Supporting Information CpG Island Methylation in Lymphoma Is Driven by the Genetic Configuration of Tumor Cells Rene Opavsky, Shu-Huei Wang, Prashant Trikha, Aparna Raval, Yuan Huang, Yue-Zhong Wu, Benjamin Rodriguez, Benjamin Keller, Sandya Liyanarachi, Guo Wei, Ramana V. Davuluri, Michael Weinstein, Dean Felsher, Michael Ostrowski, Gustavo Leone and Christoph Plass Figure S1. Methylation and Expression of RLGS Sequences (A) Southern blot analysis of control and tumor cell DNAs using RLGS fragments 6D20, 1F21 and 3F56 as probes. Control DNA (con) or Tumor DNAs (tumor) isolated from thymocytes of healthy EμSR-tTA mice or T cell lymphomas, respectively was digested either with EcoRV alone (-) or with EcoRV and NotI (+). The top bands (M) indicate methylated (not digested with NotI) and the lower bands indicate fragments digested with NotI (U). (B) Combined bisulfite restriction analysis (COBRA) analysis of bisulfite-treated DNA isolated from thymocytes of EμSR-tTA mice (con) or from nine different T cell lymphomas (tumors). PCR products were digested with restriction enzyme BstUI and loaded on PAGE gel along with 100 bp marker (M) and 100 % methylated (SssI treated DNA) control (100%). Undigested and digested fragments correspond to unmethylated and methylated DNA, respectively. (C) Expression of genes near the RLGS fragments 6D20, 5D36 and 3F70 was quantified in thymocytes isolated from three EμSR-tTA mice (open bars) and eight EμSR-tTA;Teto-MYC tumors (black bars) using real-time RT-PCR. The y-axis represents fold-decrease in gene expression relative to the levels of gene expression detected in the first control.

D A B C Figure S1 3F56 1F21 6D20 2G50 2F37 4E58 6D20 5D36 3F70 tumors con - + + + + + + + + + - M - U - + + + + + + + + + + 1F21 6D20 - + + + + + + + + + B 100% 2G50 2F37 M 4E58 con tumors undigest. fragment digest. fragments C D 6D20 5D36 3F70 tumors con 1 2 3 1 2 3 4 5 6 7 8 1 2 3 1 2 3 4 5 6 7 8 9 in gene expression Fold reduction 20 40 60 80 10 30 50 100 Figure S1