Genome-wide absolute quantification of chromatin looping

Three-dimensional genomics methods such as Hi-C and Micro-C have uncovered chromatin loops across the genome and linked these loops to gene regulation. However, these methods only measure three-dimensional interaction probabilities on a relative scale. Here we overcome this limitation by using live-imaging data to calibrate Micro-C in mouse embryonic stem cells, thus obtaining absolute looping probabilities for 65,929 Micro-C-identified chromatin loops. We find that the looped state is generally rare, with a mean pairwise looping probability of 1.2% and a maximum of 25% across the quantified loops. On average, CTCF-CTCF loops are stronger than cis-regulatory loops (2.2% versus <1%). Our findings can be extended to human cells with available Micro-C data under certain assumptions. Overall, we establish an approach for genome-wide absolute loop quantification and report that loops occur with low probabilities, generalizing recent live-imaging results to the whole genome.