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Choudhary, B.

Publications and source records attributed to Choudhary, B..

15 recordsLinked to original sources
bioRxiv2026

Spatiotemporal isoform profiling identifies a central activator of microexon splicing in C. elegans

Dynamic alternative splicing programs drive tissue specification and organismal development. Here, we present the most comprehensive, tissue-resolved alternative splicing dataset in Caenorhabditis elegans to date, spanning three major tissue types from early embryogenesis to adulthood. We uncovered broad developmental and tissue-regulated alternative splicing trends and identified putative RNA-binding proteins (RBPs) coordinating co-regulated splicing networks governing tissue identity. Among the network of regulated splice variants, we uncovered additional, unannotated microexons for further study in C. elegans. Through a forward genetic screen, we identified RBM-25, a U1 snRNP-associated regulatory protein, as a key regulator that preferentially enhances the inclusion of short exons and microexons alongside its binding partner PRP-40. Phenotypic profiling of rbm-25 mutants demonstrated significant defects in behviour, reproductive fitness, lifespan, and synaptic signalling, indicating a key role for RBM-25-regulated target transcripts in normal physiology and behaviour. Together, these findings expand our appreciation for spatiotemporal isoform diversity during animal development, and provide mechanistic insights into how microexon splicing is regulated.

molecular biology↗
bioRxiv2026

Endosulfan rewires PKA and GSK3β to disrupt primary cilia-dependent Hedgehog signalling

Primary cilium-dependent Hedgehog signalling is essential for embryonic development, tissue patterning, and organ homeostasis, and its disruption causes a spectrum of developmental disorders collectively termed ciliopathies. Whether environmental toxicants can chemically induce ciliopathy-like states by targeting this pathway, however, remains poorly understood. Here we show that endosulfan, a banned organochlorine pesticide epidemiologically linked to severe congenital and reproductive defects in exposed human populations, disrupts Hedgehog signalling by driving GLI transcription factor processing into repressor forms and suppressing target gene expression at both transcriptional and protein levels. Having excluded direct effects on core ciliary receptors and GLI-DNA binding, we identify the pathway kinases PKA and GSK3{beta} as direct targets of endosulfan: endosulfan increases PKA activity through allosteric fine-tuning, and -- in a pharmacologically rare finding -- acts as the first reported small-molecule activator of GSK3{beta}, shifting the kinase toward a catalytically active conformation. We further identify Cetn3 and Cep250 as novel GLI-regulated genes required for centriole cohesion, both of which are repressed upon endosulfan exposure, providing a mechanistic link to the reproductive defects reported in exposed populations and animal models. These findings identify endosulfan as a candidate chemical inducer of ciliopathy and reveal how an environmental toxicant can hijack core kinase signalling to disrupt Hedgehog-dependent development.

cell biology↗
bioRxiv2026

The Chromosome-Scale Genome of Phyllanthus niruri Reveals Candidate Genes and a Putative Biosynthetic Framework for Phyllanthin Formation.

Phyllanthus niruri (Phyllanthaceae) is a medicinally important herb known for producing phyllanthin, a bioactive dibenzylbutane lignan with reported hepatoprotective and antioxidant properties. However, the biosynthetic basis of phyllanthin production remains unresolved, largely due to the absence of a reference genome for the species. We report a Chromosome-Scale Assembly of P. niruri generated by integrating PacBio HiFi long reads and Illumina short reads, followed by reference-guided scaffolding against Phyllanthus cochinchinensis. The assembly has an L50 of 7 and 97.6% BUSCO completeness. Annotation predicted 19,254 protein-coding genes (91.1% functionally annotated), with phenylpropanoid biosynthesis emerging as the most enriched specialized-metabolism pathway in the genome. Using pathway-guided genome mining, structural similarity analysis, and comparative metabolic reconstruction, we propose a putative biosynthetic pathway for phyllanthin originating from the phenylpropanoid-lignan branch through secoisolariciresinol-like intermediates, followed by terminal O-methylation reactions. A total of 305 unique candidate genes associated with the proposed pathway were identified, including expanded families of dirigent proteins, peroxidases, secoisolariciresinol dehydrogenases, and O-methyltransferases. Comparative transcriptomic analyses across related Phyllanthus species further supported the proposed pathway through coordinated expression of lignan-associated genes and tissue-specific enrichment of O-methyltransferases. This work provides the first reference genome for P. niruri and a prioritized candidate gene set for functional characterization of phyllanthin biosynthesis.

genomics↗
bioRxiv2026

A consensus genome sequence for the social amoeba Dictyostelium giganteum

The life cycle of the Dictyostelid amoebae is unusual in that it alternates between a free-living solitary phase and an aggregative social phase. We used six previously collected Dictyostelium giganteum strains from distinct ecological niches in the Mudumalai Nature Reserve, India. From them, we generated short Illumina reads and assembled a consensus genome, comprising nuclear and mitochondrial genomes, representative of all six strains. The nuclear assembly has an AT content of 75.76%, accounting for 38.52 Mb, and resolves into five chromosome-scale scaffolds that are consistent with the published karyotype. Its N50 is 3.01 Mb and L50 is 5. The BUSCO analysis shows 3.9% fragmentation and 92.1% completeness. Genome assembly and completeness are also validated using [~]5,500 genes from a publicly available transcriptome dataset (PRJNA48443) derived from the post-aggregation stage. 13,251 predicted proteins are encoded by the genome, including ABC transporters, polyketide synthases, Ras/Rho GTPases, and expanded families of protein kinases. Comparative analysis demonstrates extensive conservation of syntenic blocks related to the dictyostelids D. discoideum and D. firmibasis as well as lineage-specific rearrangements. About 18% of the nuclear genome is made up of repetitive DNA, mostly in the form of simple repeats. Major transposable element classes, including piggyBac-like fragments, were found by homology searches. Long poly-asparagine/glutamine tracts are less common than in D. discoideum, but low-complexity sequences are common due to strong AT-driven codon bias. Comparative proteome-level orthology analysis across Dictyostelium species and Entamoeba identified a conserved Amoebozoan core together with a substantial Dictyostelium-specific gene repertoire. Domain-level comparisons further revealed widespread conservation of intracellular signalling and cytoskeletal modules shared with animals, whereas canonical metazoan extracellular adhesion domains were absent, highlighting the deep evolutionary roots of regulatory complexity underlying aggregative multicellularity.

