Gopal
@mkuniversity.org
Assistant Professor
Dept of Plant Biotechnology School of Biotechnology Madurai Kamaraj University Madurai Tamil Nadu India
RESEARCH INTERESTS
RNA Biology Plant Molecular Biology Virology
Scopus Publications
Scholar Citations
Scholar h-index
Scholar i10-index
Scopus Publications
Asha Anand, Shailja Chauhan, Aparna Chodon, Kavitha Velayudha Vimala Kumar, Saravanakumar S., and Gopal Pandi
Termedia Sp. z.o.o.
The microRNAs are endogenous, regulating gene expression either at the DNA or RNA level. Despite the availability of extensive studies on microRNA generation in plants, reports on their abundance, biogenesis, and consequent gene regulation in plant organelles remain naVve. Building on previous studies involving pre-miRNA sequencing in Abelmoschus esculentus, we demonstrated that three putative microRNAs were raised from the chloroplast genome. In the current study, we have characterized the genesis of these three microRNAs through a combination of bioinformatics and experimental approaches. The gene sequence for a miRNA, designated as AecpmiRNA1 (A. esculentus chloroplast miRNA), is potentially located in both the genomic DNA, i.e., nuclear and chloroplast genome. In contrast, the gene sequences for the other two miRNAs (AecpmiRNA2 and AecpmiRNA3) are exclusively present in the chloroplast genome. Target prediction revealed many potential mRNAs as targets for AecpmiRNAs. Further analysis using 5′ RACE-PCR determined the AecpmiRNA3 binding and cleavage site at the photosystem II protein N (psbN). These results indicate that AecpmiRNAs are generated from the chloroplast genome, possessing the potential to regulate mRNAs arising from chloroplast gene(s). On the other side, the possibility of nuclear genome-derived mRNA regulation by AecpmiRNAs cannot be ruled out.
Muthuramalingam Karpagavalli, Suganya Sivagurunathan, T. Sayamsmruti Panda, Nagesh Srikakulam, Reety Arora, Lamiya Dohadwala, Basant K. Tiwary, Sudha Rani Sadras, Jayamuruga Pandian Arunachalam, Gopal Pandi,et al.
Royal Society of Chemistry (RSC)
piRNAs profiled from human retina/RPE share seed sequence homology with miRNAs and lncRNAs. They play regulatory roles in intracellular transport, circadian rhythm, oxidative stress, and retinal neurodegeneration.
Ram Kumar Muthu, Thiyagarajan Sekar, Parthasarathy Ayothi, Govendan Subhas, Dinesh Babu Kandhalu Sagadevan, Gopal Pandi, Babu Rajendra Prasad Venugopal, and Kathiresan Shanmugam
South African Journal of Botany Elsevier BV
Nagesh Srikakulam, Ganapathi Sridevi, and Gopal Pandi
Frontiers Media SA
The Reference Transcriptomic Dataset (RTD) is an accurate and comprehensive collection of transcripts originating from a given organism. It holds the key to precise transcript quantification and downstream analysis of differential expressions and regulations. Currently, transcriptome annotations for most crop plants are far from complete. For example, Oryza sativa indica (O. sativa indica) is reported to have 40,759 transcripts in the Ensembl database without alternative transcript isoforms and alternative splicing (AS) events. To generate a high-quality RTD, we conducted RNA sequencing of rice leaf samples collected at various time points during Rhizoctonia solani infection. The obtained reads were analyzed by adopting the recently developed computational analysis pipeline to assemble the RTD with increased transcript and AS diversity for O. sativa indica (IndicaRTD). After stringent quality filtering, the newly constructed transcriptome annotation was comprised of 122,968 non-redundant transcripts from 53,695 genes. This study identified many novel transcripts compared to Ensembl deposited data that are important for regulating molecular and physiological processes in the plant system. Currently, the assembled IndicaRTD must allow fast quantification of transcript and gene expression with high precision.
Nagesh Srikakulam, Ashirbad Guria, Jeyalakshmi Karanthamalai, Vidya Murugesan, Vignesh Krishnan, Kasthuri Sundaramoorthy, Shakkhar Saha, Rudransh Singh, Thiveyarajan Victorathisayam, Veeraputhiran Rajapriya,et al.
Frontiers Media SA
Sheath blight (ShB) disease, caused by Rhizoctonia solani, is one of the major biotic stress-oriented diseases that adversely affect the rice productivity worldwide. However, the regulatory mechanisms are not understood yet comprehensively. In the current study, we had investigated the potential roles of miRNAs in economically important indica rice variety Pusa Basmati-1 upon R. solani infection by carrying out in-depth, high-throughput small RNA sequencing with a total data size of 435 million paired-end raw reads from rice leaf RNA samples collected at different time points. Detailed data analysis revealed a total of 468 known mature miRNAs and 747 putative novel miRNAs across all the libraries. Target prediction and Gene Ontology functional analysis of these miRNAs were found to be unraveling various cellular, molecular, and biological functions by targeting various plant defense-related genes. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to validate the miRNAs and their putative target genes. Out of the selected miRNA-specific putative target genes, miR395a binding and its cleavage site on pentatricopeptide were determined by 5’ RACE-PCR. It might be possible that R. solani instigated chloroplast degradation by modulating the pentatricopeptide which led to increased susceptibility to fungal infection.
Ashirbad Guria, Priyanka Sharma, Nagesh Srikakulam, Akhil Baby, Sankar Natesan, and Gopal Pandi
Frontiers Media SA
Covalently closed circular RNAs are neoteric to the eukaryotic family of long non-coding RNAs emerging as a result of 5′–3′ backsplicing from exonic, intronic, or intergenic regions spanning the parental gene. Owing to their unique structure and stability, circular RNAs have a multitude of functional properties such as micro-RNA and protein sponges, direct and indirect modulators of gene expression, protein translation, and many unproven activities apart from being potential biomarkers. However, due to their low abundance, most of the global circular RNA identification is carried out by high-throughput NGS-based approaches requiring millions of sequencing reads. This lag in methodological advancements demands for newer, more refined, and efficient identification techniques. Here, we aim to show an improved version of our previously reported template-dependent multiple displacement amplification (tdMDA)-NGS method by superimposing the ribosomal depletion step and use of H minus reverse transcriptase and RNase H. Implication of tdMDA using highly replicative Phi29 DNA polymerase after minimizing the linear and ribosomal RNA content further intensifies its detection limit toward even the abysmally expressing circular RNA at a low NGS depth, thereby decreasing the cost of identifying a single circular RNA. A >11-fold and >6-fold increase in total circular RNA was identified from the improved-tdMDA-NGS method over the traditional method of circRNA sequencing using DCC and CIRI2 pipelines, respectively, from Oryza sativa subsp. Indica. Furthermore, the reliability of the improved-tdMDA-NGS method was also asserted in HeLa cell lines, showing a significant fold difference in comparison with the existing traditional method of circRNA sequencing. Among the identified circular RNAs, a significant percentage from both rice (∼58%) and HeLa cell lines (∼84%) is found to be matched with the previously reported circular RNAs, suggesting that the improved-tdMDA-NGS method can be adapted to detect and characterize the circular RNAs from different biological systems.
Aparna Chodon, Jeyalakshmi Karanthamalai, Gopal Pandi, and Jebasingh Tennyson
Elsevier
Ashirbad Guria, Priyanka Sharma, Sankar Natesan, and Gopal Pandi
Springer US
Priyanka Sharma, Ashirbad Guria, Sankar Natesan, and Gopal Pandi
Springer US
Asha Anand and Gopal Pandi
MDPI AG
Regulation of gene expression in any biological system is a complex process with many checkpoints at the transcriptional, post-transcriptional and translational levels. The control mechanism is mediated by various protein factors, secondary metabolites and a newly included regulatory member, i.e., noncoding RNAs (ncRNAs). It is known that ncRNAs modulate the mRNA or protein profiles of the cell depending on the degree of complementary and context of the microenvironment. In plants, ncRNAs are essential for growth and development in normal conditions by controlling various gene expressions and have emerged as a key player to guard plants during adverse conditions. In order to have smooth functioning of the plants under any environmental pressure, two very important DNA-harboring semi-autonomous organelles, namely, chloroplasts and mitochondria, are considered as main players. These organelles conduct the most crucial metabolic pathways that are required to maintain cell homeostasis. Thus, it is imperative to explore and envisage the molecular machineries responsible for gene regulation within the organelles and their coordination with nuclear transcripts. Therefore, the present review mainly focuses on ncRNAs origination and their gene regulation in chloroplasts and plant mitochondria.
Jeyalakshmi Karanthamalai, Aparna Chodon, Shailja Chauhan, and Gopal Pandi
MDPI AG
N6-methyladenine (6mA) is a DNA base modification at the 6th nitrogen position; recently, it has been resurfaced as a potential reversible epigenetic mark in eukaryotes. Despite its existence, 6mA was considered to be absent due to its undetectable level. However, with the new advancements in methods, considerable 6mA distribution is identified across the plant genome. Unlike 5-methylcytosine (5mC) in the gene promoter, 6mA does not have a definitive role in repression but is exposed to have divergent regulation in gene expression. Though 6mA information is less known, the available evidences suggest its function in plant development, tissue differentiation, and regulations in gene expression. The current review article emphasizes the research advances in DNA 6mA modifications, identification, available databases, analysis tools and its significance in plant development, cellular functions and future perspectives of research.
Ashirbad Guria, Priyanka Sharma, Sankar Natesan, and Gopal Pandi
Frontiers Media SA
Circular RNAs are the most recent addition in the non-coding RNA family, which has started to gain recognition after a decade of obscurity. The first couple of reports that emerged at the beginning of this decade and the amount of evidence that has accumulated thereafter has, however, encouraged RNA researchers to navigate further in the quest for the exploration of circular RNAs. The joining of 5′ and 3′ ends of RNA molecules through backsplicing forms circular RNAs during co-transcriptional or post-transcriptional processes. These molecules are capable of effectively sponging microRNAs, thereby regulating the cellular processes, as evidenced by numerous animal and plant systems. Preliminary studies have shown that circular RNA has an imperative role in transcriptional regulation and protein translation, and it also has significant therapeutic potential. The high stability of circular RNA is rendered by its closed ends; they are nevertheless prone to degradation by circulating endonucleases in serum or exosomes or by microRNA-mediated cleavage due to their high complementarity. However, the identification of circular RNAs involves diverse methodologies and the delineation of its possible role and mechanism in the regulation of cellular and molecular architecture has provided a new direction for the continuous research into circular RNA. In this review, we discuss the possible mechanism of circular RNA biogenesis, its structure, properties, degradation, and the growing amount of evidence regarding the detection methods and its role in animal and plant systems.
Ashirbad Guria and Gopal Pandi
Springer Singapore
Sangeetha Elangovan, Nagesh Srikakulam, Gopal Pandi, Thomas Jacob, Usha Ramakrishnan, Venugopal Madhugiri Narayanarao, and Jebasingh Tennyson
Springer Science and Business Media LLC
Ashirbad Guria, Kavitha Velayudha Vimala Kumar, Nagesh Srikakulam, Anakha Krishnamma, Saibal Chanda, Satyam Sharma, Xiaofeng Fan, and Gopal Pandi
Hindawi Limited
Circular RNAs (circRNAs) are newly discovered incipient non-coding RNAs with potential roles in disease progression in living organisms. Significant reports, since their inception, highlight the abundance and putative functional roles of circRNAs in every organism checked for, likeO. sativa,Arabidopsis, human, and mouse. CircRNA expression is generally less than their linear mRNA counterparts which fairly explains the competitive edge of canonical splicing over non-canonical splicing. However, existing methods may not be sensitive enough for the discovery of low-level expressed circRNAs. By combining template-dependent multiple displacement amplification (tdMDA), Illumina sequencing, and bioinformatics tools, we have developed an experimental protocol that is able to detect 1,875 novel and known circRNAs fromO. sativa. The same method also revealed 9,242 putative circRNAs in less than 40 million reads for the first time from theNicotiana benthamianawhose genome has not been fully annotated. Supported by the PCR-based validation and Sanger sequencing of selective circRNAs, our method represents a valuable tool in profiling circRNAs from the organisms with or without genome annotation.
Rajkumar Verma, Rodney M. Ritzel, Nia M. Harris, Juneyoung Lee, TaeHee Kim, Gopal Pandi, Raghu Vemuganti, and Louise D. McCullough
Ovid Technologies (Wolters Kluwer Health)
Background and Purpose— Social isolation increases mortality and impairs recovery after stroke in clinical populations. These detrimental effects have been recapitulated in animal models, although the exact mechanism mediating these effects remains unclear. Dysregulation of microRNAs (miRNAs) occurs in both strokes as well as after social isolation, which trigger changes in many downstream genes. We hypothesized that miRNA regulation is involved in the detrimental effects of poststroke social isolation in aged animals. Methods— We pair-housed 18-month-old C57BL/6 male mice for 2 weeks before a 60-minute right middle cerebral artery occlusion or sham surgery and then randomly assigned mice to isolation or continued pair housing immediately after surgery. We euthanized mice either at 3, 7, or 15 days after surgery and isolated the perilesional frontal cortex for whole microRNAome analysis. In an additional cohort, we treated mice 1 day after stroke onset with an in vivo-ready antagomiR-141 for 3 days. Results— Using whole microRNAome analysis of 752 miRNAs, we identified miR-141-3p as a unique miRNA that was significantly upregulated in isolated mice in a time-dependent manner up to 2 weeks after stroke. Posttreatment with an antagomiR-141-3p reduced the postisolation-induced increase in miR-141-3p to levels almost equal to those of pair-housed stroke controls. This treatment significantly reduced mortality (by 21%) and normalized infarct volume and neurological scores in poststroke-isolated mice. Quantitative PCR analysis revealed a significant upregulation of Tgfβr1 (transforming growth factor beta receptor 1, a direct target of miR-141-3p) and Igf-1 (insulin-like growth factor 1) mRNA after treatment with antagomiR. Treatment also increased the expression of other pleiotropic cytokines such as Il-6 (interleukin 6) and Tnf-α (tumor necrosis factor-α), an indirect or secondary target) in brain tissue. Conclusions— miR-141-3p is increased with poststroke isolation. Inhibition of miR-141-3p improved mortality, neurological deficits, and decreased infarct volumes. Importantly, these therapeutic effects occurred in aged animals, the population most at risk for stroke and poststroke isolation.
Kandhalu Babu, Ashirbad Guria, Jeyalakshmi Karanthamalai, Nagesh Srikakulam, Kamlesh Kumari, Priyanka Sharma, Sam Chandran, Anburaj Barnabas, Jebasingh Tennyson, and Gopal Pandi
MDPI AG
Bhendi yellow vein mosaic virus (BYVMV) belongs to the monopartite begomovirus associated with the β satellite. As a single-stranded DNA (ssDNA) virus, it should be amenable to transcriptional and post-transcriptional gene silencing (TGS and PTGS). Previously, we had demonstrated C2, C4 and βC1 to be having different levels of influence on PTGS. Hence in the present study, a series of experiments such as agroinfiltration, chop-polymerase chain reaction (PCR), quantitative PCR (qPCR) and bisulfite next generation sequencing (NGS) were designed to analyse the involvement of BYVMV proteins on DNA methylation suppression. From the preliminary studies, we concluded that BYVMV genes were responsible for TGS suppression and C2, C4 genes from BYVMV were selected for further studies. Agroinfiltration experiments with mutant C2 and C4 partial tandem repeat (PTR) constructs of BYVMV have confirmed the role of C2 and C4 in DNA methylation impairment. The protoplast replication assay has shown that C4 was not an impediment for viral DNA replication and subsequent agroinfiltration studies with the C4 mutant BYVMV PTR construct have revealed the involvement of C4 in viral DNA movement.
Suresh L. Mehta, Gopal Pandi, and Raghu Vemuganti
Ovid Technologies (Wolters Kluwer Health)
Background and Purpose— Circular RNAs (circRNAs) are a novel class of noncoding RNAs formed from many protein-coding genes by backsplicing. Although their physiological functions are not yet completely defined, they are thought to control transcription, translation, and microRNA levels. We investigated whether stroke changes the circRNAs expression profile in the mouse brain. Methods— Male C57BL/6J mice were subjected to transient middle cerebral artery occlusion, and circRNA expression profile was evaluated in the penumbral cortex at 6, 12, and 24 hours of reperfusion using circRNA microarrays and real-time PCR. Bioinformatics analysis was conducted to identify microRNA binding sites, transcription factor binding, and gene ontology of circRNAs altered after ischemia. Results— One thousand three-hundred twenty circRNAs were expressed at detectable levels mostly from exonic (1064) regions of the genes in the cerebral cortex of sham animals. Of those, 283 were altered (>2-fold) at least at one of the reperfusion time points, whereas 16 were altered at all 3 time points of reperfusion after transient middle cerebral artery occlusion compared with sham. Postischemic changes in circRNAs identified by microarray analysis were confirmed by real-time PCR. Bioinformatics showed that these 16 circRNAs contain binding sites for many microRNAs. Promoter analysis showed that the circRNAs altered after stroke might be controlled by a set of transcription factors. The major biological and molecular functions controlled by circRNAs altered after transient middle cerebral artery occlusion are biological regulation, metabolic process, cell communication, and binding to proteins, ions, and nucleic acids. Conclusions— This is a first study that shows that stroke alters the expression of circRNAs with possible functional implication to poststroke pathophysiology.
