Involvement of JMJ15 in the dynamic change of genome-wide H3K4me3 in response to salt stress

Shen, Yuan; Chi, Yuhao; Lu, Shun; Lu, Huijuan; Shi, Lei

doi:10.3389/fpls.2022.1009723

Cited by 7 publications

(1 citation statement)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The H3K4me3 peaks corresponded with the annotated genes and were more likely to be activated, including the highly expressed genes in response to abiotic stresses, for example, 17.4 kDa class III HSP, chloroplast exonuclease V, ABA Inducible bHLH-Type (AtAIB), MADS-box protein Soc 1, NAC domain-containing protein 86, Auxin response factor 16 (ARF16), and Chromatin remodeling factor (CHD3). Most of these genes linked with stress-related processes altered by H3K4me3 have also been reported in other plant species [ 61 – 64 ]. These findings suggest that H3K4me3 probably modulates active transcription in switchgrass but with a distinct pattern of genomic distributions and regulatory roles.…”

Section: Discussionmentioning

confidence: 78%

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

Ayyappan,

Sripathi,

Xie

et al. 2024

BMC Genomics

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 78%