Towards molecular evolutionary epigenomics with an expanded nucleotide code involving methylated bases.

ABSTRACT: In molecular evolution analyses, genomic DNA sequence information is usually represented in the form of 4 bases (ATGC). However, research since the turn of the century has revealed the importance of epigenetic genome modifications, such as DNA base methylation, which can now be decoded using advanced sequence technologies. Here we provide an integrated framework for analyzing molecular evolution of nucleotide substitution, methylation, and demethylation using an expanded nucleotide code that incorporates different types of methylated bases. As a first attempt, we analysed substitution rates between bases, both unmethylated and methylated ones. As the model methylomes, we chose those of Helicobacter pylori, a unicellular bacterium with the largest known repertoire of sequence-specific DNA m

SUBMITTER: Yoshida S 

PROVIDER: S-EPMC12666383 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature