Chromatin-Based Transcriptional Reprogramming in Plants under Abiotic Stresses

Halder, Koushik; Chaudhuri, Abira; Abdin, M. Z.; Majee, Manoj; Datta, Asis

doi:10.3390/plants11111449

Cited by 13 publications

(8 citation statements)

References 150 publications

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“…The plant stress response is characterized by an intricate network of signaling cascades that trigger transcriptional reprogramming 34 . To analyze the behavior of genes in A. thaliana under control conditions and under stimulus conditions, we performed differential network analysis (Fig.…”

Section: Discussionmentioning

confidence: 99%

Inferring co-expression networks of Arabidopsis thaliana genes during their interaction with Trichoderma spp.

Vega-Arroy,

Herrera-Estrella,

Ovando-Vázquez

et al. 2024

Sci Rep

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Fungi of the Trichoderma genus are called "biostimulants" because they promote plant growth and development and induce disease resistance. We used conventional transcriptome and gene co-expression analyses to understand the molecular response of the plant Arabidopsis thaliana to inoculation with Trichoderma atroviride or Trichoderma virens. The transcriptional landscape of the plant during the interaction with these fungi showed a reduction in functions such as reactive oxygen species production, defense mechanisms against pathogens, and hormone signaling. T. virens, as opposed to T. atroviride, was more effective at downregulating genes related to terpenoid metabolism, root development, and chemical homeostasis. Through gene co-expression analysis, we found functional gene modules that closely link plant defense with hypoxia. Notably, we found a transcription factor (locus AT2G47520) with two functional domains of interest: a DNA-binding domain and an N-terminal cysteine needed for protein stability under hypoxia. We hypothesize that the transcription factor can bind to the promoter sequence of the GCC-box that is connected to pathogenesis by positioned weight matrix analysis.

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Section: Discussionmentioning

confidence: 99%

Inferring co-expression networks of Arabidopsis thaliana genes during their interaction with Trichoderma spp.

Vega-Arroy,

Herrera-Estrella,

Ovando-Vázquez

et al. 2024

Sci Rep

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show abstract

“…Chromatin accessibility and histone modifications play a significant role in plant abiotic stress responses ( Pandey et al., 2016 ; Halder et al., 2022 ; Nunez-Vazquez et al., 2022 ). Integrating chromatin regions accessibility and histone mark distribution permit to identify the location of genomic regulatory elements and understanding transcriptional regulation.…”

Section: Integrated Omics For Studying Chilling Injury Development An...mentioning

confidence: 99%

Dissecting postharvest chilling injuries in pome and stone fruit through integrated omics

Rodrigues,

Ordoñez-Trejo,

Rasori

et al. 2024

Front. Plant Sci.

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Lowering the storage temperature is an effective method to extend the postharvest and shelf life of fruits. Nevertheless, this technique often leads to physiological disorders, commonly known as chilling injuries. Apples and pears are susceptible to chilling injuries, among which superficial scald is the most economically relevant. Superficial scald is due to necrotic lesions of the first layers of hypodermis manifested through skin browning. In peaches and nectarines, chilling injuries are characterized by internal symptoms, such as mealiness. Fruits with these aesthetic or compositional/structural defects are not suitable for fresh consumption. Genetic variation is a key factor in determining fruit susceptibility to chilling injuries; however, physiological, or technical aspects such as harvest maturity and storage conditions also play a role. Multi-omics approaches have been used to provide an integrated explanation of chilling injury development. Metabolomics in pome fruits specifically targets the identification of ethylene, phenols, lipids, and oxidation products. Genomics and transcriptomics have revealed interesting connections with metabolomic datasets, pinpointing specific genes linked to cold stress, wax synthesis, farnesene metabolism, and the metabolic pathways of ascorbate and glutathione. When applied to Prunus species, these cutting-edge approaches have uncovered that the development of mealiness symptoms is linked to ethylene signaling, cell wall synthesis, lipid metabolism, cold stress genes, and increased DNA methylation levels. Emphasizing the findings from multi-omics studies, this review reports how the integration of omics datasets can provide new insights into understanding of chilling injury development. This new information is essential for successfully creating more resilient fruit varieties and developing novel postharvest strategies.

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“…Several studies have demonstrated a role for histone and DNA-modifying enzymes in stress responses in the past (reviewed by Avramova, 2015;Halder et al, 2022;L€ amke & B€ aurle, 2017;Probst & Mittelsten Scheid, 2015). A series of recent studies reported the involvement of a structural protein that is associated with the nuclear envelope (NE) in plant stress responses (Choi et al, 2019;Guo et al, 2017;Jarad et al, 2019;Sakamoto et al, 2020).…”

Section: Function Of Chromatin Regulators In Biotic and Abiotic Stres...mentioning

confidence: 99%

Conserved functions of chromatin regulators in basal Archaeplastida

Kerckhofs,

Schubert

2023

The Plant Journal

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SUMMARYChromatin is a dynamic network that regulates genome organization and gene expression. Different types of chromatin regulators are highly conserved among Archaeplastida, including unicellular algae, while some chromatin genes are only present in land plant genomes. Here, we review recent advances in understanding the function of conserved chromatin factors in basal land plants and algae. We focus on the role of Polycomb‐group genes which mediate H3K27me3‐based silencing and play a role in balancing gene dosage and regulating haploid‐to‐diploid transitions by tissue‐specific repression of the transcription factors KNOX and BELL in many representatives of the green lineage. Moreover, H3K27me3 predominantly occupies repetitive elements which can lead to their silencing in a unicellular alga and basal land plants, while it covers mostly protein‐coding genes in higher land plants. In addition, we discuss the role of nuclear matrix constituent proteins as putative functional lamin analogs that are highly conserved among land plants and might have an ancestral function in stress response regulation. In summary, our review highlights the importance of studying chromatin regulation in a wide range of organisms in the Archaeplastida.

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Chromatin-Based Transcriptional Reprogramming in Plants under Abiotic Stresses

Cited by 13 publications

References 150 publications

Inferring co-expression networks of Arabidopsis thaliana genes during their interaction with Trichoderma spp.

Inferring co-expression networks of Arabidopsis thaliana genes during their interaction with Trichoderma spp.

Dissecting postharvest chilling injuries in pome and stone fruit through integrated omics

Conserved functions of chromatin regulators in basal Archaeplastida

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