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. (DOC)