Dynamics of the 4D genome during in vivo lineage specification and differentiation

A Marieke Oudelaar,Matthew Gosden,Arun Shivalingam,Emily Georgiades,Sara De Ornellas,Jon Kerry,Tom Brown,Jelena M Telenius,Daniel Hidalgo,Douglas R Higgs,Afaf H El-Sagheer,Merav Socolovsky,Veronica J Buckle,Robert A Beagrie,Joana Carrelha,Jim R Hughes

doi:10.1038/s41467-020-16598-7

Abstract

Mammalian gene expression patterns are controlled by regulatory elements, which interact within topologically associating domains (TADs). The relationship between activation of regulatory elements, formation of structural chromatin interactions and gene expression during development is unclear. Here, we present Tiled-C, a low-input chromosome conformation capture (3C) technique. We use this approach to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. Integrated analysis of chromatin accessibility and single-cell expression data shows that regulatory elements gradually become accessible within pre-existing TADs during early differentiation. This is followed by structural re-organization within the TAD and formation of specific contacts between enhancers and promoters. Our high-resolution data show that these enhancer-promoter interactions are not established prior to gene expression, but formed gradually during differentiation, concomitant with progressive upregulation of gene activity. Together, these results provide new insight into the close, interdependent relationship between chromatin architecture and gene regulation during development.

Highlights

Mammalian gene expression patterns are controlled by regulatory elements, which interact within topologically associating domains (TADs)
Interactions within TADs are extensively restructured in differentiating cells, which involves the formation of specific interactions between enhancers and promoters[11,12,13,14,15]
It is possible that enhancers and promoters form limited interactions prior to gene activation due to changes in TAD structure during early differentiation, but that strong upregulation of gene expression is associated with more specific, subtle changes in conformation that will only be detected in data with sufficient resolution and sensitivity

Summary

Introduction

Mammalian gene expression patterns are controlled by regulatory elements, which interact within topologically associating domains (TADs). Integrated analysis of chromatin accessibility and single-cell expression data shows that regulatory elements gradually become accessible within pre-existing TADs during early differentiation This is followed by structural re-organization within the TAD and formation of specific contacts between enhancers and promoters. Our high-resolution data show that these enhancer-promoter interactions are not established prior to gene expression, but formed gradually during differentiation, concomitant with progressive upregulation of gene activity Together, these results provide new insight into the close, interdependent relationship between chromatin architecture and gene regulation during development. It is possible that enhancers and promoters form limited interactions prior to gene activation due to changes in TAD structure during early differentiation, but that strong upregulation of gene expression is associated with more specific, subtle changes in conformation that will only be detected in data with sufficient resolution and sensitivity. These findings provide new insights into the mechanisms contributing to the establishment of tissuespecific chromatin structures during development

Methods

Results

Conclusion