Epigenetic Landscapes in Breast Cancer Cells

Chromatin architecture is essential to transcriptional regulation. Cancer cells undergo critical chromatin remodeling processes that interact with the activation or silencing of oncogenes or tumor suppressor genes. These processes, together with other alterations of the functional status of chromatins, are characterized by epigenetic marks such as covalent histone modifications, DNA methylations and etc. The epigenetic landscapes defined by these marks are key to understand their regulatory mechanisms as well as the contributions to cancer onset and progression. In this study, we focus on defining the epigenetics landscapes across different breast cancer subtypes. Here we present a collection of 11 key histone modifications across 13 distinct breast cancer cell lines, representing 5 major breast cancer subtypes, including two ER positive subtypes: Lumina-A and Lumina-B, HER2 positive subtype and triple-negative subtypes TNBC-Basal and TNBC-ClaudinLow, as well as normal-like immortal breast cells. Using combinatorial patterns of multiple histone modifications, we defined the whole genome chromatin state maps and identified specific signatures in breast cancer subtypes. H3K4me1, H3K4me3, H3K27me3, H3K36me3, H3K9me3, H3K9ac, H3K79me2, H3K27ac, H2BK120ub1, H3K23ac, and H4K8ac ChIP-seq, and input in 76NF2V, MCF10A, MCF7, ZR751, MB361, UACC812, SKBR3, AU565, HCC1954, MB231, MB436, MB468, and HCC1937 cells.

染色质架构对于转录调控至关重要。癌细胞会经历关键的染色质重塑过程，这些过程与癌基因或抑癌基因的激活与沉默相互关联。这类过程连同染色质功能状态的其他改变，均以表观遗传标记为特征，例如共价组蛋白修饰、DNA甲基化等。由这些标记所定义的表观遗传图谱，是解析其调控机制以及其对癌症发生与进展贡献的关键所在。本研究聚焦于解析不同乳腺癌亚型的表观遗传图谱。在此我们提供了覆盖13种不同乳腺癌细胞系的11种关键组蛋白修饰数据集，这些细胞系对应5种主要乳腺癌亚型：两种ER（雌激素受体，Estrogen Receptor）阳性亚型——Lumina-A与Lumina-B、HER2（人表皮生长因子受体2，Human Epidermal Growth Factor Receptor 2）阳性亚型，以及三阴性乳腺癌（Triple-Negative Breast Cancer, TNBC）的Basal型与ClaudinLow型，同时还包含类正常永生化乳腺细胞系。借助多种组蛋白修饰的组合模式，我们构建了全基因组染色质状态图谱，并鉴定出乳腺癌亚型特异性特征。本数据集涵盖H3K4me1、H3K4me3、H3K27me3、H3K36me3、H3K9me3、H3K9ac、H3K79me2、H3K27ac、H2BK120ub1、H3K23ac及H4K8ac的染色质免疫共沉淀测序（Chromatin Immunoprecipitation sequencing, ChIP-seq）数据，以及对应76NF2V、MCF10A、MCF7、ZR751、MB361、UACC812、SKBR3、AU565、HCC1954、MB231、MB436、MB468与HCC1937共13种细胞系的ChIP-seq input对照数据。