Publications of NIPGR Scientists
Permanent URI for this communityhttps://ndkr-library.nipgr.ac.in/handle/123456789/1
Browse
11 results
Search Results
Item Broadening the epigenetic horizon of abiotic stress response in plants(Springer Nature Publishing AG, 2024) Chhatwal, Himani; Naik, Jogindra; Pandey, Ashutosh; Trivedi, Prabodh KumarPlants, unlike animals, cannot move from one place to another and have to face different climatic disturbances wherever they are growing. So, they have innumerable built-in mechanisms to adapt to various abiotic stressful conditions like drought, heat, cold, and salinity. The changing environmental conditions influence the expression patterns of genes. Epigenetics involves heritable changes in DNA bases or histone proteins, which ultimately create different conformational states of chromatin. The regulatory enzymes of epigenetic modifications are grouped as writers, readers and erasers, which add, recognize and remove the epigenetic marks, respectively. Here, we provide a comprehensive overview of the mechanism of DNA methylation by the RdDM pathway, its maintenance and removal, and different histone modification categories like acetylation, methylation, phosphorylation and ubiquitination. This review further discusses in detail the crucial role these modifications play in adapting to major abiotic stresses and how plants preserve these experiences as stress memory to respond to recurring stresses. It emphasizes the role of epigenetic modifications as a crucial mechanism for building plant’s tolerance and how it can be an important research priority to improve plant growth and development under abiotic stress conditions.Item A glucose-target of rapamycin signaling axis integrates environmental history of heat stress through maintenance of transcription-associated epigenetic memory in Arabidopsis(Oxford University Press, 2022) Sharma, Mohan; Sharma, Manvi; Jamsheer, Muhammed K; Laxmi, AshveryaIn nature, plants cope with adversity and have established strategies that recall past episodes and enable them to better cope with stress recurrences by establishing a 'stress memory'. Emerging evidence suggests that Glucose (Glc) and Target of Rapamycin (TOR), central regulators of plant growth have remarkable functions in stress adaptation. However, whether TOR modulates a stress memory response is so far unknown. Global transcriptome profiling identified that Glc through TOR regulates the expression of numerous genes involved in thermomemory. Priming of TOR overexpressors with mild heat showed better stress endurance, whereas TOR RNAi showed reduced thermomemory. This thermomemory is linked with histone methylation at specific sites of heat stress (HS) genes. TOR promotes long-term accumulation of H3K4me3 on thermomemory-associated gene promoters, even when transcription of those genes reverts to their basal level. Our results suggest that ARABIDOPSIS TRITHORAX 1 (ATX1), an H3K4 methyltransferase already shown to regulate H3K4me3 levels at the promoters of HS recovery genes, is a direct target of TOR signaling. The TOR activating E2Fa binds to the promoter of ATX1, regulates its expression which ultimately regulates thermomemory. Collectively, our findings reveal a mechanistic framework in which Glc-TOR signaling determines the integration of stress and energy signaling to regulate thermomemory.Item DNA methylation dynamics in response to abiotic and pathogen stress in plants(Springer Nature Publishing AG, 2022) Arora, Heena; Singh, Roshan Kumar; Sharma, Shambhavi; Sharma, Namisha; Panchal, Anurag; Das, Tuhin; Prasad, Ashish; Prasad, ManojDNA methylation is a dynamic epigenetic mechanism that plays a significant role in gene expression and also maintains chromatin stability. The process is conserved in both plants and animals, and crucial for development and stress responses. Differential DNA methylation during adverse environmental conditions or pathogen attack facilitates the selective expression of defense-related genes. Both stress-induced DNA hypomethylation and hypermethylation play beneficial roles in activating the defense response. These DNA marks may be carried to the next generation making the progenies ‘primed’ for abiotic and biotic stress responses. Over the recent years, rapid advancements in the area of high throughput sequencing have enabled the detection of methylation status at genome levels in several plant species. Epigenotyping offers an alternative tool to plant breeders in addition to conventional markers for the selection of the desired offspring. In this review, we briefly discuss the mechanism of DNA methylation, recent understanding of DNA methylation-mediated gene regulation during abiotic and biotic stress responses, and stress memory in plants.Item Histone acetylation dynamics regulating plant development and stress responses(Springer Nature Publishing AG, 2021) Kumar, Verandra; Thakur, Jitendra K.; Prasad, ManojCrop productivity is directly dependent on the growth and development of plants and their adaptation during