Publications of NIPGR Scientists
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Item UBA1-CDK16: A female-specific chimeric RNA emerging through evolution and involved in immune regulation(American Association for the Advancement of Science, 2026) Shi, Xinrui; Blackburn, Loryn; Singh, Sandeep; Glowczyk-Gluc, Martyna; Tajammal, Anam; Zahra, Shafaque; Kumar, Shailesh; Cornelison, Robert; Liang, Chen; Qin, Fujun; Liu, Aiqun; Lin, Shitong; Tang, Yue; Elfman, Justin; Manley, Thomas; Bullock, Timothy; Haverstick, Doris M.; Wu, Peng; Li, HuiChimeric RNAs resulting from intergenic splicing represent a distinct mechanism for transcriptome expansion. To explore the role of this previously unidentified layer of the transcriptome in sex-specific immunity, we analyzed RNA sequencing data from 425 blood samples and identified a female-specific chimeric RNA, UBA1-CDK16, which was further validated in more than 1200 blood samples. This chimeric RNA forms via cis-splicing between two adjacent X-linked parental genes, UBA1 and CDK16, despite both being expressed in both sexes. We demonstrated that a female-specific chromatin loop at the UBA1-CDK16 junction sites facilitates the intergenic splicing. Evolutionary analysis revealed that UBA1-CDK16 became female specific in humans through at least two independent paths. Functional studies suggested that UBA1-CDK16 is enriched in the myeloid lineage and may regulate myeloid cell development. Notably, its abnormal expression in female patients with COVID-19 correlates with altered neutrophil counts, highlighting its potential role in the disease progression.Item Molecular and expression analyses indicate the role of fusion transcripts in mediating abiotic stress responses in chickpea(Frontiers Media S.A., 2025) Hamid, Fiza; Zahra, Shafaque; Kumar, ShaileshUnderstanding the transcriptome diversity is essential for deciphering the transcriptional level regulation. High-throughput sequencing technologies have facilitated the detection of fusion transcripts (FTs), which are chimeric mRNA molecules derived from gene fusions due to chromosomal rearrangements or via the splicing machinery at the RNA level. In this study, we investigated the transcriptome complexity in Cicer arietinum resulting from fusion events using high-throughput RNA-Seq datasets from five tissues, i.e., stem, leaves, buds, flowers, and pods, and two abiotic stress conditions, i.e., drought and salinity. Of the 328 unique FTs identified, 69% exhibited the presence of canonical splice sites at their junction, indicating their generation via trans-splicing. Functional annotation and enrichment analyses of fusion partners suggested that these transcripts may expand functional diversity. A total of 10 FTs were validated via RT-PCR followed by Sanger sequencing, which are the first FTs described in the important legume chickpea. Expression analysis of fusion transcripts across various tissues and under abiotic stress conditions revealed evidence of context-dependent regulation. Furthermore, 120 fusion gene pairs were found to be conserved across 17 chickpea genotypes, highlighting their potential biological significance and stability within the species. Overall, these findings suggest that fusion transcripts may contribute to regulatory mechanisms underlying abiotic stress responses in chickpea.Item The landscape of fusion transcripts in plants: a new insight into genome complexity(BioMed Central Ltd, 2024) Chitkara, Pragya; Singh, Ajeet; Gangwar, Rashmi; Bhardwaj, Rohan; Zahra, Shafaque; Arora, Simran; Hamid, Fiza; Arya, Ajay; Sahu, Namrata; Chakraborty, Srija; Ramesh, Madhulika; Kumar, ShaileshBackground Fusion transcripts (FTs), generated by the fusion of genes at the DNA level or RNA-level splicing events significantly contribute to transcriptome diversity. FTs are usually considered unique features of neoplasia and serve as biomarkers and therapeutic targets for multiple cancers. The latest findings show the presence of FTs in normal human physiology. Several discrete reports mentioned the presence of fusion transcripts in planta, has important roles in stress responses, morphological alterations, or traits (e.g. seed size, etc.). Results In this study, we identified 169,197 fusion transcripts in 2795 transcriptome datasets of Arabidopsis thaliana, Cicer arietinum, and Oryza sativa by using a combination of tools, and confirmed the