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Review
. 2024 Oct 15.
doi: 10.1038/s41581-024-00894-2. Online ahead of print.

A guide to studying 3D genome structure and dynamics in the kidney

Brian J Beliveau  1 , Shreeram Akilesh  2
Affiliations
Review

A guide to studying 3D genome structure and dynamics in the kidney

Brian J Beliveau et al. Nat Rev Nephrol. .

Abstract

The human genome is tightly packed into the 3D environment of the cell nucleus. Rapidly evolving and sophisticated methods of mapping 3D genome architecture have shed light on fundamental principles of genome organization and gene regulation. The genome is physically organized on different scales, from individual genes to entire chromosomes. Nuclear landmarks such as the nuclear envelope and nucleoli have important roles in compartmentalizing the genome within the nucleus. Genome activity (for example, gene transcription) is also functionally partitioned within this 3D organization. Rather than being static, the 3D organization of the genome is tightly regulated over various time scales. These dynamic changes in genome structure over time represent the fourth dimension of the genome. Innovative methods have been used to map the dynamic regulation of genome structure during important cellular processes including organism development, responses to stimuli, cell division and senescence. Furthermore, disruptions to the 4D genome have been linked to various diseases, including of the kidney. As tools and approaches to studying the 4D genome become more readily available, future studies that apply these methods to study kidney biology will provide insights into kidney function in health and disease.

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References

    1. Yang, J. H. et al. Loss of epigenetic information as a cause of mammalian aging. Cell 186, 305–326.e27 (2023). - PubMed - PMC - DOI
    1. Krijger, P. H. & de Laat, W. Regulation of disease-associated gene expression in the 3D genome. Nat. Rev. Mol. Cell Biol. 17, 771–782 (2016). - PubMed - DOI
    1. Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012). - PubMed - PMC - DOI
    1. Lambert, S. A. et al. The human transcription factors. Cell 175, 598–599 (2018). - PubMed - DOI
    1. Kim, S. & Shendure, J. Mechanisms of interplay between transcription factors and the 3D genome. Mol. Cell 76, 306–319 (2019). - PubMed - DOI

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