different environmental stresses. Histone acetylation is an epigenetic modification that regulates numerous genes essential for various biological processes, including development and stress responses. Here, we have mainly discussed the impact of histone acetylation dynamics on vegetative growth, flower development, fruit ripening, biotic and abiotic stress responses. Besides, we have also emphasized the information gaps which are obligatory to be examined for understanding the complete role of histone acetylation dynamics in plants. A comprehensive knowledge about the histone acetylation dynamics will ultimately help to improve stress resistance and reduce yield losses in different crops due to climate changes.Item Surfacing the role of epigenetics in host-virus interaction(Caister Academic Press, 2018) Sharma, Namisha; Sahu, Pranav P.; Kulshreshtha, Ritika; Prasad, ManojEpigenetics is a mechanism which determines the phenotype of an organism by causing heritable (during cell division) but simultaneously reversible alterations/variations in gene expression. It is not related to alterations in the DNA sequence of the genotype. Geminiviruses are the most devastating plant viruses since they cause significant yield losses in world agriculture. The plant defense initiated against these DNA viruses is of special interest, specifically in regard to the role of epigenetic mechanism played in control of virus spread. These heritable and covalent modifications of DNA and histone in virus genome are mainly related to suppression of gene transcription, despite the differences between viruses, the role of epigenetics seems to be reasonably comparable. However, several key questions remain unanswered concerning the basic mechanism behind the epigenetic regulation of viruses via plant defense system. This book chapter specifically summarizes the recent advances on role of epigenetics in virus genome modification leading to silencing of viral genes and plant tolerance/resistance.Item Epigenetics and epigenomics of plants(Springer, 2018) Yadav, Chandra Bhan; Pandey, Garima; Muthamilarasan, MehanathanThe genetic material DNA in association with histone proteins forms the complex structure called chromatin, which is prone to undergo modification through certain epigenetic mechanisms including cytosine DNA methylation, histone modifications, and small RNA-mediated methylation. Alterations in chromatin structure lead to inaccessibility of genomic DNA to various regulatory proteins such as transcription factors, which eventually modulates gene expression. Advancements in high-throughput sequencing technologies have provided the opportunity to study the epigenetic mechanisms at genome-wide levels. Epigenomic studies using high-throughput technologies will widen the understanding of mechanisms as well as functions of regulatory pathways in plant genomes, which will further help in manipulating these pathways using genetic and biochemical approaches. This technology could be a potential research tool for displaying the systematic associations of genetic and epigenetic variations, especially in terms of cytosine methylation onto the genomic region in a specific cell or tissue. A comprehensive study of plant populations to correlate genotype to epigenotype and to phenotype, and also the study of methyl quantitative trait loci (QTL) or epiGWAS, is possible by using high-throughput sequencing methods, which will further accelerate molecular breeding programs for crop improvement.Item An insight into plant–Tomato leaf curl New Delhi virus interaction(Springer Nature, 2017) Sharma, Namisha; Prasad, ManojPlants being sessile are constantly exposed to several stresses, which involve different types of abiotic and biotic stress factors. Biotic stress in plants is caused by various living organisms called plant pathogens including bacteria, viruses, fungi and parasites. Among these pathogens, plant viruses cause severe damage to world agricultural productivity. The reason behind such widespread destruction caused by viruses is their ability to frequently evolve them through mutation and genetic recombination, to succeed over the unfavourable conditions. The virus infects both susceptible and tolerant/resistant plants by the similar and systematic manner but resistant/tolerant plants combat the virus spread and suppress the viral growth. When pathogen enters the plant system, diverse defense responses are initiated which are mediated by plant disease resistance genes (R genes) mediated resistance and hormone based signaling pathways which restrict the viral spread by initiating hypersensitive response. To further enhance our knowledge regarding resistance mechanisms, the virus infection pattern and interactions of virus within resistant and susceptible plants needs to be analysed. At present, most successful strategy involves deployment of crops possessing resistance/tolerance against viruses with the foremost interest of detecting genes associated with resistance or recovery. Among several plant viruses, ‘Geminiviruses’ are the most devastating. In this article we have provided a comprehensive overview of Tomato leaf curl New Delhi virus (ToLCNDV), a member of family Geminiviridae and the plant defense system initiated against this virus. The evaluation of ToLCNDV infection in a variety of hosts differing in their tolerance and identification of differentially expressed genes would be helpful in speculating the threats associated with similar begomoviral invasions.Item Salinity induced differential methylation patterns in contrasting cultivars of foxtail millet (Setaria italica L.)