Lattice light-sheet single-molecule imaging shows 3D Sox2 enhancer clusters in live embryonic stem cells and reveals a model linking 3D spatial distribution of cis-elements, differential target search features and localized gene regulation.
In vertebrates, large regulatory landscapes sometimes behave as coherent regulatory units, which may explain the lack of effect sometimes observed when single enhancer sequences are deleted in isolation.
Seemingly contradictory findings of single-molecule and in vivo experiments on a major mechanism of chromosome organization are reconciled by computationally investigating mechanisms of loop extrusion that are consistent with both.
Identifying the pathways that support human naive-state pluripotent stem cells provides insights into the signalling-based regulation of human pluripotency and enables informed decisions to improve conditions for pluripotent cell culture.
Sox2 transcription is not correlated with spatial proximity of its essential regulatory enhancer in embryonic stem cells, suggesting gene transcription is not limited to periods of direct enhancer-promoter contact.
Human yolk sac-like cells, which share characteristics with the post-implantation human hypoblast, can model the interaction between the epiblast and hypoblast that occurs during early human development.
CUT&RUN (Cleavage Under Targets & Release Using Nuclease) profiles antibody-targeted DNA-binding proteins in situ with high resolution and low background, providing a simple, robust and scalable alternative to chromatin immunoprecipitation.