Biology subjects

Mohapatra, T.

Publications and source records attributed to Mohapatra, T..

3 recordsLinked to original sources

bioRxiv2025

FRG1 Regulates Nonsense-Mediated mRNA Decay by Modulating UPF1 Levels

FRG1 acts as a molecular double-edged sword: while its overexpression is linked to facioscapulohumeral muscular dystrophy (FSHD), its under expression activates tumorigenic signalling pathways--highlighting the importance of tightly regulated FRG1 levels. Although prior studies have hinted at FRG1s involvement in RNA biogenesis, its core molecular functions have remained largely elusive. Our previous work identified FRG1 as a transcriptional regulator of genes in the nonsense-mediated decay (NMD) pathway; however, the underlying mechanisms were not fully delineated. In this study, using a range of cellular models with altered FRG1 expression, we demonstrate that reduced FRG1 levels enhance NMD activity. We reveal that FRG1 is a structural component of both the spliceosome and the exon junction complex (EJC), and that it directly modulates NMD by interacting with UPF1--regulating its ubiquitination and degradation. Furthermore, we show that DUX4 inversely regulates the NMD machinery through FRG1, establishing a critical molecular axis. Despite its structural association with the EJC and spliceosome, the absence of FRG1 does not compromise the integrity of these complexes. Polysome profiling showed that FRG1 co-sediments with eIF4A3, a core EJC component, across translating ribosomal fractions. This interaction was further supported by proximity ligation assays confirming the close spatial proximity of FRG1 and eIF4A3. Importantly, we validated the impact of FRG1 perturbation on NMD efficiency and UPF1 levels in vivo using a transgenic FRG1 knockout zebrafish model. Together, these findings establish a direct, DUX4-independent role for FRG1 in regulating the NMD pathway and uncover a previously unrecognized function for FRG1 in post-transcriptional gene regulation. Our work provides mechanistic insight into FRG1s molecular roles and lays the groundwork for therapeutic strategies targeting diseases associated with its dysregulation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/689056v2_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@1ef00e1org.highwire.dtl.DTLVardef@22cd63org.highwire.dtl.DTLVardef@da4080org.highwire.dtl.DTLVardef@c0d283_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

molecular biology↗

bioRxiv2020

Prediction analysis of SARS-COV-2 entry in Livestock and Wild animals

BackgroundSARS-CoV-2 is a viral pathogen causing life-threatening disease in human. Interaction between spike protein of SARS-CoV-2 and ACE2 receptor on the cells is a potential factor in the infectivity of a host. The interaction of SARS-CoV-2 spike receptor-binding domain with its receptor - ACE2, in different hosts was evaluated to understand and predict viral entry. The protein and nucleotide sequences of ACE2 were initially compared across different species to identify key differences among them. The ACE2 receptor of various species was homology modeled (6LZG, 6M0J, and 6VW1 as a reference), and its binding ability to the spike ACE2 binding domain of SARS-CoV-2 was assessed. Initially, the spike binding parameters of ACE2 of known infected and uninfected species were compared with each Order (of animals) as a group. Finally, a logistic regression model vis-a-vis the spike binding parameters of ACE2 (considering data against 6LZG and 6M0J) was constructed to predict the probability of viral entry in different hosts. ResultsPhylogeny and alignment comparison did not lead to any meaningful conclusion on viral entry in different hosts. Out of several spike binding parameters of ACE2, a significant difference between the known infected and uninfected species was observed for six parameters. However, these parameters did not specifically categorize the Orders (of animals) into infected or uninfected. The logistic regression model constructed revealed that in the mammalian class, most of the species of Carnivores, Artiodactyls, Perissodactyls, Pholidota, and Primates had high probability of viral entry. However, among the primates, African Elephant had low probability of viral entry. Among rodents, hamsters were highly probable for viral entry with rats and mice having a medium to low probability. Rabbits have a high probability of viral entry. In Birds, ducks have a very low probability, while chickens seemed to have medium probability and turkey showed the highest probability of viral entry. ConclusionsMost of the species considered in this study showed high probability of viral entry. This study would prompt us to closely follow certain species of animals for determining pathogenic insult by SARS-CoV-2 and for determining their ability to act as a carrier and/or disseminator.

microbiology↗

bioRxiv2019

Genetic Mapping Of Morpho-Physiological Traits Involved During Reproductive Stage Drought Tolerance In Rice

Reproductive stage drought stress is an important factor for yield reduction in rice. Genetic mapping of drought responsive QTLs will help to develop cultivars suitable for drought prone environments through marker-assisted breeding. QTLs linked to morpho-physiological traits under drought stress were mapped by evaluating 190 F7 recombinant inbred lines (RIL). Significant variations were observed for eleven morpho-physiological traits involved during the stress. Bulked segregant analysis (BSA) strategy was adopted for genotyping the RIL population. A total of 401 SSR primers were tested for parental polymorphism of which 77 were polymorphic. Inclusive composite interval mapping detected a total of five consistent QTLs controlling leaf rolling (qLR9.1), leaf drying (qLD9.1), harvest index (qHI9.1), spikelet fertility (qSF9.1) and relative water content (qRWC9.1) under reproductive stage drought stress. Another two non-allelic QTLs controlling leaf rolling (qLR8.1) and leaf drying (qLD12.1) were linked in a single year. QTL controlling leaf rolling, qLR8.1 was validated in this mapping population and useful in marker-assisted breeding (MAB) programs. Out of these five consistent QTLs, four (qLR9.1, qLD9.1, qHI9.1 and qRWC9.1) were detected to be novel QTLs and useful for MAB for reproductive stage drought tolerance in rice.

genetics↗