SUMMARY To infer potential causal relationships between 3D chromatin structure, enhancers, and gene transcription, we mapped each feature in a genome-wide fashion across eight narrowly-spaced timepoints of macrophage activation. Enhancers and genes connected by loops exhibited stronger correlations between histone H3K27 acetylation and expression than can be explained by genomic distance or physical proximity alone. Changes in acetylation at looped distal enhancers preceded changes in gene expression. Changes in gene expression exhibit a directional bias at differential loop anchors; gained loops are associated with increased expression of genes oriented away from the center of the loop, while lost loops were often accompanied by high levels of transcription with the loop boundaries themselves. Taken together, these results are consistent with a reciprocal relationship in which loops can facilitate increased transcription by connecting promoters to distal enhancers while high levels of transcription can impede loop formation. HIGHLIGHTS LPS + IFNγ triggers genome-wide changes in chromatin looping, enhancer acetylation, and gene expression Looped enhancer-promoter pairs exhibit ordered and correlated changes in acetylation and expression Changes in gene expression exhibit a directional bias at differential loop anchors Lost loops are associated with high levels of transcription within loop boundaries

Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription