Genome-Wide Profiling of Histone Modifications (H3K9me2 and H4K12ac) and Gene Expression in Rust (Uromyces appendiculatus) Inoculated Common Bean (Phaseolus vulgaris L.).

Vasudevan Ayyappan,Venu Kalavacharla,Venkateswara R Sripathi,Bruce Kingham,Muthusamy Manoharan,Yaqoob Thurston,Tomasz G Smolinski,Antonette Todd,Ketaki P Bhide,Jyothi Thimmapuram,Roberto Mantovani

doi:10.1371/journal.pone.0132176

Abstract

Histone modifications such as methylation and acetylation play a significant role in controlling gene expression in unstressed and stressed plants. Genome-wide analysis of such stress-responsive modifications and genes in non-model crops is limited. We report the genome-wide profiling of histone methylation (H3K9me2) and acetylation (H4K12ac) in common bean (Phaseolus vulgaris L.) under rust (Uromyces appendiculatus) stress using two high-throughput approaches, chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq). ChIP-Seq analysis revealed 1,235 and 556 histone methylation and acetylation responsive genes from common bean leaves treated with the rust pathogen at 0, 12 and 84 hour-after-inoculation (hai), while RNA-Seq analysis identified 145 and 1,763 genes differentially expressed between mock-inoculated and inoculated plants. The combined ChIP-Seq and RNA-Seq analyses identified some key defense responsive genes (calmodulin, cytochrome p450, chitinase, DNA Pol II, and LRR) and transcription factors (WRKY, bZIP, MYB, HSFB3, GRAS, NAC, and NMRA) in bean-rust interaction. Differential methylation and acetylation affected a large proportion of stress-responsive genes including resistant (R) proteins, detoxifying enzymes, and genes involved in ion flux and cell death. The genes identified were functionally classified using Gene Ontology (GO) and EuKaryotic Orthologous Groups (KOGs). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified a putative pathway with ten key genes involved in plant-pathogen interactions. This first report of an integrated analysis of histone modifications and gene expression involved in the bean-rust interaction as reported here provides a comprehensive resource for other epigenomic regulation studies in non-model species under stress.

Highlights

Plants are sessile organisms that cannot physically relocate to escape from unfavorable environmental conditions and have developed complex defense mechanisms to respond to biotic and abiotic stresses
In this study mock-inoculated (MI) samples served as background against inoculated samples, which was used for the comparison during ChIP-Seq analysis to identify differentially marked regions
Seven abundantly found transcription factor families across three time points (0, 12 and 84 hai) include WRKY, Basic Leucine Zipper Domain (bZIP), MYB, heat shock transcription factor B3 (HSFB3), GRAS, NAC and NMRA in common bean-rust interaction, which were further validated by real time PCR

Summary

Introduction

Plants are sessile organisms that cannot physically relocate to escape from unfavorable environmental conditions and have developed complex defense mechanisms to respond to biotic and abiotic stresses. The molecular mechanisms of stress-induced signaling pathways and genes differ between various stresses such as pathogen attack, cold, heat, drought, and salinity [1, 2]. In agriculturally important crops such as common bean, significant yield losses due to biotic (62%) and abiotic (37–67%) stresses have been reported [7]. Integrated molecular genetic and genomic analyses of defense responsive pathways and genes will aid in unraveling the underlying disease-resistance mechanisms, which in turn will aid in developing broader and more robust resistance in common bean cultivars while providing a more comprehensive understanding of plant disease resistance in general

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Conclusion