CE20 - Biologie des animaux, des organismes photosynthétiques et des microorganismes

Deciphering in planta CHrOmatin dynamics of a Phytopathogenic fungus during INfection – CHOPIN

Deciphering in planta CHrOmatin dynamics of a Phytopathogenic fungus during Infection

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The objective of the CHOPIN project is to understand how the epigenomic landscape of L. maculans influence gene expression at different stages of the oilseed rape infection

During infection, pathogens, including fungi, secrete an arsenal of molecules, collectively called effectors, key elements of pathogenesis. Leptosphaeria maculans is a pathogenic fungus infecting oilseed rape in two stages: an early stage on young leaves during autumn and a late stage on stems during spring. During the infection, waves of effector expression occur at different times during the infection while these genes are inhibited in vitro. ChIP-seq analysis of chromatin structure under axenic conditions showed that there are two types of heterochromatin in the L. maculans genome: regions rich in transposable elements (TEs) are enriched in the H3K9me3 modification while the H3K27me3 modification is found in gene-rich regions. Genes encoding effectors overexpressed during infection at different time points are enriched in these heterochromatin regions, explaining the inhibition of their expression in axenic condition. Our hypothesis is that chromatin dynamics would underlie the massive transcriptional reprogramming of gene expression during the life cycle of L. maculans on its host. The objective of the CHOPIN project is to decipher the dynamics of the L. maculans epigenome during host infection. We propose to analyze (i) the dynamics of histone modifications as well as the 3-D organization of nuclei at different points of host infection and (ii) the role of proteins involved in methylation/demethylation of H3K9/K27me3 in gene expression regulation and epigenome organization by performing functional analysis of these proteins; iii) integrative analysis of these data will shed light on the role of the epigenome in regulating gene expression and pathogenesis. Besides bringing an unprecedented knowledge on the plant / pathogenic fungi that can be further used to development of innovative breeding strategies for sustainable control of foliar diseases of crops.

The CHOPIN project is built around three Work-Packages. We will develop an unbiased approach to study the whole genome landscape of histone modifications and nuclear architecture dynamics underlying L. maculans transcriptome plasticity during plant infection (WP1). In a complementary approach, influence of key actors involved in chromatin remodeling on the massive transcriptome reprogramming during infection will be assessed using reverse genetics approaches (WP2). Independent and integrative analysis of the data will be managed in WP3 (Figure 4).

We have established the genome-wide map of the modifications associated to euchromatin or heterochromatin during axenic culture. Mutants of genes coding proteins involved in chromatin remodeling are available, their analyses is under going.

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Fungi are the most devastating pathogens of plants, significantly threatening food resources. During infection, pathogens, including fungi, secrete an arsenal of molecules, collectively called effectors, key elements of pathogenesis. Leptosphaeria maculans is a pathogenic fungus infecting oilseed rape in two stages: an early stage on young leaves during autumn and a late stage on stems during spring. These two stages are associated with two waves of expression of effector genes. Effector genes expressed during the early stages of infection (‘early’ effector genes) are located in transposable element (TE)-rich regions of the genome while effector genes up-regulated during late stem colonization are located in gene-rich regions (‘late’ effector genes). Recently, a detailed map of the chromatin structure in vitro of L. maculans has been generated via ChIP-seq targeting either histone modifications typical for euchromatin (dimethylation of the lysine 4 of the histone H3, H3K4me2) or heterochromatin (tri-methylation of the lysine 9 and 27 of the histone H3; H3K9me3 and H3K27me3). This analysis has shown that TE-rich regions and ‘early’ effector genes located in these regions are associated with H3K9me3. On the contrary, H3K27me3 is exclusively found within gene-rich regions and often associated with putative ‘late’ effectors. This association of two sets of effector genes - expressed at different time points during plant infection and in different plant organs - with different histone modifications typical for heterochromatin suggests that a dynamic chromatin remodeling may be involved in different waves of effector gene expression during infection. Our hypothesis is that the dynamics of chromatin, both in terms of histone modifications and three-dimensional chromosome organization within the nucleus, explain the massive transcriptional reprogramming of gene expression during the life cycle of L. maculans on its host. The objective of the CHOPIN project is to decipher the dynamics of the epigenome of L. maculans during infection of its host. To date, targeted analyses of the chromatin structure during host/pathogenic fungus interaction have been carried out in planta, but only a complete view of the chromatin structure of a pathogenic fungus during infection of its host will allow us to conclude on the role of epigenome dynamics on pathogenesis. In order to be able to carry out analyses of the epigenome of the fungus in planta, an innovative approach has been developed to sort and recover the fungal nuclei from infected plant material by flow cytometry. We propose to analyze (i) the dynamics of histone modifications as well as the 3-D organization of nuclei at different points of host infection and (ii) the role of proteins involved in methylation/demethylation of H3K9/K27me3 in gene expression regulation and epigenome organization by performing functional analysis of these proteins; iii) integrative analysis of these data will shed light on the role of the epigenome in regulating gene expression and pathogenesis. Besides bringing an unprecedented knowledge on the plant / pathogenic fungi that can be further used to development of innovative breeding strategies for sustainable control of foliar diseases of crops.

Project coordinator

Madame Jessica Soyer (Institut National de la Recherche Agronomique - BIOlogie GEstion des Risques en agriculture)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

INRA BIOGER Institut National de la Recherche Agronomique - BIOlogie GEstion des Risques en agriculture
UPSUD-IPS2 Institut des Sciences des Plantes de Paris Saclay

Help of the ANR 443,786 euros
Beginning and duration of the scientific project: December 2019 - 48 Months

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