P338
Development and Analysis of Global Reference Epigenomes for Histone H3K9me2 and H4K12ac Using ChIP-Seq in Common Bean

Date: Monday, January 13, 2014
Room: Grand Exhibit Hall
Vasudevan Ayyappan , Molecular Genetics & Epigenomics Laboratory, Delaware State University, Dover, DE
Erin Crowgey , University of Delaware, Newark, DE
Shawn Polson , Delaware State University, Newark, DE
Tomasz Smolinski , Delaware State University, Dover, DE
Muthusamy Manoharan , University of Arkansas at Pine Bluff, Pine Bluff, AR
Jyothi Thimmapuram , Purdue University, West Lafayette, IN
Venu Kalavacharla , Delaware State University, Dover, DE
The common bean (Phaseolus vulgaris) is one of the most important legumes consumed directly as part of the diet, and a valuable and cheap source for dietary minerals and micronutrients. To determine the hierarchy of chromatin modification at the whole-genome level, we used ChIP-Seq to analyze binding of H3K9me2 and H4K12ac in four different genotypes of common bean viz., Bat-93, Jalo, G19833, Sierra, and mungbean. The common bean genotype G19833 associated genomic dataset was used as a reference. We obtained a mapping rate of 87.0, 85.73, 81.10, 76.58 and 20.69% for H3K9me2 and 86.93, 86.63, 81.77, 77.34 and 20.95% for H4K12ac respectively for Bat-93, Jalo, G-19833, Sierra, and mungbean. The low mapping rate of mungbean indicates that this species is divergent from common bean. Our results indicate that high H3K9me2 and H4K12ac modification levels are seen mainly in intergenic regions of genome. These regions are thought to give rise to noncoding RNAs or microRNAs that may potentially regulate genes. The percentage of genes containing H3K9me2 or H4K12ac binding sites for all genotypes ranged from 3 to 17% and 3 to 10% respectively. The percentage of genes containing both modifications ranged from 79 to 89%. The data was filtered based on a criteria of 10kb upstream or downstream from transcription start site (TSS). Within this filtered dataset, most enrichment was seen in the region of 2kb upstream or downstream from the TSS. Based upon gene ontology enrichment analysis of highly represented genes with H3K9me2 and H4K12ac modifications, we identified that the majority of genes were expressed during various biological processes including response to hormone stimulus, regulation of transcription, ethylene signaling pathway, and response to organic stimuli in all the genotypes. This work serves as the first reference histone-DNA interaction study in common bean and lays a foundation for comprehensive analyses and large-scale studies of histone modifications, and global protein binding sites in this important plant species, and will help in further annotation of the genome sequence.
Back to: Genome Mapping, Tagging & Characterization: Legumes, Soybeans, Common Beans
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