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

Abstract

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.

Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features

“…Interestingly, 93% (75 out of 81) of gained loops that overlapped a differential gene promoter showed the same direction of change as the gene (p = 2.91 × 10 −16 , binomial test) ( Fig 2C ). This is consistent with our previous work in macrophages 30,31 and suggests that gained loops are relevant in increasing transcription of genes at their anchors. Upregulated genes found at the anchors of gained loops include TGFB1 and THBS1 , both of which are megakaryocyte-related 32,33 .…”

“…In contrast, lost loops that overlapped a differential gene promoter showed no such concordant behavior, with only 33% (15 out of 45) exhibiting the same directional change as the gene (p = 0.04, binomial test) ( Fig 2C ). These findings again agree with our previous work in macrophages 30,31 , where we did not see a significant decrease in expression of genes at lost loop anchors, suggesting that loss of looping is not sufficient to decrease transcriptional output 30,31 . This is also consistent with work by Rao et al that found almost no change in gene transcription following virtually complete abrogation of loop-extrusion 14 .…”

“…And those increased genes tend to be fairly highly expressed. We observed this exact same phenomena in macrophages responding to LPS 31 . This is consistent with transcription occurring at a high level between loop boundaries being antagonistic to loop extrusion, something that is easy to imagine given that both involve fairly large molecular complexes traversing the same stretch of DNA.…”

“…While intersecting the results of this study can provide important mechanistic insights, several of the results raise new questions that must be addressed by future functional experiments. Second, in contrast to our previous work 31 , this time-course lacked the temporal resolution to put regulatory and transcriptional events in temporal order, which makes it difficult to infer the direction of causality between any two features. This was a conscious decision as the current cost of sequencing makes it unfeasible to acquire deeply sequenced data sets across deeply sampled time courses; however, this is likely to change soon as sequencing costs continue to decrease 48,49 .…”

The 3D genome landscape: Diverse chromosomal interactions and their functional implications

“…These opposing findings have implications for our understanding of how certain factors act on distinct regulatory elements such as enhancers and promoters to orchestrate cell type-specific gene expression. Some mechanisms suggest chromosome looping may mediate enhancer-promoter contacts and could be correlated with gene activity ( Palstra et al, 2003 ; Vernimmen et al, 2007 ; Rao et al, 2014 ; Bonev et al, 2017 ; Freire-Pritchett et al, 2017 ; Ghavi-Helm, 2020 ; Oudelaar et al, 2020 ; Oudelaar and Higgs, 2021 ; Reed et al, 2022 ). Interestingly, a recent study suggests that distinct regulatory sequences, termed tethering elements, could mediate distal enhancer-promoter contacts and determine activation dynamics ( Batut et al, 2022 ).…”