Reconstitution of genome remodeling using Xenopus egg extracts

Abstract

Changes in 3D genome organization drive critical cellular transitions including cell division and differentiation. Cytoplasmic extracts derived from eggs of the African clawed frog Xenopus laevis offer a powerful system for reconstituting genome remodeling events in vitro and dissecting the underlying biochemical mechanisms. Female X. laevis produce thousands of large eggs that can be readily lysed by centrifugation to yield egg cytoplasm—commonly referred to as egg extract. This extract contains the full complement of molecules required to support multiple rounds of chromatin assembly, nuclear formation, DNA replication and repair, and chromosome segregation. Addition of an exogenous DNA source triggers rapid, highly reproducible remodeling that can be monitored by fluorescence microscopy, gel electrophoresis, or genomics approaches. The biochemical tractability of this system has historically been instrumental in revealing fundamental mechanisms of chromatin assembly and remodeling. This review summarizes the major genome remodeling assays enabled by Xenopus egg extracts and highlights recent advances in the field. We also outline promising new directions for leveraging this system to unravel the molecular basis of speciation and polyploidy.