Integrated Profiling of Histone Modifications and Gene Expression in the Rust Resistance Response of Common Bean.

Vasu Ayyappan, Delaware State University

Histone modifications such as methylation and acetylation play a substantial role in regulating gene expression in normal and stressed plants. On the other hand, transcriptome profiling using RNA-Seq analysis accounts for an array of differentially expressed transcripts between treated and untreated samples. Understanding the epigenomic and transcriptomic regulation of such stress-responsive genes in non-model crops is limited. In this study, we report the genome-wide analysis of histone methylation (H3K9_me2) and acetylation (H4K12_ac) in common bean (Phaseouls vulgaris L.) under rust (Uromyces appendiculatus) stress by using two next-generation sequencing methods - chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq). Using ChIP-Seq analysis, we discovered 1,235 histone methylation and 556 acetylation responsive genes from common bean leaves infected with rust at 0, 12, and 84h. RNA-Seq analysis revealed 145 and 1,763 differentially-expressed genes between mock-inoculated and inoculated plants, respectively. After analysis of the stressed and unstressed transcriptomes, we identified key defense responsive genes and several transcription factors upregulated in stress. The integrated ChIP-Seq and RNA-Seq analysis helped in identification of genes associated with DNA-methylation, histone-methylation, histone-acetylation, chromatin remodeling, and polycomb group of proteins. We classified the transcripts using Gene Ontology (GO) and EuKaryotic Orthologous Groups (KOGs). After assigning the GO terms to pathways, we identified a putative pathway with ten key genes involved in plant-microbe interactions. This is the first comprehensive report on integrated genome-wide profiling of bean-rust interaction and the resources developed here will be beneficial to better understand other epigenomic regulation mechanisms in non-model species under biotic and abiotic stresses.

 

Title: Integrated Profiling of Histone Modifications and Gene Expression in the Rust Resistance Response of Common Bean

Submitter’s E-mail address: vayyappan@desu.edu

Session Selection: Biotic Stress