Evolutionary dynamics of genomes and epigenomes
Cells in an individual have the exactly same genomic sequence in principle. But the genome-encoded functions are decoded in different regions in different cell types, which underlies cell-type-specific gene expression profiles. This regulatory mechanism is called epigenetics, and achieved mainly by chemical modifications (e.g., methylation) of genomic DNA and histone proteins. Epigenome is the whole of epigenetic modifications present in a cell.
Epigenetic diversity among individuals sometimes generates phenotypic diversity. We aim to understand the molecular mechanisms that generate epigenetic differences and how genome and epigenome affect each other during evolution. We study the genomic and epigenomic diversities within a species (mouse) and between species (primates) by using next generation sequencer.
Functions of retrotransposons and their regulation
In mammals including humans, protein-coding sequences make up only 1% of the genome. About a half of the rest are occupied by retrotransposons, a class of mobile genetic elements. Although retrotransposons were regarded as junk DNA, they are now recognized as a driver of genome evolution. Moreover, evidence has accumulated that retrotransposons can regulate other parts of the genome in various ways. We study such retrotransposon-encoded functions, their regulation, and the effects of retrotransposon transposition on the host epigenome.
Genomic integrity of germ cells
Germ cells are the sole type of cells that convey the genome information to the next generation. Thus, they must maintain the genomic integrity by suppressing mutagenic events, such as retrotransposon transposition and unequal crossing over in meiotic homologous DNA recombination. We study how the retrotransposons are epigenetically silenced during germ cell development and how meiotic recombination events are epigenetically regulated.