Genome-wide absolute quantification of chromatin looping

We developed a method to estimate the 3D interaction probabilities of chromatin loops across the genome on an absolute scale from Micro-C maps. To calibrate the method, we performed Micro-C on two engineered mouse embryonic stem cell (mESC) lines, each containing a fluorescently labeled chromatin loop that was quantified in previous live imaging studies. One loop is an endogenous loop containing the Fbn2 gene, and the other is a synthetic loop near the Npr3 gene. We performed two replicates of Micro-C per cell line. Using our absolute quantification method, we find that loops generally form with low probabilities. We also provide an ultra-deep merged Micro-C map for mESCs that combines all existing mESC Micro-C datasets to date, containing a total of 15.6 billion unique interactions. Overall design: Genome-wide Micro-C was performed on two replicates of the engineered cell line containing the fluorescently tagged Fbn2 loop ("Fbn2 cell line"), as well as two replicates of the engineered cell line containing the fluorescently tagged synthetic Npr3 loop ("Npr3 cell line"); all cells were in untreated condition.