N6-methyldeoxyadenosine directs nucleosome positioning in Tetrahymena DNA

N6-methyldeoxyadenosine (6mA or m6dA) was shown more than 40 years ago to exist in simple eukaryotes, yet functional studies have been limited. Recent investigations in multiple eukaryotes suggest 6mA as a potential DNA epigenetic mark that plays regulatory roles in gene regulation. Here we use Tetrahymena thermophila as a model to examine the effects of 6mA on nucleosome positioning. We have employed independent methods to identify genome-wide 6mA distribution, which revealed the enrichment after transcription start sites with a periodic pattern and a mutually exclusive relationship with the positions of nucleosomes. The exclusive distribution pattern of 6mA and nucleosome can be recapitulated by in vitro nucleosome assembly on native Tetrahymena genomic DNA, but not on DNA without 6mA. Model DNA containing artificially installed 6mA resists nucleosome assembling compared to unmodified DNA in vitro. Computational simulation revealed that 6mA increases dsDNA rigidity, which disfavors nucleosome wrapping. Knockout of a potential 6mA methyltransferase disturbs the nucleosome positioning in Tetrahymena, leading to the transcriptome-wide change of gene expression. These findings uncover a new mechanism by which DNA 6mA assists to shape the chromatin topology in order to stabilize gene expression.