Publications of NIPGR Scientists

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    ANNInter: A platform to explore ncRNA-ncRNA interactome of Arabidopsis thaliana
    (Elsevier B.V., 2025) Vivek, AT; Sahu, Namrata; Kalakoti, Garima; Kumar, Shailesh
    Eukaryotic transcriptomes are remarkably complex, encompassing not only protein-coding RNAs but also an expanding repertoire of noncoding RNAs (ncRNAs). In plants, ncRNA-ncRNA interactions (NNIs) have emerged as pivotal regulators of gene expression, orchestrating development and adaptive responses to stress. Despite their critical roles, the functional significance of NNIs remains poorly understood, largely due to a lack of comprehensive resources. Here, we present ANNInter, a comprehensive platform that integrates computational predictions with experimental datasets to systematically identify and analyze NNIs. The current version catalogs over 90,000 interactions spanning eight categories of sRNA-to-longer ncRNAs, each extensively annotated with interaction types, identification methods, and functional descriptions. The integrated schema and advanced visualization framework in ANNInter enable users to explore intricate interaction networks, providing system-wide insights into ncRNA-mediated regulation. These interaction data provide unparalleled opportunities to uncover the regulatory roles of NNIs in key biological processes such as growth regulation, stress adaptation, and cellular signaling. By providing an extensive, curated repository of computational and degradome-based interaction data, ANNInter will provide a platform to the study of ncRNA biology, elucidating the complex mechanisms of NNIs and supporting the concept of competing endogenous RNAs (ceRNAs) in gene regulation. The platform is freely accessible at https://www.nipgr.ac.in/ANNInter/.
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    Recent perspective of non-coding RNAs at the nexus of plant-pathogen interaction
    (Elsevier B.V., 2023) Sharma, Shambhavi; Sett, Susmita; Das, Tuhin; Prasad, Ashish; Prasad, Manoj
    In natural habitats, plants are exploited by pathogens in biotrophic or necrotrophic ways. Concurrently, plants have evolved their defense systems for rapid perception of pathogenic effectors and begin concerted cellular reprogramming pathways to confine the pathogens at the entry sites. During the reorganization of cellular signaling mechanisms following pathogen attack, non-coding RNAs serves an indispensable role either as a source of resistance or susceptibility. Besides the well-studied functions of non-coding RNAs related to plant development and abiotic stress responses, previous and recent discoveries have established that non-coding RNAs like miRNAs, siRNAs, lncRNAs and phasi-RNAs can fine tune plant defense responses by targeting various signaling pathways. In this review, recapitulation of previous reports associated with non-coding RNAs as a defense responder against virus, bacteria and fungus attacks and insightful discussion will lead us to conceive innovative ideas to fight against approaching threats of resistant breaking pathogens.
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    Tweaking the small non-coding RNAs to improve desirable traits in plant
    (MDPI AG, 2023) Halder, Koushik; Chaudhuri, Abira; Abdin, Malik Z; Datta, Asis
    Plant transcriptome contains an enormous amount of non-coding RNAs (ncRNAs) that do not code for proteins but take part in regulating gene expression. Since their discovery in the early 1990s, much research has been conducted to elucidate their function in the gene regulatory network and their involvement in plants' response to biotic/abiotic stresses. Typically, 20-30 nucleotide-long small ncRNAs are a potential target for plant molecular breeders because of their agricultural importance. This review summarizes the current understanding of three major classes of small ncRNAs: short-interfering RNAs (siRNAs), microRNA (miRNA), and transacting siRNAs (tasiRNAs). Furthermore, their biogenesis, mode of action, and how they have been utilized to improve crop productivity and disease resistance are discussed here.
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    Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq
    (Oxford University Press, 2021) Vivek, A.T.; Kumar, Shailesh
    Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.
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    Small RNAs in plants: recent development and application for crop improvement
    (Frontiers Media S.A., 2015) Kamthan, Ayushi; Chaudhuri, Abira; Kamthan, Mohan; Datta, Asis
    The phenomenon of RNA interference (RNAi) which involves sequence-specific gene regulation by small non-coding RNAs, i.e., small interfering RNA (siRNA) and microRNA (miRNA) has emerged as one of most powerful approaches for crop improvement. RNAi based on siRNA is one of the widely used tools of reverse genetics which aid in revealing gene functions in many species. This technology has been extensively applied to alter the gene expression in plants with an aim to achieve desirable traits. RNAi has been used for enhancing the crop yield and productivity by manipulating the gene involved in biomass, grain yield and enhanced shelf life of fruits and vegetables. It has also been applied for developing resistance against various biotic (bacteria, fungi, viruses, nematodes, insects) and abiotic stresses (drought, salinity, cold, etc.). Nutritional improvements of crops have also been achieved by enriching the crops with essential amino acids, fatty acids, antioxidants and other nutrients beneficial for human health or by reducing allergens or anti-nutrients. microRNAs are key regulators of important plant processes like growth, development, and response to various stresses. In spite of similarity in size (20–24 nt), miRNA differ from siRNA in precursor structures, pathway of biogenesis, and modes of action. This review also highlights the miRNA based genetic modification technology where various miRNAs/artificial miRNAs and their targets can be utilized for improving several desirable plant traits. microRNA based strategies are much efficient than siRNA-based RNAi strategies due to its specificity and less undesirable off target effects. As per the FDA guidelines, small RNA (sRNA) based transgenics are much safer for consumption than those over-expressing proteins. This review thereby summarizes the emerging advances and achievement in the field of sRNAs and its application for crop improvement.