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

Sex chromosomes are unique genomic regions displaying structural and evolutionary features that markedly distinguish them from autosomes. Although nuclear three dimensional (3D) folding of chromatin structure has been linked to gene expression regulation and correct developmental programs, very 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 comprehensively 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 that regulate chromatin compaction and mediate transcriptional regulation. We describe the spatial conformation and sub-nuclear positioning of the sex determining region (SDR) within the U and V chromosomes and show that these regions are insulated and span the centromeres. Moreover, 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 (EVE), providing insights regarding the impact of a latent giant dsDNA virus on the host genome’s 3D chromosomal folding.