Genome-wide shifts in histone modifications at early stage of rice infection with Meloidogyne graminicola

Epigenetic processes play a crucial role in the regulation of plant stress responses, but their role in plant-pathogen interactions remains poorly understood. Although histone modifying enzymes have been observed to be deregulated in galls induced by root-knot nematodes (RKN, Meloidogyne graminicola) in rice, their influence on plant defence and their genome-wide impact have not been comprehensively investigated. In this study, we applied 3 chemical inhibitors of histone modifying enzymes on rice 24h before inoculation with RKN. Despite their distinct described effects on histone modifications, application of different concentrations led in all cases to reduced susceptibility to RKN. Infection assays on two overexpression lines of histone lysine methyltransferases and one histone deacetylase showed contrasting results in susceptibility, indicating that each histone mark has a specific role in plant defence against RKN in rice. At genome-wide level, three histone marks, H3K9ac, H3K9me2 and H3K27me3 were studied by chromatin-immunoprecipitation (ChIP)-sequencing on RKN-induced galls at 3 days post inoculation. While levels of H3K9ac and H3K27me3 were strongly enriched, H3K9me2 was generally depleted in galls versus control root tips. Differential histone peaks were generally associated with plant defence related genes. In conclusion, our results indicate that histone modifications respond dynamically to RKN infection, and specifically target plant-defence related genes.