The proximal processes underlying the gradual loss of recombination on mating-type chromosomes in Microbotryum fungi
P. Michel
Thesis defense
14/10/2026
10:00:00
Pauline Michel, ESE
On line - visioconference
Abstract
Sex chromosomes generally possess large non-recombining regions that exhibit strong differentiation between two sex chromosomes. Several proximal mechanisms have been proposed to explain the origin, maintenance, and expansion of recombination suppression, including chromosomal inversions and epigenetic mechanisms that modify chromatin structure and recombination. Recent work has shown that non-recombining regions on mating-type chromosomes in fungi of the genus Microbotryum are numerous and have diverse evolutionary histories. These studies also revealed that not all evolutionary strata are associated with chromosomal inversions. In this context, the aim of this thesis was to investigate the proximal causes of recombination suppression on mating-type chromosomes in Microbotryum. We sought to understand the relationships between epigenetic modifications associated with chromatin accessibility and the expansion of non-recombining regions. This project addressed three main questions: (i) whether DNA methylation is associated with recombination suppression and whether it is present during the earliest stages following the cessation of recombination; (ii) how DNA methylation patterns are during meiosis. Because chromosomal recombination occurs during meiosis, a transient increase in DNA methylation during this stage could contribute to the maintenance or expansion of non-recombining regions; (iii) whether histone modifications are associated with recombination suppression. DNA methylation data were generated for 13 Microbotryum species, a group of pathogenic fungi causing anther-smut disease in plants of the genus Silene. DNA methylation profiles were obtained by whole-genome bisulfite sequencing (WGBS) from haploid sporidia and meiotic cells. In addition, ChIP-seq data were generated from haploid sporidia to characterize histone modifications and investigate their association with recombination suppression. The analyses revealed that DNA methylation levels were generally low throughout the Microbotryum genome, except in centromeres and non-recombining regions. DNA methylation levels increased with the age of non-recombining regions. Although this increase was correlated with the frequency of transposable elements, significant differences in methylation levels across different age groups strata were also observed when transposable elements were excluded from the analyses. ChIP-seq analyses revealed a strong association between transposable elements, heterochromatin-associated histone modifications, DNA methylation, and the lack of recombination. The results support a model of progressive transposable element silencing, in which newly inserted transposable elements are initially associated with facultative heterochromatin (H3K27me3) and progressively acquire H3K9me3, leading to the establishment of stable constitutive heterochromatin. Furthermore, the accumulation of heterochromatin-associated histone marks near the boundaries of the pseudoautosomal regions supports the hypothesis that chromatin remodeling contributes to the expansion of recombination suppression in Microbotryum. Together, these results suggest that histone modifications and DNA methylation act jointly in the evolution of recombination suppression. Histone modifications may promote the establishment of heterochromatic regions that are unfavorable to meiotic crossing-over, whereas DNA methylation may contribute to the long-term maintenance of these non-recombining regions.
Composition of the jury
- M. Daniel BOUYER, Chargé de recherche, ENS Lyon, Rapporteur
- M. Dirk SCHWARZER, Professeur, Université de Tuebingen - Allemagne, Rapporteur
- Mme Aurelie HUA-VAN, Professeure, Université Paris-Saclay, Examiner
- M. Florian MAUMUS, Directeur de recherche, INRAe - Université Paris-Saclay, Examiner
- Mme Elise LUCOTTE, ESE, Invited
The defense will take place online only : https://rendez-vous.renater.fr/lobby_private/PhD_defense_Pauline-Michel__mxpgp4xihdbe_5625af-b66db2-c9941f