Transient promoter interactions modulate developmental gene activation [RNA-Seq]

Transcriptional induction coincides with the formation of various chromatin topologies, including loss and gain of physical interactions between promoters and enhancers. While strong evidence supports that gene activation is accompanied by a general increase in promoter-enhancer interactions, how these topological changes are coordinated across time and space with other types of interactions to collectively enable gene activation remains unresolved. Here we combine chromatin conformation capture with the profiling of histone modifications and transcription during a finely resolved time-course of embryonic stem cell differentiation to determine how genome restructuring in 3D correlates with and informs transcriptional transitions. Our data indicates that genome restructuring follows only a few common patterns that are related to the magnitude of transcriptional induction. Using this approach we identify transiently formed interactions between gene promoters and distal regulatory elements for which we demonstrate by genetic deletion that they can contribute to the transcriptional induction of associated genes. Finally, using acute depletion of cohesin, we prevent the formation of early promoter-enhancer interactions, and show that this impairs the activation of corresponding genes, compatible with the possibility that early topological changes are instructive for transcription. Taken together, our study identifies the variety of typical topological changes during gene activation, detects an uncharacterized type of transcriptional enhancers and provides evidence that the earliest topological changes can affect the magnitude of gene activation. Our data agrees with the idea that the multitude of topological changes account for appropriate gene induction during cell differentiation. For the time-course analysis of promoter differentiation wildtype mouse embryonic stem cells (E14) were differentiated using retinoic-acid treatment and samples were collected at 0, 2, 4, 6, 24, 48 and 72 hours of treatment in biological duplicates to quadruplicates to conduct RNA-Seq. Transient enhancer within the Hoxb locus was deleted and two knockout clones (E3 and H12) as wella s one wildtuype clone (G4) were obtained with which the timecourse was also conducted. To assess how gene expression is affected by cohesin depletion, mESCs with and without acute depletion of SCC1 were differentiated for four hours. Samples were collected in triplicates.