Genome-wide DNA methylation profiling of mouse liver

To determine whether differences between background strains or housing conditions altered the hepatic methylome, We report the generation and analysis of genome-wide DNA methylation profiles at nucleotide resolution in mouse liver from two male mice on a mixed background (mixed-1, mixed-2) and two males on a pure Black-6 (B6-1, B62) background. Using Enhanced high-throughput Reduced Representation Bisulfite Sequencing (ERRBS), we enriched CpG islands in mouse liver, and covered a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse liver. We found that the total CpG methylation of each methylome was strikingly similar among the 4 mouse liver samples from two different genetic backgrounds. Analysis of all CpG sites with at least 10x coverage showed a bimodal distribution of methylation, with all samples having 25% of hypermethylated CpG sites and 60% as hypomethylated CpG sites. Given the high percent of genome coverage and robust depth at single nucleotide level, these datasets provide a resource for investigation into changes in DNA methylation patterns in liver disease, tumorigenesis and regeneration. Overall design: Ehanced reduced representation bisulfite sequencing (MspI 70~320bp size fraction) of liver tissue