Biology subjects

Bhardwaj, R.

Publications and source records attributed to Bhardwaj, R..

9 recordsLinked to original sources

bioRxiv2026

The alpine Edelweiss genome reveals a recent allotetraploid origin and localized subgenome dominance

Few plants symbolize the European Alps as profoundly as Edelweiss (Leontopodium nivale subsp. alpinum), yet its evolutionary origin and genomic constitution has remained elusive. We present a haplotype-resolved, chromosome-scale assembly of an L. n. alpinum accession from the Central Alps. The 3.15-Gb genome resolved 48 chromosomes in four phased sets with balanced gene and repeat landscapes. Phylogenomics partitioned these sets into two progenitor-derived subgenomes, DE and FG, demonstrating an allotetraploid origin. Comparison with the diploid subspecies L. n. nivale from Southern European Mountains (Appennines) linked DE to this sampled southern lineage, whereas FG derives from another distinct, unresolved diploid progenitor. Chloroplast genomes placed the plastid split between central Alps and Apennine samples in the recent Pleistocene, approximately 20,000 years ago, and LTR insertion-age profiles revealed recent retrotransposon activity consistent with genome shock following allopolyploidization. Although the subgenomes are broadly balanced,large inversions and elevated divergence concentrate on three chromosome groups. On Chromosome 3, structural complexity coincides with FG hypermethylation and DE-biased expression, revealing localized subgenome dominance. Together, these results support previous studies that suggested a westward expansion from the Asian centre of Leontopodium diversity, followed by differentiation and hybridization of closely related European lineages. Our assembly positions Edelweiss as an alpine model for recent allotetraploidy and enables genomic studies of demography, selection and high-alpine adaptation.

evolutionary biology↗

bioRxiv2025

Feedback from the Nascent Chain Triggers Ribosomal Frameshifting and Transcript Decay

Though ribosomes have several features that help them maintain their reading frame, these safeguards can be bypassed by RNA structures that promote -1 programmed ribosomal frameshifting (-1PRF). We recently found that conformational transitions in the nascent polypeptide can enhance -1PRF, though its unclear whether this feedback plays a general role in translational recoding. Here we demonstrate that the translocation of nascent transmembrane domains is sufficient to induce -1PRF during the decoding of slippery heptamers. We identify thousands of motifs that potentially trigger -1PRF along with proteomic identifications of 33 predicted human frameshift products. We also identify thousands of splicing-dependent motifs and demonstrate that the splicing-mediated reconfiguration of transmembrane domains alters -1PRF. Finally, we show that most transcripts bearing these motifs are sensitive to the nonsense-mediated decay regulator UPF1, suggesting they modulate mRNA turnover. Our findings show that the misassembly of growing polypeptides can trigger -1PRF, premature termination, and transcript decay.

biochemistry↗

bioRxiv2025

Exosome Trafficking Is a Key Regulator of Adipocyte Thermogenesis

Activation of beige adipocytes enhances energy expenditure and promotes metabolic health, presenting a promising approach for combating obesity and diabetes. As part of this process, thermogenesis, fueled in part by uncoupled mitochondrial respiration, plays a central role in converting calories into thermal energy, thereby preventing their storage as fat. Here, we identify a role for exosome trafficking as an intrinsic regulator of beige adipocyte thermogenesis. Exosomes are small extracellular vesicles that mediate cell-cell and intracellular communication by transporting regulatory cargo, including microRNAs, proteins, and lipids. Using both human cells and mouse models, we show that thermogenic activation of beige adipocytes promotes the rapid release of exosomes enriched in microRNAs known to suppress thermogenic programs. Genetic or pharmacological blockade of exosome secretion attenuates thermogenesis, whereas enhancing exosome release amplifies thermogenic output. Mice deficient in the exosome secretion regulator Rab27a exhibit reduced energy expenditure in response to both cold exposure and {beta}3-adrenergic stimulation. These findings establish exosome trafficking as a key contributor to beige adipocyte thermogenic capacity, highlighting an intracellular mechanism that may be leveraged to enhance energy expenditure and treat obesity-related metabolic diseases. Significance StatementThermogenic adipocytes, including beige fat cells, help maintain energy balance by converting excess nutrients into heat, thereby reducing fat storage and supporting metabolic function. Although these cells are known to promote energy expenditure, the intracellular processes that enable their full thermogenic response are not well defined. Here, we show that exosome secretion is required for beige adipocytes to reach their full thermogenic potential. Blocking exosome release dampens this response, while boosting it amplifies thermogenic output. These findings point to exosome release as an essential part of thermogenic regulation and a potential target for improving metabolic health.

