Institutional Publications

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    AtFusionDB: A comprehensive database of fusion transcripts in model plant Arabidopsis thaliana
    (Springer Nature Publishing AG, 2026) Shree, Tanu; Kumar, Shailesh
    Fusion transcripts are chimeric RNAs, produced by the joining of two different RNAs at the RNA level or as a product of gene fusion at the DNA level. In this era of high-throughput sequencing technologies, it is easy to identify novel molecules like fusion transcripts in different systems. That's because, initially, supposed to be the well-known cancer biomarkers, fusion transcripts are also validated in normal human physiology. In Planta, discrete reports are available, indicating the presence of fusion transcripts but no dedicated web resource is available for the plant-specific fusion transcripts. This chapter describes the first plant-specific database of fusion transcripts, i.e., AtFusionDB ( http://www.nipgr.res.in/AtFusionDB ), which contains the information on fusion transcripts identified in the model plant Arabidopsis thaliana. This database can be exploited to get significant information about gene/transcript fusion in plants.
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    Validation of plant fusion peptides using proteomics data
    (Springer Nature Publishing AG, 2026) Hamid, Fiza; Aftab, Sahrish; Shree, Tanu; Kumar, Shailesh
    Fusion transcripts and their fused protein products are emerging as exciting entities in molecular biology, offering potential applications in diagnostics and therapeutics. These fusion proteins, derived from the translation of fusion transcripts, hold promise as unique biomarkers and targets for intervention. While numerous algorithms exist to identify fusion RNAs, the detection and validation of their protein counterparts through proteomics remains a growing area of research. This challenge is particularly intriguing in plant biology, where fusion events may affect stress responses, development, and adaptation. This chapter provides an accessible and practical workflow for validating plant fusion peptides using publicly available proteomics datasets.
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    A method for isolation and transfection of arabidopsis protoplast for sucrose feeding assay
    (Springer Nature Publishing AG, 2026) Anjali, Anjali; Senthil-Kumar, Muthappa
    Protoplasts serve as a powerful system to study various plant physiological processes and to understand crucial signaling pathways within the plant system. The isolation of Arabidopsis protoplasts is a well-established technique and being utilized for wide range of assays. The method described herein includes the precise cutting of Arabidopsis leaves using extraction buffer containing cellulase and macerozyme. Further we present a polyethylene glycol [PEG]-mediated protoplast transformation method. Here, we have elucidated the methodology for isolation of protoplast for the AtSWEET-mediated sucrose uptake assay in control, and Pseudomonas syringe pv tomato DC3000 (Pst DC3000) treated leaves by utilizing GC/MS analysis. Our approach includes certain modifications to the previously published protoplast isolation technique, streamlining the process and providing a more accessible alternative to the highly specialized Xenopus oocyte uptake assay.
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    Arabidopsis ABSCISIC ACID INSENSITIVE4 targets PROTEIN L-ISOASPARTYL METHYLTRANSFERASE1 in seed
    (Springer Nature Publishing AG, 2022) Kamble, Nitin Uttam; Ghosh, Shraboni; Achary, Rakesh Kumar; Majee, Manoj
    PROTEIN L-ISOASPARTYL METHYLTRANSFERASE (PIMT) is a protein repairing enzyme (PRE) and is implicated in seed vigor and longevity. PIMT has been shown to be induced by ABA, however, its detailed regulation by ABA signaling components is unknown. Herein, we report that ABSCISIC ACID INSENSITIVE4 (ABI4) directly binds to the PIMT1 promoter and regulates its expression in Arabidopsis seeds. AtPIMT1 promoter analysis demonstrated the presence of putative ABI4 binding sites. Our Y1H analysis revealed that AtABI4 transcription factor binds to the AtPIMT1 promoter. Dual luciferase assay also demonstrated the binding of the AtABI4 transcription factor to the AtPIMT1 promoter. Subsequently, we have generated AtPIMT1 promoter GUS lines and revealed that ABA induced expression of GUS in Arabidopsis thaliana. Expression analyses exhibited reduced accumulation of PIMT1 protein and transcript with significant reduction in total PIMT activity in abi4-1 mutants as compared to that of the wild type. The AtPIMT1 promoter GUS expression in abi4-1 mutants was also found to be severely affected in both the control and ABA treatment. Hence, through molecular and genetic evidences we show that the AtABI4 plays a central role in regulating the expression of AtPIMT1 to impart seed vigor and longevity to orthodox seeds.