3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization

Pengfei Liu, Jeromine Vigneau, Rory J. Craig, Josué Barrera-Redondo, Elena Avdievich, Claudia Martinho, Michael Borg, Fabian B. Haas, Chang Liu and Susana M. Coelho ()
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Pengfei Liu: Max Planck Institute for Biology Tübingen
Jeromine Vigneau: Max Planck Institute for Biology Tübingen
Rory J. Craig: Max Planck Institute for Biology Tübingen
Josué Barrera-Redondo: Max Planck Institute for Biology Tübingen
Elena Avdievich: Max Planck Institute for Biology Tübingen
Claudia Martinho: Max Planck Institute for Biology Tübingen
Michael Borg: Max Planck Institute for Biology Tübingen
Fabian B. Haas: Max Planck Institute for Biology Tübingen
Chang Liu: University of Hohenheim
Susana M. Coelho: Max Planck Institute for Biology Tübingen

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: Abstract Nuclear three dimensional (3D) folding of chromatin structure has been linked to gene expression regulation and correct developmental programs, but little is known about the 3D architecture of sex chromosomes within the nucleus, and how that impacts their role in sex determination. Here, we determine the sex-specific 3D organization of the model brown alga Ectocarpus chromosomes at 2 kb resolution, by mapping long-range chromosomal interactions using Hi-C coupled with Oxford Nanopore long reads. We report that Ectocarpus interphase chromatin exhibits a non-Rabl conformation, with strong contacts among telomeres and among centromeres, which feature centromere-specific LTR retrotransposons. The Ectocarpus chromosomes do not contain large local interactive domains that resemble TADs described in animals, but their 3D genome organization is largely shaped by post-translational modifications of histone proteins. We show that the sex determining region (SDR) within the U and V chromosomes are insulated and span the centromeres and we link sex-specific chromatin dynamics and gene expression levels to the 3D chromatin structure of the U and V chromosomes. Finally, we uncover the unique conformation of a large genomic region on chromosome 6 harboring an endogenous viral element, providing insights regarding the impact of a latent giant dsDNA virus on the host genome’s 3D chromosomal folding.

Date: 2024
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DOI: 10.1038/s41467-024-53453-5

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