File S1 - Monoallelic Chromatin Conformation Flanking Long-Range Silenced Domains in Cancer-Derived and Normal Cells

Supporting Text and Figures S1, S2 and S3. Figure S1. Validation that BAF difference peaks reflect contiguous domains in HCT116. We reasoned that if BAF differences represented authentic differences between the two homologs, the material immunoprecitated by anti-Me should mainly be derived from one homolog, and that by anti-Ac mainly from the other throughout the length of high LD. Two regions under the long peak of BAF difference on chr1 (upper panel) were found for which HapMap data showed very high LD (r2 more than 0.9 throughout). The major allele frequency was plotted for anti-Ac (blue) and anti-Me (coral) for each SNP within the identified run of high LD. For every SNP, the anti-Ac ChIP yielded a higher BAF than the anti-Me ChIP, indicating perfect concordance between haplotype and immunoprecipitated material. Figure S2. Validation that BAF difference peaks reflect contiguous domains in HIEC. See legend to Figure S1. Three regions of high LD on chr7 are shown. Again perfect concordance was observed between haplotype and immunoprecipitated material. Figure S3. Validation that BAF difference peaks represent domains of monoallelic expression at SPRY2 (at 80.1 Mb, chr13). Genomic DNA and cDNA around rs504122 (C/T heterozygous in both HCT116 and HIEC) were amplified from both lines and sequenced. Upper panels, both alleles are expressed in HIEC, only the C in HCT116. Lower panel, BAF differences plotted for both cell lines, showing HCT116, but not HIEC, with BAF differences.
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补充材料文本及图S1、S2与S3。
图S1：验证BAF差异峰反映HCT116细胞中的连续结构域。我们推测，若BAF（等位基因频率，B Allele Frequency）差异代表两个同源染色体间的真实差异，则在高连锁不平衡（LD，Linkage Disequilibrium）区域内，抗Me免疫沉淀得到的物质应主要源自一个同源染色体，而抗Ac免疫沉淀得到的物质主要源自另一个同源染色体。在1号染色体BAF差异长峰（上方面板）下方的两个区域，经HapMap数据验证，其全程连锁不平衡程度极高（r²>0.9）。针对该高连锁不平衡区段内的每个单核苷酸多态性（SNP，Single Nucleotide Polymorphism），分别绘制抗Ac抗体（蓝色）与抗Me抗体（珊瑚色）的主要等位基因频率。结果显示，每个SNP对应的抗Ac染色质免疫沉淀（ChIP，Chromatin Immunoprecipitation）均得到高于抗Me ChIP的BAF值，表明单倍型与免疫沉淀物质之间存在完美的一致性。
图S2：验证BAF差异峰反映HIEC细胞中的连续结构域。详见图S1图例。本图展示了7号染色体上的三个高连锁不平衡区域。同样观察到单倍型与免疫沉淀物质之间存在完美的一致性。
图S3：验证BAF差异峰代表SPRY2基因（位于13号染色体80.1 Mb处）的单等位基因表达结构域。从两种细胞系中扩增并测序rs504122（在HCT116与HIEC中均为C/T杂合位点）周围的基因组DNA与互补DNA（cDNA）。上方面板结果显示：HIEC中两个等位基因均有表达，而HCT116中仅表达C等位基因；下方面板绘制了两种细胞系的BAF差异，可见仅HCT116存在BAF差异，HIEC无明显BAF差异。
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