cell biology↗

bioRxiv2025

Context-Dependent Synergism and Antagonism between IGF2BP1/3 and METTL3/14 in m6A-mediated mRNA regulation

N-6 Methyl Adenosine (m6A) methylation is primarily found in the 3-UTRs of mRNAs, near the stop codon, and at consensus sequence RRACH. The methylation reaction is catalyzed by RNA methyltransferases METTL3 and METTL14, known as writers. Readers recognize the modified mRNA, which influences mRNA stability and translation. Insulin-like growth factor-2 binding proteins 1 and 3 (IGF2BP1 and IGF2BP3) are known m6A readers, promoting mRNA stabilization. Erasers like ALKBH5 and FTO remove m6A modifications. Dysregulation of m6A machinery has been implicated in cancer progression. We analyzed the expression patterns of writers, erasers, and readers (WERs) in multiple public datasets, including NCBI-GEO, TCGA, TARGET, and normal tissue expression data from GTEx. Our findings revealed widespread dysregulation of WERs across various cancers. To investigate whether IGF2BP1/3 and METTL3/14 function synergistically in mRNA stabilization, we identified direct mRNA targets using intersection analyses of IGF2BP1/3 eCLIP and METTL3/14 knockout (KO) datasets on Galaxy server. This analysis identified METTL14-dependent targets (KDM3B, DYNLL1, CNOT1, RPL29) and METTL3-dependent targets (SREBF2, HNF4A, GNA11), all bound by IGF2BP1/3. To validate these interactions, we cloned 3-UTRs of these targets downstream of luciferase reporter and assessed mRNA stability following IGF2BP1/3 and METTL3/14 overexpression. Luciferase activity increased for RPL29, DYNLL1, SREBF2, and CNOT1 upon co-expression, indicating IGF2BP1/3-mediated mRNA stabilization in an m6A-dependent manner. In contrast, KDM3B, HNF4A, and GNA11 exhibited reduced luciferase activity, suggesting destabilization. Our study provides novel evidence that m6A readers and writers exhibit synergistic and antagonistic interactions in a target-dependent manner, underscoring the complexity of m6A-mediated gene regulation in oncogenesis.

molecular biology↗

bioRxiv2025

In vivo base editing reduces liver cysts in autosomal dominant polycystic kidney disease

Autosomal dominant polycystic kidney disease (ADPKD) is the most prevalent genetic kidney disorder, affecting over 10 million individuals worldwide. Cystic expansion typically progresses to kidney failure and also involves the liver with limited treatment options. Pathogenic variants in PKD1 or PKD2 account for 85-90% of cases. Genetic re-expression of Pkd1 or Pkd2 has been shown to partially reverse key characteristics of the disease phenotype in mice. Despite advancements in the understanding of the genetic basis, it remains unclear whether the correction of underlying pathogenic variants can effectively prevent, modify, or reverse the disease. Additionally, the feasibility of extrinsically delivered genome editing as a treatment option for ADPKD remains largely unexplored. In this study, we employed CRISPR base editing to correct a spectrum of representative pathogenic PKD1 variants selected from a patient cohort achieving precise and efficient editing in vitro. Correction of a representative murine missense variant (c.6646C>T (R2216W)) in primary renal epithelial cells successfully increased polycystin-1 expression and reduced levels of the endoplasmic reticulum stress marker sXBP1. In vivo, base editor delivery to the c.6646C>T (R2216W) knock-in mouse enabled correction of the pathogenic variant, resulting in a significant reduction in liver cysts. These findings provide the first evidence of ADPKD reversibility through genome editing, opening promising novel therapeutic perspectives for affected patients and their families.

genetics↗

bioRxiv2024

Biological activities and metabolic profile of endophytic Bacillus haynesii from Momordica charantia

