CAD-C reveals the near-perfect alignment of sister chromatids

Three-dimensional (3D) genome organization plays a central role in gene regulation, chromatin folding, and genome stability. Although chromosome-conformation capture (3C)–derived methods have revolutionized our understanding of genome architecture, most remain limited in resolution, in their capacity to detect multiway interactions and in their ability to distinguish sister chromatids. Here, we present CAD-C, a new chromatin-conformation capture strategy that uses Caspase-Activated DNase (CAD) chromatin fragmentation. The fragmentation of chromatin to the nucleosome level by CAD digestion substantially enhance the proximity ligation efficiency, enabling formation of multi-nucleosome ligation products. Nanopore sequencing of these long DNA molecules allows reconstruction of chromatin fiber connectivity and 3D contact maps at nucleosome-level resolution. CAD-C furthermore captures multiway interactions. Importantly, CAD-C is also able to identify sister-chromatid interactions at the nucleosome resolution which reveals a surprisingly tight, nucleosome-scale register of cohesion in G2 in S. cerevisiae. Together CAD-C overcome several limitations of 3C approaches and is the first assay to distinguish sister chromatids interactions at the nucleosome level. Overall design: CAD-C of yeast cells synchronized in G1 or G2, and with inducible depletion of the Scc1 subunit of Cohesin using the AID system. Datasets includes high-resolution interaction maps. And Bigwig profile of sister nucleosome overlap.