TY - JOUR T1 - Automated <em>in situ</em> profiling of chromatin modifications resolves cell types and gene regulatory programs JF - bioRxiv DO - 10.1101/418681 SP - 418681 AU - Derek H. Janssens AU - Steven J. Wu AU - Jay F. Sarthy AU - Michael P. Meers AU - Carrie H. Myers AU - James M. Olson AU - Kami Ahmad AU - Steven Henikoff Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/09/16/418681.abstract N2 - Our understanding of eukaryotic gene regulation is limited by the complexity of protein-DNA interactions that comprise the chromatin landscape and by inefficient methods for characterizing these interactions. We recently introduced CUT&amp;RUN, an antibody-targeted nuclease-cleavage method that profiles DNA-binding proteins, histones and chromatin modifying proteins in situ with exceptional sensitivity and resolution. Here we describe an automated CUT&amp;RUN platform and apply it to characterize the chromatin landscapes of human cell lines. We find that CUT&amp;RUN profiles of histone modifications crisply demarcate active and repressed chromatin regions, and we develop a continuous metric to identify cell-type specific promoter and enhancer activities. We test the ability of automated CUT&amp;RUN to profile frozen tumor samples, and find that our method readily distinguishes two diffuse midline gliomas by their subtype-specific gene expression programs. The easy, cost-effective workflow makes automated CUT&amp;RUN an attractive tool for high-throughput characterization of cell types and patient samples. ER -