Endophytes share a complex intimate relationship due to which they are capable of synthesizing metabolites that are either similar or derivative of host bioactive compounds. Such endophytes especially from medicinal plants can be prospected for commercial-scale production of the therapeutic compound. Thus, the study evaluates the antioxidant and anti-inflammatory potential of Momordica charantia fruit endophyte Bacillus haynesii R2MCFF61, and determines its metabolite profile through LC-Q-TOF-MS for the bioactive compounds produced. B. haynesii R2MCFF61 showed significant antioxidant and anti-inflammatory potential with increased DPPH scavenging activity in the standard compound and inhibition of protein denaturation respectively. The metabolic profile of this endophyte showed 23 compounds, mostly consisting of metabolites from lipid, phenylpropanoid and triterpenoid pathways. B. haynesii R2MCFF61 showed production of cucurbitane-triterpenoids namely Momordicoside K, 19-dimethoxycucurbita-5(10),6,22(E),24-tetraen-3{beta}-ol and 23(E)-7{beta}-methoxycucurbita-5,23,25-trien-3{beta}-ol. These compounds are mainly produced by M. charantia fruit and their production by its endophyte is reported for the first time. Thus, these results indicate the promising therapeutic potential of B. haynesii R2MCFF61 which can be utilized as a low-cost sustainable source of these bioactive compounds.

microbiology↗

bioRxiv2024

GenomicLinks: Deep learning predictions of 3Dchromatin loops in the maize genome

Gene regulation in eukaryotes is partly shaped by the 3D organization of chro]matin within the cell nucleus. Distal interactions between cis-regulatory elements and their target genes are widespread and many causal loci underlying heritable agricultural traits have been mapped to distal non-coding elements. The biology underlying chromatin loop formation in plants is poorly understood. Dissecting the sequence features that mediate distal interactions is an important step toward identifying putative molecular mechanisms. Here, we trained GenomicLinks, a deep learning model, to identify DNA sequence features predictive of 3D chromatin interactions in maize. We found that the presence of binding motifs of specific Transcription Factor classes, especially bHLH, are predictive of chromatin interaction specificities. Using an in silico mutagenesis approach we show the removal of these motifs from loop anchors leads to reduced interaction probabilities. We were able to validate these predictions with single-cell co-accessibility data from different maize genotypes that harbor natural substitutions in these TF binding motifs. GenomicLinks is currently implemented as an open-source web tool, which should facilitate its wider use in the plant research community.

genomics↗

bioRxiv2023

An associative transcriptomics study on rice bean (Vigna umbellata) provides new insights into genetic basis and candidate genes governing flowering, maturity and seed weight

Rice bean is an underrated legume with significant potential to support food and nutritional security worldwide, being a rich source of proteins, minerals, and essential fatty acids. Therefore, we considered three pivotal production traits of rice bean; flowering, maturity and seed weight, to identify associated candidate genes. One-hundred diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank were considered for phenotypic data collection and genotyping by transcriptome sequencing approach. Association analysis involving various GWAS models was conducted to identify significant marker-trait associations. The results revealed association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The annotation of associated transcripts unraveled the functional genes related to the considered traits. Among the significant candidate genes identified, HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A were found associated with flowering. Further, associations of WRKY1 and DEAD-box-RH27 with seed weight, PIF3 and pentatricopeptide-repeat-containing-gene with maturity & seed weight and aldo-keto-reductase with flowering & maturity have been revealed. The present investigation provides insights into the genetic mechanisms governing economically-essential traits like flowering, maturity and seed weight that can be potentially utilized for rice bean improvement. HighlightsThe present investigation is the first associative transcriptomics approach implemented on Vigna umbellata. Based on the marker-trait association analysis, candidate genes for flowering, maturity and seed weight traits are reported.

bioinformatics↗

bioRxiv2021

Dissecting gating mechanisms of Orai calcium channel paralogs using constitutively active Orai mutants that mimic STIM1-gated state

In humans, there are three paralogs of the Orai Ca2+ channel, which lie at the heart of the store-operated calcium entry (SOCE) machinery. While the STIM-mediated gating mechanism of Orai channels is still being actively investigated, several artificial and natural variants are known to cause constitutive activity of the human Orai1 channel. Surprisingly, little is known about the conservation of the gating mechanism among the different human Orai paralogs and orthologs in other species. In our work, we show that the mutation corresponding to the activating mutation H134A in transmembrane helix 2 (TM2) of human Orai1 also activates Orai2 and Orai3, likely via a similar mechanism. However, this cross-paralog conservation does not apply to the "ANSGA" nexus mutations in TM4 of human Orai1 which mimic the STIM1-activated state of the channel. Investigating the mechanistic background of these differences, we identified two positions, H171 and F246 in human Orai1, which directly control the channel activation triggered by the "ANSGA" mutations in Orai1. Our results shed new light on these important gating checkpoints and show that the gating mechanism of the Orai channels is affected by multiple factors that are not necessarily evolutionarily conserved, such as the TM4-TM3 coupling.

cell biology↗