Supplemental Materials: Evolutionary Expansion of DNA Hypomethylation in the Mammalian Germline Genome
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چکیده
Supplemental Methods 15 Sperm sample collection and library preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Hierarchical clustering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Orthologous promoter HMR sizes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Ultra-conserved HMRs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 Species-specific hypomethylation and methylation . . . . . . . . . . . . . . . . . . . . . . . . . . 16 Phylogenetic tree from multiple genome alignment . . . . . . . . . . . . . . . . . . . . . . . . . 16 State space and units of measurement for DNA methylation . . . . . . . . . . . . . . . . . . . . . 16 Phylo-epigenetic model with independent sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 Phylo-epigenetic model with interdependent sites . . . . . . . . . . . . . . . . . . . . . . . . . . 18 Model learning and inference for phylo-epigenetic model with interdependent sites . . . . . . . . 22 Sperm methylome evolution at well-conserved elements . . . . . . . . . . . . . . . . . . . . . . . 29 Sperm methylome evolution with mouse as reference species . . . . . . . . . . . . . . . . . . . . 29 Hypomethylation expansion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 Relative sequence substitution rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 Enrichment of histone modifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 Enrichment of transcription factor binding sites . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Gene ontology analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
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Evolutionary expansion of DNA hypomethylation in the mammalian germline genome.
DNA methylation in the germline is among the most important factors influencing the evolution of mammalian genomes. Yet little is known about its evolutionary rate or the fraction of the methylome that has undergone change. We compared whole-genome, single-CpG DNA methylation profiles in sperm of seven species-human, chimpanzee, gorilla, rhesus macaque, mouse, rat, and dog-to investigate epigen...
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