SummaryChromatin modifying activities inherent to polycomb repressive complexes PRC1 and PRC2 play an essential role in gene regulation, cellular differentiation, and development. However, the mechanisms by which these complexes recognize their target sites and function together to form repressive chromatin domains remain poorly understood. Recruitment of PRC1 to target sites has been proposed to occur through a hierarchical process, dependent on prior nucleation of PRC2 and placement of H3K27me3. Here, using a de novo targeting assay in mouse embryonic stem cells we unexpectedly discover that PRC1-dependent H2AK119ub1 leads to recruitment of PRC2 and H3K27me3 to effectively initiate a polycomb domain. This activity is restricted to variant PRC1 complexes, and genetic ablation experiments reveal that targeting of the variant PCGF1/PRC1 complex by KDM2B to CpG islands is required for normal polycomb domain formation and mouse development. These observations provide a surprising PRC1-dependent logic for PRC2 occupancy at target sites in vivo.

Summary A class of cis-regulatory elements called enhancers plays a central role in orchestrating spatio-temporally precise gene expression programs during development. Consequently, divergence in enhancer sequence and activity is thought to be an important mediator of inter- and intra-species phenotypic variation. Here, we give an overview of emerging principles of enhancer function, current models of enhancer architecture, genomic substrates from which enhancers emerge during evolution and the influence of three-dimensional genome organization on long-range gene regulation. We discuss intricate relationships between distinct elements within complex regulatory landscapes and consider their potential impact on specificity and robustness of transcriptional regulation.

CpG islands (CGIs) are associated with most mammalian gene promoters. A subset of CGIs act as polycomb response elements (PREs) and are recognized by the polycomb silencing systems to regulate expression of genes involved in early development. How CGIs function mechanistically as nucleation sites for polycomb repressive complexes remains unknown. Here we discover that KDM2B (FBXL10) specifically recognizes non-methylated DNA in CGIs and recruits the polycomb repressive complex 1 (PRC1). This contributes to histone H2A lysine 119 ubiquitylation (H2AK119ub1) and gene repression. Unexpectedly, we also find that CGIs are occupied by low levels of PRC1 throughout the genome, suggesting that the KDM2B-PRC1 complex may sample CGI-associated genes for susceptibility to polycomb-mediated silencing. These observations demonstrate an unexpected and direct link between recognition of CGIs by KDM2B and targeting of the polycomb repressive system. This provides the basis for a new model describing the functionality of CGIs as mammalian PREs.DOI: http://dx.doi.org/10.7554/eLife.00205.001

Melanoma is a tumor of transformed melanocytes, which are derived from the embryonic neural crest. It is unknown to what extent the programs regulating neural crest development interact with mutations in the BRAF oncogene, the gene most commonly mutated in human melanoma1. We have utilized the zebrafish embryo to identify initiating transcriptional events upon BRAFV600E activation in the neural crest lineage. Transgenic mitf-BRAFV600E;p53-/- zebrafish embryos demonstrate a gene signature enriched for markers of multipotent neural crest cells, and exhibit a failure of terminal differentiation of neural crest progenitors. To determine if these early transcriptional events were important for melanoma pathogenesis, we performed a chemical genetic screen to identify small molecule suppressors of the neural crest lineage, which were then tested for effects in melanoma. One class of compounds, inhibitors of dihydroorotate dehydrogenase (DHODH) such as leflunomide, led to an almost complete abrogation of neural crest development in the zebrafish and a reduction in self-renewal of mammalian neural crest stem cells. Leflunomide exerts these effects by inhibiting transcriptional elongation of genes required for neural crest development and melanoma growth. When used alone or in combination with a specific inhibitor of the BRAFV600E oncogene, DHODH inhibition led to a marked decrease in melanoma growth both in vitro and in mouse xenograft studies. Taken together, these studies highlight developmental pathways in neural crest cells that have direct bearing upon subsequent melanoma formation.