Browsing by Author "Yadav, Vikash Kumar"

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Deciphering shared attributes of plant long non-coding RNAs through a comparative computational approach
(Springer Nature Publishing AG, 2023) Yadav, Vikash Kumar; Jalmi, Siddhi Kashinath; Tiwari, Shalini; Kerkar, Savita
Over the past decade, long non-coding RNA (lncRNA), which lacks protein-coding potential, has emerged as an essential regulator of the genome. The present study examined 13,599 lncRNAs in Arabidopsis thaliana, 11,565 in Oryza sativa, and 32,397 in Zea mays for their characteristic features and explored the associated genomic and epigenomic features. We found lncRNAs were distributed throughout the chromosomes and the Helitron family of transposable elements (TEs) enriched, while the terminal inverted repeat depleted in lncRNA transcribing regions. Our analyses determined that lncRNA transcribing regions show rare or weak signals for most epigenetic marks except for H3K9me2 and cytosine methylation in all three plant species. LncRNAs showed preferential localization in the nucleus and cytoplasm; however, the distribution ratio in the cytoplasm and nucleus varies among the studied plant species. We identified several conserved endogenous target mimic sites in the lncRNAs among the studied plants. We found 233, 301, and 273 unique miRNAs, potentially targeting the lncRNAs of A. thaliana, O. sativa, and Z. mays, respectively. Our study has revealed that miRNAs, which interact with lncRNAs, target genes that are involved in a diverse array of biological and molecular processes. The miRNA-targeted lncRNAs displayed a strong affinity for several transcription factors, including ERF and BBR-BPC, mutually present in all three plants, advocating their conserved functions. Overall, the present study showed that plant lncRNAs exhibit conserved genomic and epigenomic characteristics and potentially govern the growth and development of plants.
ReDtool: a Python-based command line tool for restriction digestion analysis of large DNA sequences
(Springer Nature Publishing AG, 2024) Brahmam, Guntha Shiva; Mishra, Divya; Yadav, Vikash Kumar
Developing an in-silico restriction digestion tool is vital in modern molecular biology and genomics. We develop ReDtool, a Python 3-based command-line toolkit to simulate restriction digestion processes. ReDtool offers a virtual digestion function, simulating restriction digestion on a provided sequence by specifying any desired restriction site. We validated the output of ReDtool experimentally using restriction analysis and Sanger sequencing. ReDtool processes large genomic sequences efficiently, accepting FASTA or text format as input. The output file includes detailed information such as restriction site position, fragment length, and fragment sequence. With its high throughput and precision, ReDtool enables comprehensive restriction digestion analysis of chromosomes or genomes, addressing a critical need in genomic research with its straightforward approach (https://github.com/CBL205NIPGR/ReDtool).