Statham Aaron L, Taberlay Phillippa C, Kelly Theresa K, Jones Peter A, Clark Susan J
Epigenetics Research Program, Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
Epigenetics Research Program, Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia ; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Australia, Darlinghurst, NSW 2010, Australia.
Genom Data. 2014 Dec 8;3:94-6. doi: 10.1016/j.gdata.2014.11.012. eCollection 2015 Mar.
DNA methylation and nucleosome positioning are two key mechanisms that contribute to the epigenetic control of gene expression. During carcinogenesis, the expression of many genes is altered alongside extensive changes in the epigenome, with repressed genes often being associated with local DNA hypermethylation and gain of nucleosomes at their promoters. However the spectrum of alterations that occur at distal regulatory regions has not been extensively studied. To address this we used Nucleosome Occupancy and Methylation sequencing (NOMe-seq) to compare the genome-wide DNA methylation and nucleosome occupancy profiles between normal and cancer cell line models of the breast and prostate. Here we describe the bioinformatic pipeline and methods that we developed for the processing and analysis of the NOMe-seq data published by (Taberlay et al., 2014 [1]) and deposited in the Gene Expression Omnibus with accession GSE57498.
DNA甲基化和核小体定位是促成基因表达表观遗传控制的两个关键机制。在致癌过程中，许多基因的表达会随着表观基因组的广泛变化而改变，被抑制的基因通常与局部DNA高甲基化以及其启动子处核小体的增加有关。然而，在远端调控区域发生的改变谱尚未得到广泛研究。为了解决这个问题，我们使用核小体占据率和甲基化测序（NOMe-seq）来比较乳腺和前列腺正常及癌细胞系模型之间全基因组的DNA甲基化和核小体占据率图谱。在这里，我们描述了为处理和分析（Taberlay等人，2014 [1]）发表并保存在基因表达综合数据库（登录号GSE57498）中的NOMe-seq数据而开发的生物信息学流程和方法。
