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

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 time points of macrophage activation. Enhancers and genes connected by loops exhibit stronger correlations between histone H3K27 acetylation and expression than can be explained by genomic distance or physical proximity alone. At these looped enhancer-promoter pairs, changes in acetylation at distal enhancers precede 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, and lost loops are often accompanied by high levels of transcription within the loop boundaries themselves. These results are consistent with a reciprocal relationship where loops can facilitate increased transcription by connecting promoters to distal enhancers, whereas high levels of transcription can impede loop formation.

Automated summary

In this study, potential causal relationships between 3D chromatin structure, enhancers, and gene transcription were investigated using genome-wide mapping in macrophage activation. The results suggest that chromatin loops can facilitate transcription by connecting promoters to distal enhancers, while high levels of transcription may impede loop formation.