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Evolution of 3D chromatin organization at different scales

Most animal genomes fold in 3D chromatin domains called topologically associated domains (TADs) that facilitate interactions between cis-regulatory elements (CREs) and promoters. Owing to their critical role in the control of developmental gene expression, we explore how TADs have shaped animal evol...

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Bibliographic Details
Published in:Current opinion in genetics & development 2023-02, Vol.78, p.102019-102019, Article 102019
Main Authors: Acemel, Rafael D, Lupiáñez, Darío G
Format: Article
Language:English
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Summary:Most animal genomes fold in 3D chromatin domains called topologically associated domains (TADs) that facilitate interactions between cis-regulatory elements (CREs) and promoters. Owing to their critical role in the control of developmental gene expression, we explore how TADs have shaped animal evolution. In the light of recent studies that profile TADs in disparate animal lineages, we discuss their phylogenetic distribution and the mechanisms that underlie their formation. We present evidence indicating that TADs are plastic entities composed of genomic strata of different ages: ancient cores are combined with newer regions and brought into extant TADs through genomic rearrangements. We highlight that newly incorporated TAD strata enable the establishment of new CRE-promoter interactions and in turn new expression patterns that can drive phenotypical innovation. We further highlight how subtle changes in chromatin folding may fine-tune the expression levels of developmental genes and hold a potential for evolutionary significance. •Chromatin folding into topologically associated domains (TADs) is pervasive across animal groups.•TADs are plastic entities composed of genomic strata from different ages.•Incorporated TAD strata can promote adaptive gene expression through novel enhancer-promoter interactions.•Subtle changes in 3D chromatin organization may fine-tune developmental gene expression in evolutionary contexts.
ISSN:0959-437X
1879-0380
DOI:10.1016/j.gde.2022.102019