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Evolutionary analysis of gene ages across TADs associates chromatin topology with whole-genome duplications

Lookup NU author(s): Caelinn James, Dr Marco Trevisan-HerrazORCiD

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

Abstract

© 2024 The AuthorsTopologically associated domains (TADs) are interaction subnetworks of chromosomal regions in 3D genomes. TAD boundaries frequently coincide with genome breaks while boundary deletion is under negative selection, suggesting that TADs may facilitate genome rearrangements and evolution. We show that genes co-localize by evolutionary age in humans and mice, resulting in TADs having different proportions of younger and older genes. We observe a major transition in the age co-localization patterns between the genes born during vertebrate whole-genome duplications (WGDs) or before and those born afterward. We also find that genes recently duplicated in primates and rodents are more frequently essential when they are located in old-enriched TADs and interact with genes that last duplicated during the WGD. Therefore, the evolutionary relevance of recent genes may increase when located in TADs with established regulatory networks. Our data suggest that TADs could play a role in organizing ancestral functions and evolutionary novelty.

Publication metadata

Author(s): James C, Trevisan-Herraz M, Juan D, Rico D

Publication type: Article

Publication status: Published

Journal: Cell Reports

Year: 2024

Volume: 43

Issue: 4

Print publication date: 23/04/2024

Online publication date: 21/03/2024

Acceptance date: 16/02/2024

Date deposited: 04/04/2024

ISSN (electronic): 2211-1247

Publisher: Elsevier B.V.

URL: https://doi.org/10.1016/j.celrep.2024.113895

DOI: 10.1016/j.celrep.2024.113895

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