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Boundary stacking interactions enable cross-TAD enhancer–promoter communication during limb development
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Boundary stacking interactions enable cross-TAD enhancer–promoter communication during limb development
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Journal Article
Boundary stacking interactions enable cross-TAD enhancer–promoter communication during limb development
2024
Overview
Although promoters and their enhancers are frequently contained within a topologically associating domain (TAD), some developmentally important genes have their promoter and enhancers within different TADs. Hypotheses about molecular mechanisms enabling cross-TAD interactions remain to be assessed. To test these hypotheses, we used optical reconstruction of chromatin architecture to characterize the conformations of the
Pitx1
locus on single chromosomes in developing mouse limbs. Our data support a model in which neighboring boundaries are stacked as a result of loop extrusion, bringing boundary-proximal
cis
-elements into contact. This stacking interaction also contributes to the appearance of architectural stripes in the population average maps. Through molecular dynamics simulations, we found that increasing boundary strengths facilitates the formation of the stacked boundary conformation, counter-intuitively facilitating border bypass. This work provides a revised view of the TAD borders’ function, both facilitating and preventing
cis
-regulatory interactions, and introduces a framework to distinguish border-crossing from border-respecting enhancer–promoter pairs.
A combination of single-cell imaging and dynamic polymer simulation shows that stacked boundary conformation facilitates
cis
-regulatory elements communication across topologically associating domain (TAD) borders at the Pitx1 locus in developing mouse limbs.
Publisher
Nature Publishing Group US,Nature Publishing Group
Subject
/ 13/56
/ 14
/ 14/32
/ 14/63
/ 45
/ 631/136
/ 64
/ 64/60
/ Animal Genetics and Genomics