(Springer, 2017) Pandey, Garima; Yadav, Chandra Bhan; Sahu, Pranav Pankaj; Muthamilarasan, Mehanathan; Prasad, ManojReduced productivity and significant yield loss are the adverse effects of environmental conditions on physiological and biochemical pathways in crop plants. In this context, understanding the epigenetic machinery underlying the tolerance traits in a naturally stress tolerant crop is imperative. Foxtail millet (Setaria italica) is known for its better tolerance to abiotic stresses compared to other cereal crops. In the present study, methylation-sensitive amplified polymorphism (MSAP) technique was used to quantify the salt-induced methylation changes in two foxtail millet cultivars contrastingly differing in their tolerance levels to salt stress. The study highlighted that the DNA methylation level was significantly reduced in tolerant cultivar compared to sensitive cultivar. A total of 86 polymorphic MSAP fragments were identified, sequenced and functionally annotated. These fragments showed sequence similarity to several genes including ABC transporter, WRKY transcription factor, serine threonine-protein phosphatase, disease resistance, oxidoreductases, cell wall-related enzymes and retrotransposon and transposase like proteins, suggesting salt stress-induced methylation in these genes. Among these, four genes were chosen for expression profiling which showed differential expression pattern between both cultivars of foxtail millet. Altogether, the study infers that salinity stress induces genome-wide DNA demethylation, which in turn, modulates expression of corresponding genes.Item Post-transcriptional and epigenetic arms of RNA silencing: a defense machinery of naturally tolerant tomato plant against Tomato leaf curl New Delhi virus(Springer, 2014) Sahu, Pranav Pankaj; Sharma, Namisha; Puranik, Swati; Prasad, ManojTomato leaf curl disease (ToLCD), caused by strains of Tomato leaf curl virus, is major constraint to tomato production globally. The present study was aimed to understand the mechanisms of ToLCD tolerance in a naturally tolerant tomato cultivar through post-transcriptional and DNA methylation-specific RNA silencing. We evaluated the distribution of virus-derived short-interfering RNAs (siRNAs) throughout the Tomato leaf curl New Delhi virus (ToLCNDV) genome along with DNA methylation patterns in intergenic (IR) and Rep (AC1) regions in two tomato cultivars differing in their ToLCNDV tolerance. The methylation pattern was correlated by expression analysis of key methyltransferases genes. In the tolerant cultivar, higher accumulation of viral IR-specific 24-nucleotides (nt) siRNA and AC1-specific 21-nt siRNA were found. Higher methylation levels were observed in various regions of IR. Additionally, AC1 region which facilitates binding of plant nuclear proteins was hypermethylated. DNA methylation in the key regulating region may control the expression of AC1, AC2, and AC3 genes. Components of RNA silencing and DNA methylation machinery were found to be differentially expressed in both the cultivar of tomato at 21 dpi. Thus, we infer that both viral DNA methylation and siRNA-mediated RNA degradation play an important role in conferring tolerance against Tomato leaf curl New Delhi virus. Due to the inability to achieve field resistance in transgenic tomato by deploying the viral genes, targeting the viral genomic regions through RNAi technology reported here could offer an alternate defense strategy for generating transgenics to prevent yield loss.Item Involvement of host regulatory pathways during geminivirus infection: a novel platform for generating durable resistance(Springer, 2014) Sahu, Pranav Pankaj; Sharma, Namisha; Puranik, Swati; Muthamilarasan, Mehanathan; Prasad, ManojGeminiviruses are widely distributed throughout the world and cause devastating yield losses in almost all the economically important crops. In this review, the newly identified roles of various novel plant factors and pathways participating in plant–virus interaction are summarized with a particular focus on the exploitation of various pathways involving ubiquitin/26S proteasome pathway, small RNA pathways, cell division cycle components, and the epigenetic mechanism as defense responses during plant–pathogen interactions. Capturing the information on these pathways for the development of strategies against geminivirus infection is argued to provide the basis for new genetic approaches to resistance.