Abstract 210: Direct multiomic mapping of chromatin proteins and DNA methylation

DNA methylation (DNAme) is a class of epigenetic marks that includes the methylation of cytosine residues (5mC) within CpG islands. In addition to well characterized roles regulating gene expression, imprinting, and silencing parasitic DNA elements, misregulation of DNAme is implicated in multiple cancers. Evidence is emerging that DNAme is not an independent epigenetic mark but rather closely linked to chromatin proteins. However, examining the relationships between DNAme and chromatin proteins is hampered by correlative analyses that cannot establish a direct mechanistic link. Furthermore, the traditional approach to measure DNAme relies upon harsh bisulfite chemical conversion, which introduces DNA breaks and systemic biases. To address these limitations, we developed CUT&RUN-EM: an ultra-sensitive multiomic technology that integrates EpiCypher's CUT&RUN genomic mapping with New England Biolab’s Enzymatic Methyl-seq (EM-seq). Together, these technologies permit high-resolution, simultaneous profiling of chromatin proteins and DNAme, enabling direct interrogation of the complex molecular crosstalk between these genomic features. To quantify the capabilities and limitations of the assay, we tested CUT&RUN-EM across chromatin proteins and cell lines. We show that CUT&RUN-EM is highly reproducible, specific, sensitive, and efficient, requiring as few as 5 million short-read sequences per reaction (10-100x less than whole-genome DNAme sequencing). The advent of CUT&RUN-EM will enable detailed interrogation of the cancer epigenome, providing insights into new therapeutic targets. Citation Format: Jen Spengler, Bryan J. Venters, Vishnu U. Sunitha Kumary, Allison Hickman, Anup Vaidya, Jonathan M. Burg, Louise Williams, Louise Williams, Chaithanya Ponnaluri, Pierre-Olivier Esteve, Issac Meek, Sriharsa Pradhan, Zu-Wen Sun, Martis W. Cowles, Michael-Christopher Keogh. Direct multiomic mapping of chromatin proteins and DNA methylation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 210.