour progression of malignant melanoma. Loss of mH2A isoforms, histone variants generally associated with condensed chromatin and fine-tuning of developmental gene expression programs1-4, is positively correlated with increasing malignant phenotype of melanoma cells in culture and human tissue samples. Knockdown of mH2A isoforms in melanoma cells of low malignancy results in significantly increased proliferation and migration in vitro and growth and metastasis in vivo. Restored expression of mH2A isoforms rescues these malignant phenotypes in vitro and in vivo. We demonstrate that the tumour promoting function of mH2A loss is mediated, at least in part, through direct transcriptional up-regulation of CDK8. Suppression of CDK8, a colorectal cancer oncogene5, 6, inhibits proliferation of melanoma cells, and knockdown of CDK8 in cells depleted of mH2A suppresses the proliferative advantage induced by mH2A loss. Moreover, a significant inverse correlation between mH2A and CDK8 expression levels exists in melanoma patient samples. Taken together, our results demonstrate that mH2A is a critical component of chromatin that suppresses the development of malignant melanoma, a highly intractable cutaneous neoplasm.

SUMMARY Histone variants are emerging as key regulatory molecules in cancer. Here we report a novel role for the H2A.Z isoform H2A.Z.2 as a driver of malignant melanoma. H2A.Z.2 is highly expressed in metastatic melanoma, correlates with decreased patient survival, and is required for cellular proliferation. Our integrated genomic analyses reveal that H2A.Z.2 controls the transcriptional output of E2F target genes in melanoma cells. These genes are highly expressed and display a distinct signature of H2A.Z occupancy. We identify BRD2 as an H2A.Z interacting protein, whose levels are also elevated in melanoma. We further demonstrate that H2A.Z.2 regulated genes are bound by BRD2 and E2F1 in a H2A.Z.2-dependent manner. Importantly, H2A.Z.2 deficiency sensitizes melanoma cells to chemotherapy and targeted therapies. Collectively, our findings implicate H2A.Z.2 as a mediator of cell proliferation and drug sensitivity in malignant melanoma, holding translational potential for novel therapeutic strategies.

Histone variants are key players in shaping chromatin structure, and, thus, in regulating fundamental cellular processes such as chromosome segregation and gene expression. Emerging evidence points towards a role for histone variants in contributing to tumor progression, and, recently, the first cancer-associated mutation in a histone variant-encoding gene was reported. In addition, genetic alterations of the histone chaperones that specifically regulate chromatin incorporation of histone variants are rapidly being uncovered in numerous cancers. Collectively, these findings implicate histone variants as potential drivers of cancer initiation and/or progression, and, therefore, targeting histone deposition or the chromatin remodeling machinery may be of therapeutic value. Here, we review the mammalian histone variants of the H2A and H3 families in their respective cellular functions, and their involvement in tumor biology.

The histone variant macroH2A generally associates with transcriptionally inert chromatin; however, the factors that regulate its chromatin incorporation remain elusive. Here, we identify the SWI/SNF helicase ATRX (a-thalassemia/ MR, X-linked) as a novel macroH2A-interacting protein.Unlike its role in assisting H3.3 chromatin deposition, ATRX acts as a negative regulator of macroH2A's chromatin association. In human erythroleukemic cells deficient for ATRX, macroH2A accumulates at the HBA gene cluster on the subtelomere of chromosome 16, coinciding with the loss of a-globin expression. Collectively, our results implicate deregulation of macroH2A's distribution as a contributing factor to the a-thalassemia phenotype of ATRX syndrome. The replacement of canonical histones with histone variants contributes to the dynamic nature of chromatin.Due to amino acid differences and, in turn, unique posttranslational modifications, histone variants can alter nucleosome structure, stability, and binding of effector proteins. Histone variants have unique genomic localization patterns, and thus specialized roles such as regulating gene expression or chromosome segregation during cell division . Therefore, the differential genomic incorporation of histone variants directly impacts critical cellular functions.The histone variant macroH2A (mH2A) is a vertebratespecific member of the H2A family and is unusual due to the presence of a C-terminal macro domain (Pehrson and Fried 1992). Two different genes encode mH2A1 and mH2A2 (H2AFY and H2AFY2, respectively), and two splice forms of mH2A1 exist: mH2A1.1 and mH2A1.2 (Costanzi and Pehrson 2001). mH2A is abundant in heterochromatin, including senescence-associated heterochromatic foci (SAHF) and the inactivated X chromosome (Xi) (Costanzi and Pehrson 1998;Zhang et al. 2005). In vitro studies suggest that the macro domain sterically hinders access of transcription factors to DNA, while mH2A's L1 loop produces inflexible nucleosomes (Angelov et al. 2003;Chakravarthy et al. 2005).Our group has recently demonstrated a role for mH2A isoforms in suppressing melanoma progression, and others have linked mH2A expression or its splice patterns to breast and lung cancer (Sporn et al. 2009;Kapoor et al. 2010;Novikov et al. 2011). However, the factors that regulate the association of mH2A with chromatin remain obscure. Therefore, identifying regulators of the incorporation of histone variants at distinct genomic loci is key to understanding how chromatin domains are established and maintained and how these may go awry in disease.A second group of factors contributing to chromatin dynamics are ATP-dependent chromatin remodeling complexes that rearrange or mobilize nucleosomes. Deregulation of members of the SWI/SNF family is implicated in various cancers and mental retardation (MR) syndromes, including ATRX (a-thalassemia/MR, X-linked), (Wilson and Roberts 2011). Mutations in ATRX, predominantly found in the H3K9me3-binding ADD (ATRX-DNMT3-DNMT3L) and/or helicase domains, are associated with ATRX sy...

SUMMARY Bromodomain and extraterminal domain inhibitors (BETi) represent promising therapeutic agents for metastatic melanoma, yet their mechanism of action remains unclear. Here we interrogated the transcriptional effects of BETi and identified AMIGO2, a trans-membrane molecule, as a BET target gene essential for melanoma cell survival. AMIGO2 is upregulated in melanoma cells and tissues compared to human melanocytes and nevi, and AMIGO2 silencing in melanoma cells induces G1/S arrest followed by apoptosis. We identified the pseudokinase PTK7 as an AMIGO2 interactor whose function is regulated by AMIGO2. Epigenomic profiling and genome editing revealed that AMIGO2 is regulated by a melanoma-specific BRD2/4-bound promoter and super-enhancer configuration. Upon BETi treatment, BETs are evicted from these regulatory elements, resulting in AMIGO2 silencing and changes in PTK7 proteolytic processing. Collectively, this study uncovers mechanisms underlying the therapeutic effects of BETi in melanoma and reveals the AMIGO2-PTK7 axis as a targetable pathway for metastatic melanoma.