Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development

Area of Science:

• Genomics
• Molecular Biology
• Developmental Biology

Background:

• Topologically associating domains (TADs) are crucial for organizing the genome into functional units.
• Promoters and enhancers are typically found within the same TAD, but exceptions exist for developmentally important genes, suggesting mechanisms for cross-TAD interactions.

Purpose of the Study:

• To investigate the molecular mechanisms underlying enhancer-promoter interactions across different TADs.
• To test hypotheses regarding chromatin conformation and the role of TAD boundaries in regulating gene expression.

Main Methods:

• Utilized optical reconstruction of chromatin architecture to analyze single-chromosome conformations of the Pitx1 locus in developing mouse limbs.
• Employed molecular dynamics simulations to model the effects of boundary strength on chromatin structure.

Main Results:

• Data support a model where stacked neighboring TAD boundaries, formed by loop extrusion, bring boundary-proximal cis-regulatory elements into contact.
• Stacking interactions contribute to observed architectural stripes in population-averaged maps.
• Increased boundary strength paradoxically facilitates stacked boundary formation, promoting border bypass.

Conclusions:

• TAD borders have a dual function, capable of both facilitating and inhibiting cis-regulatory interactions.
• Introduced a framework to differentiate between enhancer-promoter pairs that cross TAD borders and those that respect them.
• Provides a revised understanding of TAD border function in genome organization and gene regulation.