Dual Cross-Linking Improves Ability to Map Chromatin Loops

Hi-C is a method that maps the 3D architecture and folding pattern of the genome generating annotations of features, like DNA loops and domains, that bring distal elements in proximity and influence their regulation. Cross-linking samples is the first step in Hi-C and can greatly affect the quality of contacts observed in the Hi-C data. Here we are testing the quality of data processed with formaldehyde cross-linking versus formaldehyde plus DSG dual cross-linking in cell lines and human tissues, using standard Intact Hi-C protocol and Juicer 2 pipeline. We found that dual cross-linking improves noise statistics and DNA yield that can be attributed to heightened chromatin stability from the addition of DSG. Furthermore, we can see that looping signal, regulatory, and architectural features present are enhanced with dual cross-linking. After further investigation for robustness, dual cross-linking can be adopted as a new standard protocol for Hi-C tissue processing.