Genome-wide shifts in histone modification patterns at early stage of rice infection with root-knot nematode 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 are deregulated in galls induced by root-knot nematode (RKN, Meloidogyne graminicola) in rice, their influence on plant defence and their genome-wide impact has not been comprehensively investigated. 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. Total RNA sequencing was performed to assess the effect of histone modification changes on gene expression. Overall design: Total RNA sequencing was done on RNA extracted from rice roots under two eperimental conditions: infection with Meloidogyne graminicola and mock infection (three replicates per condition).