Anti-DAPT: A “One-Pot” Multi-Omics Assay for Antibody-Directed DNA, RNA, and Protein Tagging

Abstract

The role of epigenetic modifications in gene regulation is well established, with mechanisms such as histone modification and DNA methylation playing pivotal roles in gene expression and cellular identity. Elucidating the molecular compositions and local environments at these epigenetic markers may uncover new mechanisms and therapeutic targets in diseases ranging from cancer to neurodegeneration. While recent methods such as CUT&Tag can efficiently identify the DNA sequences associated with such epigenetic features, there remains a lack of robust methodologies that allow simultaneous profiling of local protein and RNA environments that are also compatible with clinical specimens. Here, we present Antibody-directed DNA And Protein Tagging (Anti-DAPT), a novel epigenomic profiling assay that extends our previous iDAPT technology. Anti-DAPT employs an antibody-tethered protein A–Tn5 transposase–APEX2 peroxidase (pA-Tn5-APX) fusion protein to simultaneously tag DNA, RNA, and protein molecules proximal to epigenetic features of interest. As proof of concept, we demonstrate that all three protein domains of the pA-Tn5-APX fusion protein are appropriately functional for the purposes of the assay. Future application of the Anti-DAPT assay to various chromatin features, cell types, and tissues will enable unprecedentedly comprehensive and multi-omic mapping of the regulatory microenvironments that shape gene expression and drive human disease.