Annie Maslan from the University of California, Berkley spoke about “Mapping protein-DNA interactions genome-wide with DiMeLo-seq as part of the Nanopore Community Meeting 2021. They explained that existing methods for mapping protein binding use coverage as a proxy for binding.” Maslan noted that short-read methods obscure or complicate the interpretation of joint and independent binding events, don’t include methylation information, and cannot map interactions in repetitive regions. The lab Maslan is in developed DiMeLo-seq: directed methylation with long-read sequencing. They first permeabilized nuclei, bind an antibody, and then bind protein A-HiA5 and add SAM. Next they sequence and detect mA with long-read sequencing. Now, joint binding events on a single molecule can be interpreted. Protein-DNA interactions can be mapped in repetitive regions and methylation patterns can also be detected, as endogenous CpG methylation information is retained. Joint binding events on single molecules and coordinated protein-DNA dynamics are now interpretable. The method is available on Protocols.io and is a creative and powerful way of using Nanopore long-read sequencing.
