Browsing by Author "Shree, Tanu"

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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.
Identification of tRNA-derived fragments in legumes
(Springer Nature Publishing AG, 2026) Arora, Simran; Aftab, Sahrish; Shree, Tanu; Kumar, Shailesh
The tRNA-derived noncoding RNAs (tncRNAs) belong to the novel class of noncoding RNAs, acting as important components of genome regulatory circuits. In planta, the mechanism of generation and function of tncRNAs is not fully elucidated. Production of important leguminous plants like chickpea, Medicago and soybean is majorly hampered due to different biotic and abiotic stresses. Identification and characterization of tncRNAs in legumes may open a new paradigm for molecular biologists to make novel tools for the improved varieties of legumes for sustainable agriculture. The first step in the study of tncRNAs is to identify and annotate them in small RNA sequencing datasets. Here, we have demonstrated the tncRNA Toolkit for the identification and annotation of tncRNAs in a small RNA sequencing dataset of the important legume crop chickpea.
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.