Fortin Jean-Philippe, Hansen Kasper D
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Road, Baltimore, 21205, MD, USA.
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 1900 East Monument Street, Baltimore, 21205, MD, USA.
Genome Biol. 2015 Aug 28;16(1):180. doi: 10.1186/s13059-015-0741-y.
Analysis of Hi-C data has shown that the genome can be divided into two compartments called A/B compartments. These compartments are cell-type specific and are associated with open and closed chromatin. We show that A/B compartments can reliably be estimated using epigenetic data from several different platforms: the Illumina 450 k DNA methylation microarray, DNase hypersensitivity sequencing, single-cell ATAC sequencing and single-cell whole-genome bisulfite sequencing. We do this by exploiting that the structure of long-range correlations differs between open and closed compartments. This work makes A/B compartment assignment readily available in a wide variety of cell types, including many human cancers.
对Hi-C数据的分析表明，基因组可分为两个称为A/B区室的部分。这些区室具有细胞类型特异性，并与开放和封闭的染色质相关。我们表明，可以使用来自几个不同平台的表观遗传数据可靠地估计A/B区室：Illumina 450 k DNA甲基化微阵列、DNase超敏性测序、单细胞ATAC测序和单细胞全基因组亚硫酸氢盐测序。我们通过利用开放和封闭区室之间远距离相关性的结构差异来做到这一点。这项工作使得A/B区室分配在多种细胞类型中都很容易实现，包括许多人类癌症。
