Realizing the clinical potential of epigenomic technologies requires robust, scalable approaches that can profile large numbers of patient samples in parallel. Characterizing cell-type-specific chromatin landscapes is essential for this atlas however, technical limitations have prevented implementation of traditional approaches for genome-wide profiling of chromatin proteins on the scales necessary for this project.ĭespite the growing awareness that epigenetic derangements underlie many human diseases, very few methods for high-throughput profiling of epigenomic information are available. To provide a reference for molecular diagnosis of patient samples, efforts are underway to generate a comprehensive atlas of cells in the human body.

However, we are only just beginning to appreciate how assessing the activity of cis-regulatory elements may be used in clinical settings for patient diagnosis. Defects in the nuclear proteins that recognize these cis-regulatory elements underlie many human diseases that often manifest in specific tissues and cell types. Promoter elements lie near the 5′ transcriptional start sites (TSSs) of all genes, whereas distal cis-regulatory elements such as enhancers often bridge long stretches in the DNA to interact with select promoters and direct cell-type-specific gene expression.

The easy, cost-effective workflow makes automated CUT&RUN an attractive tool for high-throughput characterization of cell types and patient samples.Ĭells establish their distinct identities by altering activity of the cis-regulatory DNA elements that control gene expression. We test the ability of automated CUT&RUN to profile frozen tumor samples and find that our method readily distinguishes two pediatric glioma xenografts by their subtype-specific gene expression programs. We find that automated CUT&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. Here, we describe an automated CUT&RUN platform and apply it to characterize the chromatin landscapes of human cells. We recently introduced CUT&RUN, an antibody-targeted nuclease cleavage method that profiles DNA-binding proteins, histones and chromatin-modifying proteins in situ with exceptional sensitivity and resolution. 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.

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