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.
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.
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.
Deep imaging, machine-learning-based segmentation, and tissue annotation resulted in a developmental series of 3D digital ovules with cellular resolution allowing next-level analysis of the ontogenesis of this complex organ.