title: Genome-Wide Profiling of Histone Modifications (H3K9me2 and H4K12ac) and Gene Expression in Rust (Uromyces appendiculatus) Inoculated Common Bean (Phaseolus vulgaris L.).
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.
authors.affiliation: Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, Delaware, United States of America.
authors.forename: Vasudevan
authors.initials: V
authors.lastname: Ayyappan
authors.affiliation: Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, Delaware, United States of America; Center for Integrated Biological and Environmental Research (CIBER), Delaware State University, Dover, Delaware, United States of America.
authors.forename: Venu
authors.initials: V
authors.lastname: Kalavacharla
authors.affiliation: Bioinformatics Core, Purdue University, West Lafayette, Indiana, United States of America.
authors.forename: Jyothi
authors.initials: J
authors.lastname: Thimmapuram
authors.affiliation: Bioinformatics Core, Purdue University, West Lafayette, Indiana, United States of America.
authors.forename: Ketaki P
authors.initials: KP
authors.lastname: Bhide
authors.affiliation: Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, Delaware, United States of America.
authors.forename: Venkateswara R
authors.initials: VR
authors.lastname: Sripathi
authors.affiliation: Computational Intelligence and Bio(logical)informatics Laboratory (CIBiL), Delaware State University, Dover, Delaware, United States of America.
authors.forename: Tomasz G
authors.initials: TG
authors.lastname: Smolinski
authors.affiliation: Department of Agriculture, University of Arkansas, Pine Bluff, Arkansas, United States of America.
authors.forename: Muthusamy
authors.initials: M
authors.lastname: Manoharan
authors.affiliation: Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, Delaware, United States of America.
authors.forename: Yaqoob
authors.initials: Y
authors.lastname: Thurston
authors.affiliation: Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, Delaware, United States of America.
authors.forename: Antonette
authors.initials: A
authors.lastname: Todd
authors.affiliation: Sequencing and Genotyping Center, Delaware Biotechnology Institute, Newark, Delaware, United States of America.
authors.forename: Bruce
authors.initials: B
authors.lastname: Kingham
mesh_terms: D000107:Acetylation; D001487:Basidiomycota / Q000235:genetics*; D047369:Chromatin Immunoprecipitation; D044127:Epigenesis, Genetic / Q000235:genetics; D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D042421:Histone Code / Q000235:genetics*; D054884:Host-Pathogen Interactions / Q000235:genetics; D008745:Methylation; D020411:Oligonucleotide Array Sequence Analysis; D027805:Phaseolus / Q000235:genetics* / Q000382:microbiology; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology*; D016415:Sequence Alignment