Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation [RNA-Seq]

Estrogen hormones are implicated in a majority of breast cancers and estrogen receptor alpha (ER) orchestrates a complex molecular circuitry that is not yet fully elucidated. Here we investigated genome-wide DNA methylation, histone acetylation and transcription after estradiol (E2) deprivation and re-stimulation to better characterise the ability of ER to coordinate gene regulation. We found that E2 deprivation mostly resulted in DNA hypermethylation and histone deacetylation in enhancers. Transcriptome analysis revealed that E2 deprivation leads to a global down-regulation in gene expression. Enrichment analysis of transcription factor (TF) binding and motif occurrence in the proximity of E2 deprivation-mediated differentially methylated and acetylated sites reinforces the importance of AP-1 and FOX proteins, Finally, most deprivation-dependent epigenetic changes were reversed following E2 re-stimulation. Control MCF-7 HTB-22 breast cancer cells (CTR) were cultured continuously for 14 days in E2-containing medium, while E2-deprived cells (E2D) were cultured in the same conditions as CTR only lacking E2. The re-stimulated cells (ReSt) were E2-deprived for 4 days and re-stimulated for the 10 following. Each treatment (CTR, E2D and ReSt) and timepoint (d0, d4, d14) is available in triplicates. See publication for schematic design

雌激素与绝大多数乳腺癌的发生发展密切相关，而雌激素受体α（ER，estrogen receptor alpha）所构建的复杂分子调控网络尚未被完全阐明。本研究通过对雌二醇（E2，estradiol）剥夺及再刺激处理后的样本开展全基因组DNA甲基化、组蛋白乙酰化与转录组水平分析，以更深入地解析ER介导的基因调控能力。研究发现，E2剥夺主要会导致增强子区域出现DNA高甲基化与组蛋白去乙酰化现象。转录组分析结果显示，E2剥夺会引发全基因组范围内的基因表达整体下调。对E2剥夺介导的差异甲基化与乙酰化位点周边的转录因子（TF，transcription factor）结合事件及基序分布进行富集分析，进一步验证了AP-1与FOX家族蛋白的关键作用。最终，绝大多数依赖于E2剥夺的表观遗传变化在E2再刺激后均得到了逆转。本研究设置的对照组MCF-7 HTB-22乳腺癌细胞（CTR）在含E2的培养基中连续培养14天；E2剥夺组细胞（E2D）则在与对照组一致的培养条件下培养，仅去除培养基中的E2。再刺激组细胞（ReSt）先经4天的E2剥夺处理，随后再进行10天的E2再刺激培养。各处理组（CTR、E2D与ReSt）及各时间点（d0、d4、d14）的样本均设置3次生物学重复。具体实验设计示意图详见相关发表论文。