Nucleosome spacing regulates linker methylation by DNMT3A2/3B3

Although cells contain millions of unique linkers, the rules that dictate which linkers get targeted by DNMT3 enzymes are not understood. Here, we show that nucleosome spacing governs linker DNA methylation and H3K36me2 recognition by the DNMT3A2/3B3 tetramer, directly linking de novo methylation to chromatin structure and nucleosome remodeling.

We present the first structures of DNMT3A2/3B3 bound to di-nucleosomes, revealing inter-nucleosome interactions that control methylation. DNMT3A2/3B3 bridges nucleosomes separated by short DNA linkers, suppressing methylation, while long linkers allow DNMT3A2/3B3 to engage each nucleosome separately, promoting methylation. Finally, DNMT3A2/3B3 scans for properly modified substrates by positioning its PWWP domain at the H3 tail exit site, however H3K36me2 recognition is blocked when DNMT3A2/3B3 bridges di-nucleosomes with short linkers.