Gene expression analysis of breast cancer (HCC1954) and normal breast cells (HMEC)

While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors as well as changes in chromatin modifications as caused by genetic mutations of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe the first complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. We find widespread DNA hypomethylation in the cancer cell, primarily at partially methylated domains (PMDs) in normal breast cells. Unexpectedly, genes within these regions are largely silenced in cancer cells. The loss of DNA methylation in these regions is accompanied by formation of repressive chromatin, with a significant fraction displaying allelic DNA methylation where one allele is DNA methylated while the other allele is occupied by histone modifications H3K9me3 or H3K27me3. Our results show a mutually exclusive and complementary relationship between DNA methylation and H3K9me3 or H3K27me3. These results suggest that global DNA hypomethylation in breast cancer is tightly linked to the formation of repressive chromatin domains and gene silencing, thus identifying a potential epigenetic pathway for gene regulation in cancer cells and suggesting a possible new approach toward the development of cancer therapeutics. mRNA-Seq of polyA-selected RNA from breast cancer HCC1954 and normal breast HMEC. 36 cycles of sequencing on Illumina platform.

尽管基因突变是癌症的标志性特征，但多数癌症在肿瘤发生过程中还会获得表观遗传改变（epigenetic alterations），包括抑癌基因的DNA异常高甲基化，以及由染色质修饰机器（chromatin-modifying machinery）突变引发的染色质修饰改变。
然而，目前尚未完全解析癌细胞中表观遗传改变的全貌。
本研究首次构建了低传代乳腺癌细胞系与原代人乳腺上皮细胞的单核苷酸分辨率全基因组甲基化组（methylome）图谱。我们发现癌细胞中存在广泛的DNA低甲基化现象，这类低甲基化区域主要对应正常乳腺细胞中的部分甲基化区域（partially methylated domains, PMDs）。出乎意料的是，这些区域内的基因在癌细胞中大多处于沉默状态。
这些区域的DNA甲基化丢失同时伴随抑制性染色质的形成，其中相当一部分区域呈现等位基因特异性DNA甲基化：一个等位基因发生DNA甲基化，而另一个等位基因则带有组蛋白修饰（histone modifications）H3K9me3或H3K27me3。我们的研究结果表明，DNA甲基化与H3K9me3或H3K27me3之间存在互斥且互补的关系。
上述结果提示，乳腺癌中全局性DNA低甲基化与抑制性染色质结构域的形成及基因沉默紧密相关，这不仅明确了癌细胞中基因调控的一条潜在表观遗传通路，也为癌症治疗药物的开发提供了全新的思路。
本研究对乳腺癌细胞系HCC1954与正常乳腺细胞HMEC的聚腺苷酸富集RNA（polyA-selected RNA）开展了mRNA测序（mRNA-Seq）。本次测序采用Illumina平台，测序循环数为36个。