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DNA methylation is an epigenetic modification that transfers a methyl group onto the C-5 position of the cytosine to form 5-methylcytosine. DNA methylation regulates gene expression by recruiting proteins involved in gene repression or by inhibiting the binding of transcription factor(s) to DNA, especially in regulation of Allele Specific Expression (ASE). In this study, we used Oxford Nanopore long-read sequencing technology to profile methylome in the two inbred mouse strains, C57BL/6J (B6) and DBA/2J (D2). Compared with bisulfite conversion followed by Illumina Sequencing, long-read sequencing technology allows us to achieve much longer read length of 4,653.675 base pairs on average while maintaining an average percent identity of 90.775%. We detected millions of methylation events and 1,465 differentially methylated regions (DMRs) between B6 and D2. Understanding more about how DNA methylation patterns of these mice affect neurological phenotype will further research into drug development for neurodegenerative diseases, such as Alzheimer’s disease (AD) and Parkinson’s disease (PD).

This work was conducted in the UND Department of Biology under the advisement of Dr. Xusheng Wang and supported by The UND Center for Biomedical Research Excellence (CoBRE) for Epigenomics of Development and Disease (X.W.), the UND CoBRE for Host-Pathogen Interactions (HPI) (X.W.), the ND EPSCoR STEM program (X.W.), the UND Vice President for Research & Economic Development (VPRED) seed program (X.W.), the American Society for Pharmacology & Experimental Therapeutics (ASPET) SURF Program, the Chair of the Department of Biomedical Sciences, the Division of Research & Economic Development at the University of North Dakota , an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103442, the Dean of the University of North Dakota School of Medicine & Health Sciences.

A special thanks to all my peers in the Xusheng Wang Laboratory: He Huang, Ling Li, Kincaid Rowbotham, Alyssa Erickson, and the UND Genomics Core for performing the DNA extraction and sequencing.

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Presented at the Fall 2021 Virtual UNDergraduate Showcase, Grand Forks, ND, December 9, 2021.

Genome-Wide Analysis of Methylome in the Mouse Brain using Long-Read Sequencing Technology

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