Focal DNA hypo-methylation in cancer is mediated by transcription factors binding

Abstract

Aberrant DNA methylation has emerged as a hallmark of cancer cells and profiling their epigenetic landscape has widely been carried out in many types of cancer. However, the mechanisms underlying changes in DNA methylation remain elusive. Transcription factors, initially thought to be repressed from binding by DNA methylation, have recently emerged as potential drivers of DNA methylation patterns. Here we perform a rigorous bioinformatic analysis integrating the massive amount of data available from The Cancer Genome Atlas to identify transcription factors driving aberrant DNA methylation. We predict TFs known to be involved in cancer as well as novel candidates to drive hypo-methylated regions such as FOXA1 and GATA3 in breast cancer, FOXA1 and TWIST1 in prostate cancer and NFE2L2 in lung cancer. We also predict TFs that lead to hyper-methylated regions upon TF loss such as EGR1 in several cancer types. Finally, we validate experimentally that FOXA1 and GATA3 mediate hypo-methylated regions in breast cancer cells. Our work shows the importance of TFs as upstream regulators shaping DNA methylation patterns in cancer.