Biology subjects

Vigneau, J.

Publications and source records attributed to Vigneau, J..

3 recordsLinked to original sources

bioRxiv2025

Rewiring of chromatin regulation underlies the evolution of brown algal multicellularity

Chromatin structure plays a central role in regulating transcription, genome stability, and epigenetic inheritance in eukaryotes. Much of our understanding of chromatin architecture and histone post-translational modifications (hPTMs) comes from a narrow set of animal and plant models, but emerging data from non-model lineages are challenging canonical views of how chromatin functions across the tree of life. Brown algae are complex multicellular eukaryotes that provide a unique perspective on chromatin evolution given their independent origin of complex multicellularity. Here, we compile the chromatin toolkit of brown algae and show that canonical silencing systems involving DNA cytosine methylation and PRC2-mediated H3K27 methylation were lost early in their evolution. By generating hPTM profiles from diverse brown algal clades, we resolve the nature and regulatory roles of chromatin states in this lineage and show how H3K79 methylation emerged and diversified as a repressive system. We further uncover sex-specific reconfigurations in species with varying degrees of sexual dimorphism and reconstruct the ancestral regulatory landscape that likely preceded the emergence of brown algae. Together, our findings illuminate the dynamic evolution of chromatin regulation in a distinct multicellular lineage and challenge assumptions about the universality of chromatin-based mechanisms across eukaryotes.

evolutionary biology↗

bioRxiv2024

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

Sex chromosomes are unique genomic regions displaying structural and evolutionary features that distinguish them markedly from autosomes. Although nuclear three dimensional (3D) folding of chromatin structure is im-portant for 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 function 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 retrotranspos-ons. 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 pro-teins that regulate chromatin compaction and mediate transcriptional regulation. We describe the spatial confor-mation and sub-nuclear positioning of the sex determining region (SDR) within the U and V chromosomes and show that these regions are very insulated and span the centromeres. Moreover, we link sex-specific chromatin dynamics and gene expression levels to the 3D chromatin structure of 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 functional significance of the chromatin organisation of latent giant dsDNA virus.

genomics↗

bioRxiv2023

Sex chromosome dominance in a UV sexual system

The alternation between multicellular haploid gametophytes and diploid sporophytes is a defining feature of most plant and algal life cycles. In such organisms, male and female sexes are determined in the haploid gametophyte with a female (U) or male (V) sex chromosome. Once the U and V chromosomes unite at fertilisation, sex determination no longer occurs, raising key questions about the fate of UV sex chromosomes in the diploid sporophyte stage of the life cycle. Here, we unravel the genetic and molecular interactions between the U and V chromosomes by assessing transcriptional and chromatin states across the life cycle of the brown alga Ectocarpus alongside ouroboros mutants that decouple life cycle stage from ploidy. We reveal how sex chromosome genes are developmentally regulated across the life cycle, with genes involved in female sex determination in particular undergoing strong down-regulation in the sporophyte. Diploid ouroboros mutants containing both a U and V sex chromosome behave as functional male gametophytes yet still exhibit feminized transcription, suggesting that presence of the V chromosome alone is insufficient to fully suppress female developmental program. Although the silencing of sex chromosome genes in the diploid sporophyte does not appear to correlate with localised changes in chromatin state, small RNAs may play a role in the repression of a female sex-linked gene. Finally, we show how histone H3K79me2 is globally re-configured in the diploid phase of the life cycle, including the sex determining region of the UV sex chromosomes. Contrary to its pattern in the haploid gametophyte, H3K79me2 no longer associates with repressed genes in the diploid sporophyte, suggesting that the function of this histone mark in Ectocarpus may be more complex than previously appreciated.

evolutionary biology↗