Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription [ChIP-Seq]

3D chromatin structure, enhancers, and gene transcription function together to regulate cellular differentiation, establish cellular identity, and respond to external stimuli; however, the functional interplay between these regulatory elements remains incompletely understood. To infer potential causal relationships, we mapped 3D chromatin architecture, histone H3 K27 acetylation, chromatin accessibility, and gene expression across eight narrowly-spaced time points of macrophage activation. Enhancers and genes that were connected by a loop exhibited stronger correlation between histone H3K27 acetylation and expression than can be explained by distance or proximity alone, suggesting that the presence of a chromatin loop may facilitate functional regulatory connections via methods beyond simply increasing their frequency of physical proximity. Changes in enhancer acetylation preceded changes in gene expression by 30-60 minutes further supporting a causal relationship. Changes in gene expression exhibit a directional bias at differential loop anchors. The anchors of gained enhancer-promoter loops are associated with increased gene expression of genes oriented away from the center of the loop. Surprisingly, lost enhancer-promoter loops were also associated with increased gene expression, particularly within the bounds of the loop. Analysis of absolute levels of transcription revealed that lost loops were characterized by particularly high levels of internal transcription. Taken together, these results are consistent with a reciprocal relationship between looping and transcription. In this model, loops can enhance transcription by facilitating enhancer-promoter contacts, but also high levels of transcription can negatively impact loop strength by antagonizing loop extrusion mechanisms. Overall design: Genome-wide time course of enhancer activity (H3K27ac ChIP-Seq) in human THP-1-derived macrophages treated with LPS/IFNg for 0, 0.5, 1, 1.5, 2, 4, 6, and 24 hours. Coupled with datasets of chromatin accessibility (ATAC-Seq), chromatin structure (in situ Hi-C), and gene expression (RNA-Seq).