Skene and Henikoff. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 6, e21856 (2017). (PMID: 28079019)
In 2017, Steven Henikoff’s lab at the Fred Hutchinson Cancer Research Center published their first paper describing CUT&RUN. This in situ chromatin mapping assay builds on ChIC technology from Ulrich Laemmli’s group, using a protein A-fused micrococcal nuclease (pA-MNase) to selectively cleave antibody-bound chromatin loci in intact cells and nuclei. Skene et al. describes the assay and uses it to profile several transcription factors in yeast and human nuclei. Head-to-head comparisons with ChIP-seq assays further highlights the enhanced sensitivity, improved signal : noise, and reduced sequencing requirement of CUT&RUN vs. leading assays.
Meers et al. Improved CUT&RUN chromatin profiling tools. eLife 8, e46314 (2019). (PMID: 31232687)
This 2019 paper from the Henikoff lab reports the development of a novel protein A-protein G fused micrococcal nuclease (pAG-MNase), for use in CUT&RUN. pAG-MNase expands antibody species compatibility in CUT&RUN assays and forms the basis for EpiCypher’s CUTANA CUT&RUN technology. This paper also describes the use of E. coli DNA for assay calibration and a modified MNase digestion strategy for improved yield with minimal background, representing significant breakthroughs for CUT&RUN assays.
Yusufova et al. Histone H1 Loss drives lymphoma by disrupting 3D chromatin architecture. Nature AOP (2020). (PMID: 33299181)
Linker histone H1 proteins are important components of chromatin structure and are frequently mutated in B-cell lymphoma, but their role in cancer development has been unclear. Here, Yusufova et al. establish H1 as a bona fide tumor suppressor protein, demonstrating that H1 mutations alter chromatin structure to support re-expression of developmental genes and subsequent cancer development. EpiCypher’s use of CUTANA CUT&RUN technology to examine changes in H3K9me2 and H3K9me3 was key to uncovering this complex mechanism.
Wilson et al. ARID1A mutations promote P300-dependent endometrial invasion through super-enhancer hyperacetylation. Cell Rep. 33, 108366 (2020). (PMID: 33176148)
ARID1A is a key subunit of the SWI/SNF chromatin remodeling complex and is commonly mutated in severe forms of endometriosis; however, its function is not well defined. Here, Wilson et al. show that ARID1A co-localizes with and represses the p300 lysine acetyltransferase. Mutation of ARID1A results in increased H2K27ac at super-enhancers and supports invasive endometrial growth. To profile H3K27ac at super-enhancers, Wilson et al. applied EpiCypher’s CUTANA pAG-MNase for ultra-sensitive CUT&RUN assays.
Stengel et al. Definition of a small core transcriptional circuit regulated by AML1-ETO. Mol Cell AOP (2020). (PMID: 33382982)
Chromosomal translocations in cancer can result in fusions of transcription factors to other protein domains, altering gene expression to drive oncogenesis. In acute myeloid leukemia (AML), the most common fusion protein is AML-ETO, combining the DNA binding domain of AML/RUNX1 to the transcriptional corepressor ETO. Here, Stengel et al. performed a comprehensive analysis of AML-ETO function, utilizing PRO-seq, CRISPR-based mutagenesis, and EpiCypher CUT&RUN technology to define AML-ETO targets and downstream effects.