Single cell genome structures of mouse diploid ES cells [CUT&Run]

We describe the first integrated 3D structural models of an entire mammalian diploid genome using data derived from both chromosome conformation capture and microscopy imaging. This has allowed us to study the association of open DNA regions imaged by ATAC-see and histone with the folding of chromosomes down to a scale of 100kb. Overall design: Cut and Run data for various histone modifications was collected in a diploid mouse ES cell line as it exited pluripotency. Using a genome build specific for this diploid mouse ES cell line we analysed the Cut and Run data for these histone modifications across the two parental genomes and in genome structures derived from single cell Hi-C.