translational activity of 150 fusion transcripts through proteomic datasets. Analysis of the FT junction sequences and their association with epigenetic factors, as revealed by ChIP-Seq datasets, demonstrated an organised process of fusion formation at the DNA level. We investigated the possible impact of three-dimensional chromatin conformation on intra-chromosomal fusion events by leveraging the Hi-C datasets with the incidence of fusion transcripts. We further utilised the longread RNA-Seq datasets to validate the most reoccurring fusion transcripts in each plant species followed by further authentication through RT-PCR and Sanger sequencing. Conclusions Our findings suggest that a significant portion of fusion events may be attributed to alternative splicing during transcription, accounting for numerous fusion events without a proportional increase in the number of RNA pairs. Even non-nuclear DNA transcripts from mitochondria and chloroplasts can participate in intra- and inter-chromosomal fusion formation. Genes in close spatial proximity are more prone to undergoing fusion formation, especially in intra-chromosomal FTs. Most of the fusion transcripts may not undergo translation and serve as long non-coding RNAs. The low validation rate of FTs in plants indicated that the fusion transcripts are expressed at very low levels, like in the case of humans. FTs often originate from parental genes involved in essential biological processes, suggesting their relevance across diverse tissues and stress conditions. This study presents a comprehensive repository of fusion transcripts, offering valuable insights into their roles in vital physiological processes and stress responses.Item Genome-wide characterization and comparative analysis of the OSCA gene family and identification of its potential stress-responsive members in legumes(Nature Publishing Group, 2023) Chakraborty, Srija; Gangwar, Rashmi; Zahra, Shafaque; Poddar, Nikita; Singh, Amarjeet; Kumar, ShaileshCicer arietinum, Cajanus cajan, Vigna radiata, and Phaseolus vulgaris are economically important legume crops with high nutritional value. They are negatively impacted globally by different biotic and abiotic stresses. Hyperosmolality-gated calcium-permeable channels (OSCA) have been characterized as osmosensors in Arabidopsis thaliana but have not previously reported in legumes. This study provides a genome-wide identification, characterization, and comparative analysis of OSCA genes in legumes. Our study identified and characterized 13 OSCA genes in C. cajan, V. radiata, P. vulgaris, and 12 in C. arietinum, classified into four distinct clades. We found evidence to suggest that the OSCAs might be involved in the interaction between hormone signalling pathways and stress signalling pathways. Furthermore, they play a major role in plant growth and development. The expression levels of the OSCAs vary under different stress conditions in a tissue-specific manner. Our study can be used to develop a detailed understanding of stress regulatory mechanisms of the OSCA gene family in legumes.Item tncRNA Toolkit: A pipeline for convenient identification of RNA (tRNA)-derived non-coding RNAs(Elsevier B.V., 2023) Zahra, Shafaque; Singh, Ajeet; Kumar, ShaileshInsights into the eukaryotic gene regulation networks have improved due to the advent of diverse classes of non-coding RNAs. The transfer RNA (tRNA)-derived non-coding RNAs or tncRNAs is a novel class of non-coding RNAs, shown to regulate gene expression at transcription and translation levels. Here, we present a pipeline 'tncRNA Toolkit' for accurately identifying tncRNAs using small RNA sequencing (sRNA-seq) data. Previously, we identified tncRNA in six major angiosperms by utilizing our pipeline and highlighted the significant points regarding their generation and functions. The 'tncRNA Toolkit' is available at the URL: http://www.nipgr.ac.in/tncRNA. The scripts are written in bash and Python3 programming languages. The program can be efficiently run as a standalone command-line tool and installed in any Linux-based Operating System (OS). The user can run this program by providing the input of sRNA-seq data and genome file.The various features of the 'tncRNA Toolkit' are as follows:•Major tncRNA classes identified by this tool include tRF-5, tRF-3, tRF-1, 5'tRH, 3'tRH, and leader tRF. Also, it categorizes miscellaneous tncRNAs as other tRF.