Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

• DOI: 10.15252/msb.20167311
• Publication Date: 2016-12-10T04:24:26Z
• Authors: Lilija Brant; Theodore Georgoma...; Milos Nikolic; Chris A Brackley; Petros Kolovos; Wilfred van Ijcken; Frank G Grosveld; Davide Marenduzzo; Argyris Papantonis
• Keywords: Chromosome conformation capture; CTCF; Folding (DSP implementation)

Abstract Mammalian interphase chromosomes fold into a multitude of loops to fit the confines cell nuclei, and looping is tightly linked regulated function. Chromosome conformation capture (3C) technology has significantly advanced our understanding this structure‐to‐function relationship. However, all 3C‐based methods rely on chemical cross‐linking stabilize spatial interactions. This step remains “black box” as regards biases it may introduce, some discrepancies between microscopy 3C studies have now been reported. To address these concerns, we developed “i3C”, novel approach for capturing interactions without need cross‐linking. We apply i3C intact nuclei living cells exploit native forces that chromatin folding. Using different types loci, computational modeling, methylation‐based orthogonal validation method, “ TALE ‐ iD ”, show resemble cross‐linked ones, but display improved signal‐to‐noise ratios are more focal regulatory elements CTCF sites, while strictly abiding topologically associating domain restrictions.