Bivalent and Broad Chromatin Domains Regulate Pro-metastatic Drivers in Melanoma

Abstract

25Chromatin deregulation is an emerging hallmark of cancer. However, the extent of 26 epigenetic aberrations during tumorigenesis and their relationship with genetic 27 aberrations are poorly understood. Using ChIP-sequencing for enhancers (H3K27ac and 28 H3K4me1), promoters (H3K4me3), active transcription (H3K79me2) and polycomb 29 (H3K27me3) or heterochromatin (H3K9me3) repression we generated chromatin state 30 profiles in metastatic melanoma using 46 tumor samples and cell lines. We identified a 31 strong association of NRAS, but not BRAF mutations, with bivalent states harboring 32H3K4me3 and H3K27me3 marks. Importantly, the loss and gain of bivalent states 33 occurred on important pro-metastasis regulators including master transcription factor 34 drivers of mesenchymal phenotype including ZEB1, TWIST1, SNAI1 and CDH1. 35Unexpectedly, a subset of these and additional pro-metastatic drivers (e.g. POU3F2, 36 SOX9 and PDGFRA) as well as melanocyte-specific master regulators (e.g. MITF, ZEB2, 37and TFAP2A) were regulated by exceptionally wide H3K4me3 domains that can span 38 tens of thousands of kilobases suggesting roles of this new epigenetic element in 39 melanoma metastasis. Overall, we find that BRAF, NRAS and WT melanomas may use 40 bivalent states and broad H3K4me3 domains in a specific manner to regulate pro-41 metastatic drivers. We propose that specific epigenetic traits -such as bivalent and broad 42 domains -get assimilated in the epigenome of pro-metastatic clones to drive evolution of 43 cancer cells to metastasis. 44 45 46 47 Results 103 Bivalent polycomb repressive chromatin domains distinguish metastatic 104 melanoma tumors based on mutational subtypes. 105Chromatin state profiling remains a powerful tool for determining the regulatory status of 106 annotated genes and identifying novel elements in non-coding genomic regions 3,4 . Using 107ChIP-sequencing for enhancers (H3K27ac and H3K4me1), promoters (H3K4me3), active 108 transcription (H3K79me2) and polycomb (H3K27me3) or heterochromatin (H3K9me3) 109repression coupled with tissue-matched mutation, transcriptomic and methylation data, 110we describe the cis-regulatory landscape across 46 melanoma samples. These 111 constituted 20 metastatic melanoma tumors (profiled by the TCGA study 6 ), 10 patient-112

Interrogating Epigenome toward Personalized Approach in Cutaneous Melanoma

“…However, Terranova at al. found that metastatic melanomas harbor exceptionally wide H3K4me3 domains [ 119 ]. These domains can span tens of thousands of kilobases, and appear to be involved in the regulation of several EMT transcription factors (POU3F2, SOX9, and PDGFRA) as well as melanocyte-specific master regulators (MITF, ZEB2, and TFAP2A) [ 120 ].…”

“…These domains can span tens of thousands of kilobases, and appear to be involved in the regulation of several EMT transcription factors (POU3F2, SOX9, and PDGFRA) as well as melanocyte-specific master regulators (MITF, ZEB2, and TFAP2A) [ 120 ]. Terranova et al finally highlighted that particular events such as BRAF or NRAS mutations may employ specific chromatin states (bivalent states and broad H3K4me3 domains) to orchestrate transcriptional changes unique to a genotype, suggesting that epigenetic mechanisms play important roles in regulating CM behaviors [ 119 ].…”