An Epic Advance in Epigenomics: Automated CUT & RUN Enables Chromatin Profiling for Scaled Research & Drug Discovery Applications

Oktober 24, 2023


Dynamic changes in chromatin drive gene expression programs during cellular development and contribute to pathological changes underlying disease. To date, efforts to characterize chromatin dynamics have largely focused on chromatin accessibility (ATAC-seq) and DNA methylation profiling (bisulfite-seq). However, these assays provide a binary view of chromatin (open vs. closed), limiting their ability to decipher clear determinants of cellular identity or derive mechanistic insight into disease etiology.

Epigenomic features – such as histone post-translational modifications (PTMs) and chromatin-associated proteins (e.g., transcription factors) – regulate chromatin structure, gene expression, and cell function. Mapping these features provides a rich context to study cell fate and offers the potential for discovering new biomarkers and drug targets. Despite widespread interest, efforts to integrate epigenomics into large-scale cell-type profiling and drug development pipelines have been hampered by the poor sensitivity, low throughput, and high costs of traditional chromatin mapping technology (ChIP-seq).

During this webinar, EpiCypher's Andrea Johnstone will present a breakthrough automated CUT&RUN (autoCUT&RUN) assay for rapid, ultra-sensitive epigenomics. This workflow generates reliable profiles down to 10,000 cells and is supported by rigorous optimization, high-quality antibodies, robust spike-in controls, and streamlined DNA cleanup using magnetic SPRI beads.

Andrea will also discuss how autoCUT&RUN can be applied at-scale to map the epigenome in challenging clinical samples, detect dynamic changes after drug treatment, and identify cell-specific chromatin signatures. This technology has broad applications in fields where the potential of epigenomics has yet to be fully realized, including cell identity fingerprinting and translational research.

At-a-Glance Insights:

  • Improved technologies are needed to fully realize the potential of chromatin research to illuminate cell development pathways and disease pathology.
  • EpiCypher has leveraged rigorous R&D efforts, proprietary spike-in control technology, and best-in-class reagents to develop the first commercial automated CUT&RUN assay.
  • AutoCUT&RUN enables highly sensitive, low-cost epigenomics at the scale required to study chromatin dynamics for advanced applications, including cell type profiling, biomarker discovery, and therapeutic development.

Meet the Speakers

Andrea Johnstone, Ph.D., is the Senior Director of Product Development at EpiCypher, where she leads the commercialization of novel chromatin research technologies. She earned her PhD under the mentorship of Dr. John Bixby at the University of Miami Miller School of Medicine, in the Miami Project to Cure Paralysis. Her predoctoral studies, supported by a Ruth L. Kirschstein National Research Service Award, used phenotypic high-throughput screening to identify and characterize novel therapeutic approaches for spinal cord injury.

As a Postdoctoral Fellow in the laboratory of Dr. Claes Wahlestedt (Department of Psychiatry, University of Miami Miller School of Medicine), Andrea studied novel epigenetic signaling pathways underlying neuropsychiatric disease. She applied these insights to establish and implement drug development pipelines, leading to the identification of preclinical candidate compounds. In 2016, Andrea joined EpiCypher to apply her background in drug discovery to develop innovative tools for the epigenetics research community.

Lori Euler has over 20 years of experience working in research and development labs in the areas of microbiology and molecular biology. In 1999, Lori joined DuPont as a staff scientist. Throughout her 16 years with the company, she helped engineer bacterial strains to produce a variety of compounds as part of their Green Chemistry initiative. She then went on to hold product management roles with Pall Corporation before joining Beckman Coulter Life Sciences in 2022, where she’s a senior manager of the genomics drug discovery product management team.

Lori earned a Bachelor of Science degree in microbiology at Rutgers University and a Master of Science degree in biomedical chemistry at Thomas Jefferson University. She has extensive publications, presentations and patents in her name, detailing her protocol and process development in the areas of metabolic engineering and bacterial strain analysis.