•It provides the following information for each identified tncRNA viz. tncRNA class, raw and normalized read count (RPM), read length, progenitor tRNA information (amino acid, anticodon, locus, strand), tncRNA sequence, and tRNA modification sites.•We hope to facilitate quick and reliable tncRNA identification, which will boost the exploration of this novel class of non-coding RNAs and their relevance in the living world, including plants.Item PtncRNAdb: plant transfer RNA-derived non-coding RNAs (tncRNAs) database(Springer Nature Publishing AG, 2022) Zahra, Shafaque; Bhardwaj, Rohan; Sharma, Shikha; Singh, Ajeet; Kumar, ShaileshSpecific endonucleolytic cleavage of tRNA molecules leads to the biogenesis of heterogeneously sized fragments called tRNA-derived non-coding RNAs (tncRNAs). The role of tncRNAs is well studied in human processes, and diseases including different types of cancers and other ailments. They are also generated under stress conditions in plants. Considering the potential role of tncRNAs in the plant system, we have developed a user-friendly, open-access web resource, PtncRNAdb (https://nipgr.ac.in/PtncRNAdb). PtncRNAdb consists of 4,809,503 tncRNA entries identified from ~ 2500 single-end small RNA-seq libraries from six plants, viz., Arabidopsis thaliana, Cicer arietinum, Zea mays, Oryza sativa, Medicago truncatula, and Solanum lycopersicum. It is provided with assorted options to search, browse, visualize, interpret, and download tncRNAs data. Users can perform query search using ‘BLASTN’ against PtncRNAdb entries. Highcharts have been included for better statistical PtncRNAdb data readability to the users. Additionally, PtncRNAdb includes ‘DE tncRNAs’ module for differentially expressed tncRNAs under various conditions. Their secondary structure, putative targets, interactive networks of target enrichment, and related publications are also incorporated for further interpretation of their biological functions. PtncRNAdb is an efficient, user-friendly, and exhaustive database, which will aid the ongoing research in plant tncRNAs as well as help in deciphering their role in gene regulation. We hope that it provides a promising platform for researchers to facilitate the understanding of tncRNAs, and their involvement in numerous pathways related to plant development and stress tolerance.Item Transfer RNA-derived non-coding RNAs (tncRNAs): Hidden regulation of plants' transcriptional regulatory circuits(Elsevier B.V., 2021) Zahra, Shafaque; Singh, Ajeet; Poddar, Nikita; Kumar, ShaileshThe emergence of distinct classes of non-coding RNAs has led to better insights into the eukaryotic gene regulatory networks. Amongst them, the existence of transfer RNA (tRNA)-derived non-coding RNAs (tncRNAs) demands exploration in the plant kingdom. We have designed a methodology to uncover the entire perspective of tncRNAome in plants. Using this pipeline, we have identified diverse tncRNAs with a size ranging from 14 to 50 nucleotides (nt) by utilizing 2448 small RNA-seq samples from six angiosperms, and studied their various features, including length, codon-usage, cleavage pattern, and modified tRNA nucleosides. Codon-dependent generation of tncRNAs suggests that the tRNA cleavage is highly specific rather than random tRNA degradation. The nucleotide composition analysis of tncRNA cleavage positions indicates that they are generated through precise endoribonucleolytic cleavage machinery. Certain nucleoside modifications detected on tncRNAs were found to be conserved across the plants, and hence may influence tRNA cleavage, as well as tncRNA functions. Pathway enrichment analysis revealed that common tncRNA targets are majorly enriched during metabolic and developmental processes. Further distinct tissue-specific tncRNA clusters highlight their role in plant development. Significant number of tncRNAs differentially expressed under abiotic and biotic stresses highlights their potential role in stress resistance. In summary, this study has developed a platform that will help in the understanding of tncRNAs and their involvement in growth, development, and response to various stresses. The workflow, software package, and results are freely available at http://nipgr.ac.in/tncRNA.Item Bioinformatics tools for epitope prediction(Springer Nature Publishing AG, 2020) Jaiswal, Mohini; Zahra, Shafaque; Kumar, ShaileshImmunological