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Abstract DNA methylation (DNAme) is an epigenetic mark that includes the modification of cytosine resides (5mC) within CpG islands. In addition to well characterized roles regulating gene expression, imprinting and silencing parasitic DNA elements, the misregulation of DNAme is implicated in multiple diseases. Evidence is emerging that DNAme is not an independent epigenetic mark but rather closely linked to the post translational modification (PTM) of histone proteins. However, examining the relationship between 5mC and PTMs are hampered by the usual approach of independent analyses that cannot establish a direct linkage. Furthermore, the traditional approach to measure 5mC relies upon harsh bisulfite chemical conversation of DNA, which introduces damage and systemic biases. To address these limitations, we developed Targeted Enzymatic Methylation-sequencing (TEM-seq): an ultra-sensitive multi-omic genomic mapping technology that delivers high resolution DNAme profiles at epitope-defined chromatin features. Importantly this assay is capable of directly examining the link between 5mC and histone PTMs and/or chromatin associated proteins (ChAPs). The TEM-seq workflow integrates CUT10% off-target binding, 90% enzymatic conversion of DNAme, 0. 5% conversion of unmethylated DNA). TEM-seq is also highly-sensitive, requiring only five million short-read sequences per assay (10-50x less than whole-genome 5mC-sequencing), demonstrating the disruptive potential of the assay to enable cost-effective approach for targeted DNAme analysis. Finally, we leveraged TEM-seq to gain mechanistic insights to Rett syndrome a neurodegenerative disorder that results from mutations in the 5mC-binding domain of the MECP2 gene. Citation Format: Keith E. Maier, Vishnu U. Sunitha Kumary, Bryan J. Venters, Allison Hickman, Anup Vaidya, James Anderson, Ryan Ezell, Jonathan M. Burg, Louise Williams, Chaithanya Ponnaluri, Pierre Esteve, Isaac Meek, Zu-wen Sun, Martis W. Cowles, Sriharsa Pradhan, Michael-Christopher Keogh. Direct multi-omics for the masses: Linking DNA methylation to chromatin targets via TEM-seq abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts) ; 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84 (6Suppl): Abstract nr 7027.
Maier et al. (Fri,) studied this question.