CBCB scientists Mahfuza Sharmin, Hector Corrada Bravo, and Sridhar Hannenhalli publish a paper in BMC Cancer on hypomethylated blocks in colon cancer

Lead author and CBCB doctoral student Mahfuza Sharmin, and CBCB faculty Hector Corrada Bravo and Sridhar Hannenhalli, have published a paper titled "Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer" on February 11, 2016 in the journal BMC Cancer. In this paper, they found that the classical promoter epigenomic mark - H3K4me3, is highly enriched at Hypomethylated Block (HMB) boundaries, as are insulator protein CTCF bound sites. HMB boundaries harbor distinct combinations of transcription factor (TF) motifs. A Random Forest machine learning model based on TF motifs can accurately distinguish boundaries not only from regions inside and outside HMBs, but surprisingly, from active promoters as well. Interestingly, the distinguishing TFs and their interacting proteins are involved in chromatin modification. Finally, HMB boundaries significantly coincide with the boundaries of Topologically Associating Domains of the chromatin. Their analyses suggest that the overall architecture of HMBs is guided by pre-existing chromatin architecture, and are associated with aberrant activity of promoter-like sequences at the boundary.

"Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer" article: https://bmccancer.biomedcentral.com/articles/10.1186/s12885-016-2128-1