protection is conferred by immune cells, i.e., B and T cells, which can efficiently develop pathogen-specific memory and thus involved in adaptive immunity. More specifically, these immune cells can recognize a specific portion of their respective antigens termed as epitopes which possess their own significant values. There is a noble reason to identify the antigenic region of an antigen as it is having a great empirical cause, which includes exploration of disease etiology, the advancement of diagnosis assays, immune monitoring, and to design epitope-based vaccines. It requires detection and prediction of epitopes which is a considerable concern in the preparation of a peptide-based vaccine that is the centralized issue of immunoinformatics. Experimental screening is involved for large arrays of probable epitope candidates; thereby it is pricey and tedious. There is a requirement of more-advanced immunoinformatics tools as a prodigious amount of information has accumulated because of the onset of next-generation sequencing approaches for collection, analysis, and interpretation of data. Further, development of in silico epitope prediction methods has substantially reduced the difficulties related to epitope mapping by shortening potential epitope candidates list for experimental testing. These software tools have diverse applications in diagnosis of infectious diseases and allergies, understanding immune system function, vaccine designing, and prognosis of cancer. This chapter presents an outlook on how these tools are capable to predict epitopes of various antigens.Item From current knowledge to best practice: A primer on Viral diagnostics using deep sequencing of virus-derived small interfering RNAs (vsiRNAs) in infected plants(Elsevier B.V., 2020) Vivek, A.T.; Zahra, Shafaque; Kumar, ShaileshPlants have evolved many defense strategies for combating viral infections. One major surveillance strategy adopted by them is manipulating viral sequences to generate distinct small RNA products via Dicer-like enzymes (DCL), and thereby restricting virus multiplication through the RNA interference (RNAi) mechanism. The power of high-throughput sequencing technologies, with diverse computational tools to handle small RNA sequencing (sRNA-Seq) data, bestows unprecedented opportunities to answer fundamental questions in plant virology. Here, we present some basic concepts of virus-derived, small interfering RNA (vsiRNA) biogenesis in plants, optimization strategies, caveats, and best practices for efficient discovery and diagnosis of known as well as novel plant viruses/viroids using deep sequencing of small RNA (sRNA) pools.Item In-silico tools in phytochemical research(Springer Nature Publishing AG, 2019) Singh, Ajeet; Zahra, Shafaque; Kumar, ShaileshThe enormous and highly diversified plant kingdom bears a potpourri of phytochemicals, which offers a lot of chance in the pharmaceutical field for researchers to scout new drugs for treating a large number of diseases. The surplus amount of biomedical knowledge accumulated so far has led to the use of bioinformatics approaches for the analysis of genomics, proteomics, and metabolomics datasets. With the help of available data and computational analysis techniques, it has become possible to explore and analyze the multifarious molecular targets of individual phytochemical compounds. Web-based cheminformatics databases have assisted in extensive data mining, modeling of biochemical pathways and protein-protein interactions, and they are gainful for phytochemical research surpassing the narrow spectrum of their old and conventional uses. Genome-wide functional screening for probable pharmacological targets, pharmacophore generation, Quantitative or qualitative structure-activity relationship (QSAR) modeling, molecular docking, and systems biology approaches in this current post-genomic era have now become an indispensable part of the drug discovery process. Although, currently known phytoconstituents and their structures represent only an infinitesimal portion of the total diversity of plant phytocomponents, with the emergence in ‘in silico’ based approaches, many new phytoconstituents, and their respective targets will be discovered in the future. This chapter sheds light on the key elements of drug designing and available user-oriented ‘in silico’ tools helpful in phytochemical research.