Data from: Monoallelic chromatin conformation flanking long-range silenced domains in cancer-derived and normal cells

Epigenetic inactivation of chromatin plays an important role in determining cell phenotype in both normal and cancer cells, but our knowledge is still incomplete with respect to any potential monoallelic nature of the phenomenon. We have genotyped DNA isolated from chromatin of two colorectal cancer-derived lines and a culture of normal human intestinal epithelial cells (HIEC), which was immunoprecipitated with antibodies to acetylated vs. methylated histone H3K9, and presented the data as B allele frequency differences over multiple single-nucleotide polymorphism (SNP) moving window averages. [B allele is an arbitrary term defined as one of the two alleles at any given SNP, named A and B]. Three different validation tests confirmed that peaks exhibiting differences represented monoallelic domains. These complementary tests confirmed the following: 1) genes in the regions of high B allele frequency difference were expressed monoallelically; 2) in normal cells all five imprinting control regions which carried heterozygous SNPs were characterized by B allele difference peaks; and 3) the haplotypes in the B allele difference peaks were faithfully maintained in the chromatin immunoprecipitated with the respective antibodies. In both samples most of the monoallelic domains were found at the boundaries between regions of open and closed chromatin. With respect to the cancer line, this supports the established concept of conformation spreading, but the results from the normal cells were unexpected. Since these cells were polyclonal, the monoallelic structures were probably not determined by random choice as occurs in X-inactivation, so we propose that epigenetic inactivation in some domains may be heritable and polymorphic in normal human cells.

染色质的表观遗传失活在正常细胞与癌细胞中均对细胞表型的确定发挥关键作用，但目前学界对该现象潜在的单等位基因特性的认知仍存在显著不足。我们对两株结直肠癌来源细胞系以及正常人肠上皮细胞（HIEC）的染色质分离所得DNA进行了基因分型，分别使用靶向乙酰化与甲基化组蛋白H3K9的抗体进行染色质免疫沉淀，并将数据以多个单核苷酸多态性（SNP）滑动窗口平均后的B等位基因频率差异形式呈现。[B等位基因为任意定义术语，指任一给定SNP位点的两个等位基因之一，分别命名为A和B]。三项独立验证实验证实，呈现频率差异的峰代表单等位基因结构域。这些互补验证实验确认了以下三点：1）高B等位基因频率差异区域内的基因以单等位基因形式表达；2）在正常细胞中，所有携带杂合SNP的五个印记控制区域均表现出B等位基因差异峰；3）经对应抗体免疫沉淀的染色质中，B等位基因差异峰所在的单倍型得到了忠实保留。在两类样本中，绝大多数单等位基因结构域均定位于开放染色质与闭合染色质的边界区域。针对癌细胞系的分析结果支持了已确立的构象扩散概念，但正常细胞的实验结果却出人意料。由于这批细胞为多克隆群体，单等位基因结构的形成可能并不如X染色体失活那般由随机选择决定，因此我们提出假说：正常人类细胞的部分结构域中，表观遗传失活或许具备可遗传性与多态性。