Publications of NIPGR Scientists

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Subject: search.filters.subject.bisulphite sequencing

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    Genome-wide DNA methylation dynamics at "heading" stage of panicle and flag leaf in contrasting rice cultivars under field drought conditions
    (Frontiers Media S.A., 2025) Jajo, Ringyao; Kansal, Shivani; Mathur, Saloni; Raghuvanshi, Saurabh
    Abstract Introduction: Drought stress induces widespread genome-wide alterations in DNA methylation of rice. These changes work to alter gene expression and are relatively unexplored in reproductive tissues like flag leaf and panicle under field drought conditions. This study aims to explore the same in the panicle and flag leaf tissue of IR64 (drought-sensitive) and N22 (drought-tolerant) rice cultivars under field-drought conditions during the 'heading' stage of development. Methods: For the same, we generated whole-genome bisulfite sequencing libraries from the corresponding tissues and analysed them in detail. Results and discussion: The DNA methylation dynamics in adult tissue (flowering stage) was found to be clearly distinct from that of the seedling stage. Further, the contrasting rice genotypes also exhibited cultivar-specific and drought-induced dynamism in the methylation signatures. Notably, the two cultivars demonstrate inherent distinctions in sequence preferences of hyper- and hypo-methylation even prior to experiencing drought stress, and these preferences persist under the influence of the stress. Approximately 90% of the drought-induced differentially methylated region (DMR) are cultivar-specific, and about 70% of the cultivar differences (cultivar-DMR) under stress are unique compared to control condition. There is higher prevalence of hyper-methylated DMR that co-localized with differentially expressed genes in panicle. DMR of CHH sequence exhibit stronger negative correlation with expression compared to CpG and CHG sequence. Examination of differentially expressed genes with DMR highlights their functional relevance under drought stress, especially with DMR found in gene bodies and promoter regions. Notably, in panicle, methylation divergence of the two cultivars influences flowering regulation genes. Additionally, the findings also suggest a regulatory role for DNA methylation in drought induced response of miRNA genes, particularly in the panicle of N22 cultivars.
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    Cytosine hypomethylation at CHG and CHH sites in the pleiotropic mutants of Mendelian inheritance in Catharanthus roseus
    (Indian Academy of Sciences, 2013) Kumari, Renu; Yadav, Gitanjali; Sharma, Vishakha; Sharma, Vinay; Kumar, Sushil
    The 5S and 18S rDNA sequences of Catharanthus roseus cv 'Nirmal' (wild type) and its leafless inflorescence (lli), evergreen dwarf (egd) and irregular leaf lamina (ill) single mutants and lli egd, lli ill and egd ill double mutants were characterized. The lli, egd and ill mutants of Mendelian inheritance bore the names after their most conspicuous morphological feature(s). They had been chemically induced and isolated for their salt tolerance. The double mutants were isolated as morphological segregants from crosses between single mutants. The morphological features of the two parents accompanied salt tolerance in the double mutants. All the six mutants were hypomethylated at repeat sequences, upregulated and downregulated for many genes and carried pleiotropic alterations for several traits. Here the 5S and 18S rDNAs of C. roseus were found to be relatively low in cytosine content. Cytosines were preponderantly in CG context (53%) and almost all of them were methylated (97%). The cytosines in CHH and CHG (where H = A, T or C) contexts were largely demethylated (92%) in mutants. The demethylation was attributable to reduced expression of RDR2 and DRM2 led RNA dependant DNA methylation and CMT3 led maintenance methylation pathways. Mutants had gained some cytosines by substitution of C at T sites. These perhaps arose on account of errors in DNA replication, mediated by widespread cytosine demethylation at CHG and CHH sites. It was concluded that the regulation of cytosine ethylation mechanisms was disturbed in the mutants. ILL, EGD and LLI genes were identified as the positive regulators of other genes mediating the RdDM and CMT3 pathways, for establishment and maintenance of cytosine methylation in C. roseus.