UMI-4C for quantitative and targeted chromosomal contact profiling. Drosophila melanogaster

We developed a targeted chromosome conformation capture (4C) approach that uses unique molecular identifiers (UMI) to derive high complexity quantitative chromosome contact profiles with controlled signal to noise ratios. We demonstrate that the method improves the sensitivity and specificity for detection of long-range chromosomal interactions, and that it allows the design of interaction screens with predictable statistical power. UMI-4C robustly quantifies contact intensity changes between cell types and conditions, opening the way toward incorporation of long-range interactions in quantitative models of gene regulation. Overall design: We constructed UMI-4C profiles of 5 different genomic loci (viewpoints) in one cell line under four different conditions, and two larval tissues, in order to study the 3D chromatin contact maps of these selected loci. The coordinates for these viewpoints are: BaitB1 chrX:1609904; BaitB2 chrX:1619649; BaitX1 chrX:158064; BaitX2 chrX:1829722; BaitX3 chrX:1945463