Mapping protein-DNA interactions genome-wide with DiMeLo-seq
About Annie Maslan
Annie Maslan is a 5th-year graduate student in the lab of Aaron Streets at the University of California, Berkeley. Annie develops new methods to measure protein-DNA interactions and genome conformation.
Molecular studies of genome regulation often rely on the ability to map where specific proteins interact with genomic DNA. Existing techniques for genome-wide mapping of protein-DNA interactions rely on DNA amplification followed by sequencing with short reads, which dissociates joint binding information at neighboring sites, removes endogenous DNA methylation information, and precludes the ability to reliably map interactions in repetitive regions of the genome. To address these limitations, we created a new protein-DNA mapping method, called Directed Methylation with Long-read sequencing (DiMeLo-seq), which methylates DNA near each target protein’s DNA binding site in situ, then leverages the ability to distinguish methylated and unmethylated bases on long, native DNA molecules using nanopore sequencing.