Maintenance of histone crotonylation by YEATS2 and GCDH drives EMT in head and neck cancer [ChIP-seq]

Regulation of gene expression is an integral cellular process, fine-tuned by epigenetic marks like histone modifications. Perturbations in the activity or abundance of epigenetic factors can lead, or contribute to tumorigenesis in healthy cells. Remarkably, the addition of epigenetic marks is dependent on the metabolites produced during several essential cellular pathways. Here, we have explored the interplay between a highly expressed epigenetic factor YEATS2, and a metabolic enzyme GCDH in regulating epithelial to mesenchymal transition in head and neck cancer. We report the results of RNA-seq in YEATS2-silenced BICR10 cells to investigate the effect of YEATS2 in influencing gene expression globally. We have also performed ChIP-seq using YEATS2 antibody in BICR10 cells to obtain the globally occupied sites of YEATS2. Lastly, we report the changes in crotonylation at histone 3 lysine 27 (H3K27Cr) upon YEATS2 downregulation in BICR10 by performing ChIP-seq in shControl vs. shYEATS2 cells. ChIP-seq for YEATS2 performed in BICR10 cells. ChIP-seq for H3K27Cr was performed in shControl vs shYEATS2 BICR10 cells.

基因表达调控是细胞的核心生理过程，可通过组蛋白修饰等表观遗传标记(epigenetic marks)进行精细调控。表观遗传因子(epigenetic factors)的活性或丰度异常扰动，可直接引发或促进健康细胞的肿瘤发生。值得注意的是，表观遗传标记的添加依赖于多种核心细胞代谢通路所产生的代谢产物。本研究探讨了高表达表观遗传因子YEATS2与代谢酶GCDH之间的相互作用，及其在头颈癌(head and neck cancer)上皮间质转化(epithelial to mesenchymal transition)调控中的作用。本研究通过对YEATS2沉默的BICR10细胞开展RNA测序(RNA-seq)，以探究YEATS2对全基因组基因表达的全局影响。此外，本研究在BICR10细胞中使用YEATS2抗体进行染色质免疫共沉淀测序(ChIP-seq)，以获取YEATS2的全基因组结合位点。最后，本研究通过对比阴性对照短发卡RNA（shControl）与靶向YEATS2的短发卡RNA（shYEATS2）转染的BICR10细胞的ChIP-seq结果，分析了YEATS2下调后组蛋白3赖氨酸27巴豆酰化(H3K27Cr)的水平变化。本研究完成了BICR10细胞中YEATS2的ChIP-seq实验，以及shControl与shYEATS2转染的BICR10细胞中H3K27Cr的ChIP-seq实验。