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.

Spot blotch disease of wheat: the current status of research on genetics and breeding

“…The work involving the role of methylation/demethylation and chromatin remodelling involving histone modifications in plant immunity has recently been reviewed (Ding & Wang, ; Deleris et al ., ). Genome‐wide profiling of histone modifications (H3K9me2 and H4K12ac) and gene expression has also been conducted in common bean ( Phaseolus vulgaris ) inoculated with rust ( Uromyces appendiculatus ) (Ayyappan et al ., ). Noncoding RNAs including miRNAs, target mimics (TM) and other long noncoding RNAs (lncRNAs) may also be involved in response to spot blotch disease and need to be examined (for a review, see Gupta, ), as has been done in the case of yellow rust and some abiotic stresses in wheat (Feng et al ., ).…”

Transcriptional regulatory mechanism of alcohol dehydrogenase 1-deficient mutant of rice for cell survival under complete submergence

“…Corresponding with these expression data, we also identified putative w-box-like elements in the promoter regions of some of the key upregulated metabolic genes which might be linked to the reduced coleoptile elongation in rad mutant. Examples of such genes are as follows: i) UDP-glucuronosyl/UDP-glucosyltransferase family protein (Os06g0220500), which plays a major role in cell homeostasis (Vogt and Jones 2000 ) and potentially contributes to chemical stability and reduced chemical activity of the cell under stress conditions, ii) similar to cytochrome P450 family (Os12g0268000), induced by environmental stresses, which contains binding sites for MYB, MYC, and WRKY in their promoters and is involved in the catabolism of plant hormones (Ayyappan et al 2015 ), and iii) methyltransferase type 12 domain containing protein (Os01g0716500), which may control the synthesis of cell building blocks by repressing their transcription. Taken together, our results demonstrate a possible link between WRKY TF and metabolic alteration that supports rad mutant for the cell survival.…”

Characterization and Expression Analysis of Common BeanHistone Deacetylase 6during Development and Cold Stress Response

“…Phaseolus vulgaris cultivar “Sierra” (Mesoamerican and resistant to Uromyces appendiculatus race 53), which was previously used for studying transcriptome and genome-wide histone binding analysis and global leaf HDAC activity [22, 29], was also used throughout the study. Phaseolus vulgaris genotypes “Olathe” (Mesoamerican and susceptible to Uromyces appendiculatus race 53) and “G19833” (Andean origin and reference genotype in Phytozome, http://www.phytozome.org) were used for cloning and sequence analysis.…”

“…The seedlings were then transferred to poly pots filled with Promix soil. The plants were allowed to grow in the greenhouse under natural light until pod formation according to Ayyappan et al 2015 [29], with samples collected as per the experimental protocol below.…”