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

Autor: Ayyappan V; Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA. vasudevanbiotech@gmail.com., Sripathi VR; Center for Molecular Biology, Alabama A&M University, Normal, AL, 35762, USA., Xie S; Bioinformatics Core, Purdue University, West Lafayette, IN, 47907, USA., Saha MC; Noble Research Institute, LLC, Ardmore, OK, 73401, USA., Hayford R; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA., Serba DD; USDA-ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, 85138, USA. des.serba@usda.gov., Subramani M; Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA., Thimmapuram J; Bioinformatics Core, Purdue University, West Lafayette, IN, 47907, USA., Todd A; Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA., Kalavacharla VK; Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA.; Center for Integrated Biological and Environmental Research (CIBER), Delaware State University, Dover, DE, 19901, USA.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2024 Feb 29; Vol. 25 (1), pp. 223. Date of Electronic Publication: 2024 Feb 29.
DOI: 10.1186/s12864-024-10068-w
Abstrakt: 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.
Conclusion: Our study provides a comprehensive and reproducible epigenomic analysis of drought, heat, and combined stress responses in switchgrass. Significant enrichment of H3K4me3 peaks downstream of the TSS of protein-coding genes was observed. In addition, the cost-effective experimental design, modified ChIP-Seq approach, and analyses presented here can serve as a prototype for other non-model plant species for conducting stress studies.
(© 2024. The Author(s).)
Databáze: MEDLINE
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