Publications of NIPGR Scientists

Permanent URI for this communityhttps://ndkr-library.nipgr.ac.in/handle/123456789/1

Browse

Author: search.filters.author.Zahra, ShafaqueHas files: No

Search Results

Now showing 1 - 4 of 4
  • No Thumbnail Available
    Item
    In silico identification of tRNA fragments, novel candidates for cancer biomarkers, and therapeutic targets
    (Springer Nature Publishing AG, 2024) Singh, Ankita; Zahra, Shafaque; Arora, Simran; Hamid, Fiza; Kumar, Shailesh
    The identification of a wide variety of RNA molecules using high-throughput sequencing techniques in the transcriptome pool of living organisms has revealed hidden regulatory insights in the cell. The class of non-coding RNA fragments produced from transfer RNA, or tRFs, is one such example. They are heterogeneously sized molecules with lengths ranging between 15 and 50 nt. They have a history of being dysregulated in human malignancies and other illnesses. The detection of these molecules has been made easier by a variety of bioinformatics techniques. The various types of tRFs and how they relate to cancer are covered in this chapter. It also provides a summary of the biological significance of tRFs reported in human cancer. Additionally, it emphasizes the utilities of databases and computational tools that have been created by different research teams for the investigation of tRFs. This will further aid the exploration and analysis of tRFs in cancer research and will support future advancement and a better comprehension of these molecules.
  • No Thumbnail Available
    Item
    PtRNAdb: a web resource of plant tRNA genes from a wide range of plant species
    (Springer Nature Publishing AG, 2022) Singh, Ajeet; Zahra, Shafaque; Das, Durdam; Kumar, Shailesh
    tRNA, as well as their derived products such as short interspersed nuclear elements (SINEs), pseudogenes, and transfer RNA (tRNA)-derived fragments (tRFs), have now been shown to be vital for cellular life, functioning, and adaptation during different stress conditions in all diverse life forms. In this study, we have developed PtRNAdb (www.nipgr.ac.in/PtRNAdb), a plant-exclusive tRNA database containing 113,849 tRNA gene sequences from phylogenetically diverse plant species. We have analyzed a total of 106 nuclear, 89 plastidial, and 38 mitochondrial genomes of plants by the tRNAscan-SE software package, and after careful curation of the output data, we integrated the data and developed this database. The information about the tRNA gene sequences obtained was further enriched with a consensus sequence-based study of tRNA genes based on their isoacceptors and isodecoders. We have also built covariance models based on the isoacceptors and isodecoders of all the tRNA sequences using the infernal tool. The user can also perform BLAST not only against PtRNAdb entries but also against all the tRNA sequences stored in the PlantRNA database and annotated tRNA genes across the plant kingdom available at NCBI. This resource is believed to be of high utility for plant researchers as well as molecular biologists to carry out further exploration of the plant tRNAome on a wider spectrum, as well as for performing comparative and evolutionary studies related to tRNAs, and their derivatives across all domains of life. Database URL: http://www.nipgr.ac.in/PtRNAdb/
  • No Thumbnail Available
    Item
    In silico methods for the identification of viral-derived small interfering RNAs (vsiRNAs) and their application in plant genomics
    (Springer Nature Publishing AG, 2022) Narayan, Aditya; Zahra, Shafaque; Singh, Ajeet; Kumar, Shailesh
    The current era of high-throughput sequencing (HTS) technology has expedited the detection and diagnosis of viruses and viroids in the living system including plants. HTS data has become vital to study the etiology of the infection caused by both known as well as novel viral elements in planta, and their impact on overall crop health and productivity. Viral-derived small interfering RNAs are generated as a result of defence response by the host via RNAi machinery. They are immensely exploited for performing exhaustive viral investigations in plants using bioinformatics as well as experimental approaches. This chapter briefly presents the basics of virus-derived small interfering RNAs (vsiRNAs) biology in plants and their applications in plant genomics and highlights in silico strategies exploited for virus/viroid detection. It gives a systematic pipeline for vsiRNAs identification using currently available bioinformatics tools and databases. This will surely work as a quick beginner’s recipe for the in silico revelation of plant vsiRNAs as well as virus/viroid diagnosis using high-throughput sequencing data.
  • No Thumbnail Available
    Item
    PtRFdb: Plant tRNA-derived fragments database
    (Springer Nature Publishing AG, 2019) Zahra, Shafaque; Kumar, Shailesh
    The transfer RNA-derived fragments or tRFs represent a distinct class of small non-coding RNAs, and have been detected in evolutionarily divergent organisms. The role of tRFs in human cancers and infectious diseases as well as in gene regulation has been well established in diverse organisms. However, in plants, there is a need to further consolidate the tRF research by identification and characterization of tRFs because this domain is still unexplored across the plant kingdom. This chapter discusses about PtRFdb (www.nipgr.res.in/PtRFdb), a web-based repository harbouring the valuable information related to transfer RNA derived fragments (tRFs) in 10 different plant species. This database is believed to be beneficial for molecular biologists in facilitating future survey and characterization of tRFs across the plant kingdom.