Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development

Interphase chromatin is organized into topologically associating domains (TADs). Within TADs, chromatin looping interactions are formed between DNA regulatory elements, but their functional importance for the establishment of the 3D genome organization and gene regulation during development is unclear. Using high-resolution Hi-C experiments, we analyze higher order 3D chromatin organization during Drosophila embryogenesis and identify active and repressive chromatin loops that are established with different kinetics and depend on distinct factors: Zelda-dependent active loops are formed before the midblastula transition between transcribed genes over long distances. Repressive loops within polycomb domains are formed after the midblastula transition between polycomb response elements by the action of GAGA factor and polycomb proteins. Perturbation of PRE function by CRISPR/Cas9 genome engineering affects polycomb domain formation and destabilizes polycomb-mediated silencing. Preventing loop formation without removal of polycomb components also decreases silencing efficiency, suggesting that chromatin architecture can play instructive roles in gene regulation during development. [Display omitted] [Display omitted] •Two waves of active chromatin loops during early Drosophila embryogenesis•Repressive loops within polycomb domains are formed after the midblastula transition•GAF-dependent looping between PREs is dispensable to recruit PcG proteins•Looping between PREs stabilizes gene silencing during development Ogiyama et al. used a combination of Hi-C analysis, microscopy, and genome engineering to analyze the kinetics of 3D chromatin interactions during Drosophila development and the consequences of the perturbation of chromatin contacts on genome function, indicating that the 3D genome architecture can play instructive roles in gene regulation.