Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass

Authors: AYYAPPAN, VASUDEVAN - Delaware State University; XIE, SHAOJUN - Purdue University; SAHA, MALAY - Noble Research Institute; HAYFORD, RITA - University Of Delaware; Serba, Desalegn; SRIPATHI, VENKATESWARA - Alabama A & M University; DUBRAMANI, MAYAVAN - Delaware State University; THIMMAPURAM, JYOTHI - Purdue University; TODD, ANTONETTE - Delaware State University; KALAVACHARLA, VENU - Delaware State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/30/2024
Publication Date: 2/29/2024
Citation: Ayyappan, V., Xie, S., Saha, M.C., Hayford, R., Serba, D.D., Sripathi, V.R., Dubramani, M., Thimmapuram, J., Todd, A., Kalavacharla, V. 2024. Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass. BMC Genomics. 25. Article 223. https://doi.org/10.1186/s12864-024-10068-w.
DOI: https://doi.org/10.1186/s12864-024-10068-w

Interpretive Summary: The effect of drought is often accompanied by heat stress in many places. The combined drought and heat stress have more detrimental effect on the plant growth and development. Switchgrass is one of the environmental stress tolerant herbaceous plants being evaluated as a non-food crop biomass source for biofuel production. However, the molecular mechanisms of switchgrass drought and heat stress characteristics are not fully understood. In this study, we analyzed the epigenetic modification using chromatin immunoprecipitation and sequencing (ChIP-Seq) analysis with emphasis on the activation of histone mark ‘H3K4me3’ for its involvement in the regulation of stress responsive gene expression. A total of 1,374,515 H3K4me3 peaks were identified in this study. Among them, 6,510 peaks were activated under combined drought and heat (DTHT) stress. Out of which 121 DTHT responsive peaks overlapped with 110 DTHT responsive genes. These genes are involved in biological processes, molecular functions, and as cellular components with significantly over-represented members. Quantitative real-time polymerase chain reaction (qRT-PCR) revealed the relative expressions of six abiotic stress responsive-genes that were significantly (P<0.05) marked under drought and heat stresses compared to combined stress treatment. This result in heat and drought response epigenetic regulation in switchgrass will provide valuable information in related non-model plant species epigenetic studies for stress tolerance.

Technical Abstract: Background: Switchgrass (Panicum virgatum L.) is a warm-season perennial (C4) grass identified as an important biofuel crop in the United States. It is well adapted to the marginal environment where heat and moisture stresses predominantly affect crop growth. However, the underlying molecular mechanisms associated with heat and drought stress tolerance still need to be fully understood in switchgrass. The methylation of H3K4 is often associated with transcriptional activation of genes, including stress-responsive. Therefore, this study aimed to analyze genome-wide histone H3K4-tri-methylation in switchgrass under heat, drought, and combined stress. Results: In total, ~ 1.3 million H3K4me3 peaks were identified in this study using SICER. Among them, 7,342; 6,510; and 8,536 peaks responded under drought (DT), drought and heat (DTHT), and heat (HT) stresses, respectively. Most DT and DTHT peaks spanned 0 to + 2000 bases from the transcription start site [TSS]. By comparing differentially marked peaks with RNA-Seq data, we identified peaks associated with genes: 155 DT-responsive peaks with 118 DT-responsive genes, 121 DTHT-responsive peaks with 110 DTHT-responsive genes, and 175 HT-responsive peaks with 136 HT-responsive genes. We have identified various transcription factors involved in DT, DTHT, and HT stresses. Gene Ontology analysis using the AgriGO revealed that most genes belonged to biological processes. Most annotated peaks belonged to metabolite interconversion, RNA metabolism, transporter, protein modifying, defense/immunity, membrane traffic protein, transmembrane signal receptor, and transcriptional regulator protein families. Further, we identified significant peaks associated with TFs, hormones, signaling, fatty acid and carbohydrate metabolism, and secondary metabolites. qRT-PCR analysis revealed the relative expressions of six abiotic stress-responsive genes (transketolase, chromatin remodeling factor-CDH3, fatty-acid desaturase A, transmembrane protein 14C, beta-amylase 1, and integrase-type DNA binding protein genes) that were significantly (P < 0.05) marked during drought, heat, and combined stresses by comparing stress-induced against un-stressed and input controls.