Browsing by Author "Bhardwaj, Rohan"

Now showing 1 - 3 of 3

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, Shailesh
Background 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.
MedProDB: A database of mediator proteins
(Elsevier B.V., 2021) Bhardwaj, Rohan; Thakur, Jitendra K.; Kumar, Shailesh
In the last three decades, the multi-subunit Mediator complex has emerged as the key component of transcriptional regulation of eukaryotic gene expression. Although there were initial hiccups, recent advancements in bioinformatics tools contributed significantly to in-silico prediction and characterization of Mediator subunits from several organisms belonging to different eukaryotic kingdoms. In this study, we have developed the first database of Mediator proteins named MedProDB with 33,971 Mediator protein entries. Out of those, 12531, 11545, and 9895 sequences belong to metazoans, plants, and fungi, respectively. Apart from the core information consisting of sequence, length, position, organism, molecular weight, and taxonomic lineage, additional information of each Mediator sequence like aromaticity, hydropathy, instability index, isoelectric point, functions, interactions, repeat regions, diseases, sequence alignment to Mediator subunit family, Intrinsically Disordered Regions (IDRs), Post-translation modifications (PTMs), and Molecular Recognition Features (MoRFs) may be of high utility to the users. Furthermore, different types of search and browse options with four different tools namely BLAST, Smith-Waterman Align, IUPred, and MoRF-Chibi_Light are provided at MedProDB to perform different types of analysis. Being a critical component of the transcriptional machinery and regulating almost all the aspects of transcription, it generated lots of interest in structural and functional studies of Mediator functioning. So, we think that the MedProDB database will be very useful for researchers studying the process of transcription. This database is freely available at http://14.139.61.8/MedProDB/index.html
PtncRNAdb: plant transfer RNA-derived non-coding RNAs (tncRNAs) database
(Springer Nature Publishing AG, 2022) Zahra, Shafaque; Bhardwaj, Rohan; Sharma, Shikha; Singh, Ajeet; Kumar, Shailesh
Specific 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.