Bapatla Kesava Pavan Kumar, S. Kanakala, V. G. Malathi, P. Gopal, and R. Usha
Springer Science and Business Media LLC
Kavitha Velayudha Vimala Kumar, Nagesh Srikakulam, Priyavathi Padbhanabhan, and Gopal Pandi
MDPI AG
MicroRNAs (miRNAs) are crucial regulatory RNAs, originated from hairpin precursors. For the past decade, researchers have been focusing extensively on miRNA profiles in various plants. However, there have been few studies on the global profiling of precursor miRNAs (pre-miRNAs), even in model plants. Here, for the first time in a non-model plant—Abelmoschus esculentus with negligible genome information—we are reporting the global profiling to characterize the miRNAs and their associated pre-miRNAs by applying a next generation sequencing approach. Preliminarily, we performed small RNA (sRNA) sequencing with five biological replicates of leaf samples to attain 207,285,863 reads; data analysis using miRPlant revealed 128 known and 845 novel miRNA candidates. With the objective of seizing their associated hairpin precursors, we accomplished pre-miRNA sequencing to attain 83,269,844 reads. The paired end reads are merged and adaptor trimmed, and the resulting 40–241 nt (nucleotide) sequences were picked out for analysis by using perl scripts from the miRGrep tool and an in-house built shell script for Minimum Fold Energy Index (MFEI) calculation. Applying the stringent criteria of the Dicer cleavage pattern and the perfect stem loop structure, precursors for 57 known miRNAs of 15 families and 18 novel miRNAs were revealed. Quantitative Real Time (qRT) PCR was performed to determine the expression of selected miRNAs.
K. Shanmugha Rajan, Ganesan Velmurugan, Pandi Gopal, Tharmarajan Ramprasath, D.D. Venkatesh Babu, S. Krithika, Y. Christy Jenifer, Allen Freddy, George William, Krishnan Kalpana,et al.
Elsevier BV
P. Priyavathi, V. Kavitha, and P. Gopal
Current Science Association
Abelmoschus esculentus (Bhendi) is a traditional vege-table crop widely cultivated and consumed commonly in India. Yellow vein mosaic disease (YVMD) caused by Bhendi yellow vein mosaic virus (BYVMV) is a major constraint for Bhendi cultivation in India. To study the nature of infection in the field, we collected leaves which showed typical YVMD in Madurai (9 plants) and carried out rolling circle amplification (RCA) for plant #6. Intriguingly, the digestion of RCA product did not yield expected fragments. This sug-gests that there may be new viruses due to recombina-tion or mutation or mixed infection. However, on digesting the RCA product of plant #1 with Sac I, monomers of 2.7 and 1.3 kb were released and each was cloned into the pOK12 vector. Sequenced RCA digested products showed mixed infection by BYVMV DNA A, Okra enation leaf curl virus (OELCuV) DNA A, beta, alphasatellite with the nanovirus origin of replication. Consequently, mixed infection was also confirmed by Southern hybridization and qPCR in all the analysed plant samples. In the mixed infection of BYVMV and OELCuV, we examined high level of OELCuV DNA A accumulation.
K. Shanmugha Rajan, G. Velmurugan, Gopal Pandi, and Subbiah Ramasamy
Elsevier BV
Ashutosh Dharap, Courtney Pokrzywa, Shruthi Murali, Gopal Pandi, and Raghu Vemuganti
Public Library of Science (PLoS)
MicroRNAs (miRNAs) are known to repress translation by binding to the 3’UTRs of mRNAs. Using bioinformatics, we recently reported that several miRNAs also have target sites in DNA particularly in the promoters of the protein-coding genes. To understand the functional significance of this phenomenon, we tested the effects of miR-324-3p binding to RelA promoter. In PC12 cells, co-transfection with premiR-324-3p induced a RelA promoter plasmid in a dose-dependent manner and this effect was lost when the miR-324-3p binding site in the promoter was mutated. PremiR-324-3p transfection also significantly induced the endogenous RelA mRNA and protein expression in PC12 cells. Furthermore, transfection with premiR-324-3p increased the levels of cleaved caspase-3 which is a marker of apoptosis. Importantly, the miR-324-3p effects were Ago2 mediated as Ago2 knockdown prevented RelA expression and cleavage of caspase-3. Thus, our studies show that miRNA-mediated transcriptional activation can be seen in PC12 cells which are neural in origin.
S. A. Chandran, R. M. Packialakshmi, K. Subhalakshmi, C. Prakash, K. Poovannan, A. Nixon Prabu, P. Gopal, and R. Usha
Springer Science and Business Media LLC