Genomic architecture of promoters and transcriptional regulation of candidate genes in rice involved in tolerance to anaerobic germination

Mohanty, Bijayalaxmi

doi:10.1016/j.cpb.2022.100236

Cited by 8 publications

(5 citation statements)

References 195 publications

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“…AT2G20110/TCX6 (Tesmin/TSO1-like CXC domain-containing protein) and AS2 are two transcriptional repressors that play roles in the repression of maintenance of DNA methylation and silencing of genes related with leaf polarity establishment and shoot apical meristem development [ 52 ]. ASHR1 was recently reported to regulate gene expression during anaerobic germination in rice [ 53 ]. The down-regulation of these factors (Fig.…”

Section: Discussionmentioning

confidence: 99%

Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis

Mladenov,

Wang,

Yang

et al. 2023

BMC Plant Biol

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Background Drought is one of the main consequences of global climate change and this problem is expected to intensify in the future. Resurrection plants evolved the ability to withstand the negative impact of long periods of almost complete desiccation and to recover at rewatering. In this respect, many physiological, transcriptomic, proteomic and genomic investigations have been performed in recent years, however, few epigenetic control studies have been performed on these valuable desiccation-tolerant plants so far. Results In the present study, for the first time for resurrection plants we provide evidences about the differential chromatin accessibility of Haberlea rhodopensis during desiccation stress by ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing). Based on gene similarity between species, we used the available genome of the closely related resurrection plant Dorcoceras hygrometricum to identify approximately nine hundred transposase hypersensitive sites (THSs) in H. rhodopensis. The majority of them corresponds to proximal and distal regulatory elements of different genes involved in photosynthesis, carbon metabolism, synthesis of secondary metabolites, cell signalling and transcriptional regulation, cell growth, cell wall, stomata conditioning, chaperons, oxidative stress, autophagy and others. Various types of binding motifs recognized by several families of transcription factors have been enriched from the THSs found in different stages of drought. Further, we used the previously published RNA-seq data from H. rhodopensis to evaluate the expression of transcription factors putatively interacting with the enriched motifs, and the potential correlation between the identified THS and the expression of their corresponding genes. Conclusions These results provide a blueprint for investigating the epigenetic regulation of desiccation tolerance in resurrection plant H. rhodopensis and comparative genomics between resurrection and non-resurrection species with available genome information.

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Section: Discussionmentioning

confidence: 99%

Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis

Mladenov,

Wang,

Yang

et al. 2023

BMC Plant Biol

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“…The regulation of ABA-signaling genes was associated with the overexpression of TFs, with their highest values observed at 15 min. TFs are members of the HD-ZIP, bZIP, C2H2, and AP2 families, such as ZAT12 (C2H2 family), that participate in the induction and repression of cold-responsive and oxidative stress genes [ 60 ]; HOX22 (HD-ZIP family) is involved in the defense mechanism of pathogen-related stress response of fungi [ 61 ], and drought- [ 62 ] and heat-stress-tolerance-induced HOX24 [ 63 ] and MYBS1 [ 64 ] are the essential components of the sugar signaling pathway regulating the α-amylase gene promoter [ 65 ]. A high expression level was found for DREB1G (AP2 family), which is a typical C-repeat-binding factor (CBF/DREB1) whose specific functions was found to be related to cold stress response [ 66 , 67 ].…”

Section: Discussionmentioning

confidence: 99%

‘Garlic-lipo’4Plants: Liposome-Encapsulated Garlic Extract Stimulates ABA Pathway and PR Genes in Wheat (Triticum aestivum)

Kutasy

Kiniczky²,

Decsi

et al. 2023

Plants

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Recently, environmentally friendly crop improvements using next-generation plant biostimulants (PBs) come to the forefront in agriculture, regardless of whether they are used by scientists, farmers, or industries. Various organic and inorganic solutions have been investigated by researchers and producers, focusing on tolerance to abiotic and biotic stresses, crop quality, or nutritional deficiency. Garlic has been considered a universal remedy ever since antiquity. A supercritical carbon dioxide garlic extract encapsulated in nanoscale liposomes composed of plant-derived lipids was examined as a possible PB agent. The present study focused on the characterization of the genes associated with the pathways involved in defense response triggered by the liposome nanoparticles that were loaded with supercritical garlic extracts. This material was applied to Triticum aestivum in greenhouse experiments using foliar spraying. The effects were examined in a large-scale genome-wide transcriptional profiling experiment by collecting the samples four times (0 min, used as a control, and 15 min, 24 h, and 48 h after spraying). Based on a time-course expression analysis, the dynamics of the cellular response were determined by examining differentially expressed genes and applying a cluster analysis. The results suggested an enhanced expression of abscisic acid (ABA) pathway and pathogenesis-related (PR) genes, of which positive regulation was found for the AP2-, C2H2-, HD-ZIP-, and MYB-related transcription factor families.

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“…There are still limited numbers of reports available about the role of GATA TFs in regulation of plant development and physiology. For example, role of these TFs in response to anaerobic germination is not well studied yet ( Gupta et al, 2017 ; Mohanty, 2022 ). However, it is known that genes related with stress-response, metabolism, and hormone signaling are controlled by the GATA TFs ( Gupta et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

In-Silico Study of Brassinosteroid Signaling Genes in Rice Provides Insight Into Mechanisms Which Regulate Their Expression

Ahmar

Gruszka

2022

Front. Genet.

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Brassinosteroids (BRs) regulate a diverse spectrum of processes during plant growth and development and modulate plant physiology in response to environmental fluctuations and stress factors. Thus, the BR signaling regulators have the potential to be targeted for gene editing to optimize the architecture of plants and make them more resilient to environmental stress. Our understanding of the BR signaling mechanism in monocot crop species is limited compared to our knowledge of this process accumulated in the model dicot species - Arabidopsis thaliana. A deeper understanding of the BR signaling and response during plant growth and adaptation to continually changing environmental conditions will provide insight into mechanisms that govern the coordinated expression of the BR signaling genes in rice (Oryza sativa) which is a model for cereal crops. Therefore, in this study a comprehensive and detailed in silico analysis of promoter sequences of rice BR signaling genes was performed. Moreover, expression profiles of these genes during various developmental stages and reactions to several stress conditions were analyzed. Additionally, a model of interactions between the encoded proteins was also established. The obtained results revealed that promoters of the 39 BR signaling genes are involved in various regulatory mechanisms and interdependent processes that influence growth, development, and stress response in rice. Different transcription factor-binding sites and cis-regulatory elements in the gene promoters were identified which are involved in regulation of the genes’ expression during plant development and reactions to stress conditions. The in-silico analysis of BR signaling genes in O. sativa provides information about mechanisms which regulate the coordinated expression of these genes during rice development and in response to other phytohormones and environmental factors. Since rice is both an important crop and the model species for other cereals, this information may be important for understanding the regulatory mechanisms that modulate the BR signaling in monocot species. It can also provide new ways for the plant genetic engineering technology by providing novel potential targets, either cis-elements or transcriptional factors, to create elite genotypes with desirable traits.

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Genomic architecture of promoters and transcriptional regulation of candidate genes in rice involved in tolerance to anaerobic germination

Cited by 8 publications

References 195 publications

Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis

Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis

‘Garlic-lipo’4Plants: Liposome-Encapsulated Garlic Extract Stimulates ABA Pathway and PR Genes in Wheat (Triticum aestivum)

In-Silico Study of Brassinosteroid Signaling Genes in Rice Provides Insight Into Mechanisms Which Regulate Their Expression

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