genomics↗
bioRxiv2025

QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5' splice sites

During organogenesis, precise pre-mRNA splicing is essential to assemble tissue architecture. Many developmentally essential exons bear weak 5' splice sites (5'SS) yet are spliced with high precision, implying unknown yet active splicing fidelity mechanisms. By combining transcriptome and alternative splicing profiling with temporal eCLIP mapping of RNA interactions across development, we identify the RNA-binding protein QKI as an essential direct regulator of splicing fidelity in key cardiac transcripts. Although QKI is dispensable for cardiac specification, its loss disrupts sarcomere assembly despite intact expression of sarcomere mRNAs through exon skipping and nuclear retention of mis-spliced RNAs. QKI-dependent exons in essential cardiac genes have weak 5'SS and frequently show poor complementarity with U6 snRNA. We show that QKI directly interacts with U6 snRNA using an overlapping interface to its traditional intronic binding activity, securing U4/U6{middle dot}U5 tri-snRNP to ensure splicing fidelity. Thus, QKI exemplifies how context-aware RBPs enforce splicing fidelity at structurally vulnerable splice sites during organogenesis.

cell biology↗
bioRxiv2024

Conserved role for spliceosomal component PRPF40A in microexon splicing

Microexons (exons [≤]30 nts) are important features of neuronal transcriptomes, but pose mechanistic challenges to the splicing machinery. We previously showed that PRP-40, a component of the U1 spliceosome, is globally required for microexon splicing in C. elegans. Here we show that the homologous PRPF40A is also globally required for microexon splicing in mouse neuroblastoma cells. We find that PRPF40A co-regulates microexons along with SRRM4, a neuron-specific regulator of microexon splicing. The relationship between exon size and dependence on PRPF40A/SRRM4 is distinct, with SRRM4-dependence exhibiting a size threshold ([~]30 nts) and PRPF40A-dependence exhibiting a graded decrease as exon size increases. Finally, we show that PRPF40A knockdown causes an increase in productive splicing of its spliceosomal binding partner Luc7l by skipping of a small "poison exon." Similar homeostatic cross-regulation is often observed across paralogous RNA binding proteins. Here we find this concept likewise applies across evolutionarily unrelated but functionally and physically coupled spliceosomal components.

molecular biology↗
bioRxiv2024

The first assembled chromosome-level genome of an individual from Karnataka, India

We present the first chromosome-level assembled genome of an individual from Karnataka, India (KIn1), using de novo assembly of 12x coverage of PacBio HiFi reads generated in-house and 30x Hi-C data from the most ethnically related individual to KIn1 from Andhra Pradesh (HG04712), publicly available under International Genome Sample Resource (IGSR). We achieved an N50 of 137 Mb and an L50 of 9--very close to the maximum achievable N50 of 147 Mb and minimum achievable L50 of 8 respectively for human genomes. A comparison of the KIn1 assembly with assemblies of four other individual genomes from a Puerto Rican (PR1), Ashkenazi (Ash1), Hans Chinese (Hans1), and Northern European (T2T) reported to date from resources like IGSR and/or Genome-in-a-Bottle (GIBR) collections shows that the longest scaffolds from KIn1 cover 80-90% of the reference chromosomes and exhibit near collinearity. We find a unique inversion in the chromosome 7 euchromatic region and other major translocations in chromosomes 17 and 20 in KIn1. We also produced a chromosome-level assembly for another individual from Punjab, Lahore (HG03492), for use in our comparison. The analysis of variants among select IGSR individuals using the KIn1 assembly as a reference reveals that the Indian Telugu from the UK (ITU) population in IGSR is ethnically closest to KIn1, followed by the Sri Lankan Tamil from the UK (STU) as representatives of South Asian ancestry.

genomics↗
bioRxiv2024

SbPIP2 Mediated Improvements in Plant Resilience: Physiological and Molecular Insights into Abiotic Stress Response

Understanding the mechanisms behind plant resilience to abiotic stresses is essential for enhancing crop yield and sustainability. This study integrates findings from a comprehensive investigation into the function of the SbPIP2 gene, which encodes an aquaporin protein, in improving the abiotic stress tolerance of transgenic plants. Our integrated approach revealed that transgenic plants overexpressing SbPIP2 significantly reduce reactive oxygen species (ROS) accumulation and exhibit enhanced physiological attributes, including higher seed germination rates, improved growth, early flowering, and better seed setting under stress conditions. Notably, these plants also showed a quicker recovery and completion of their lifecycle post-stress treatment. The transcriptomic analysis provided a deeper understanding of the genetic modifications contributing to stress resilience, highlighting the involvement of genes associated with oxidative stress response, calcium and sugar signaling pathways, stomatal regulation, phytohormone biosynthesis, and flower development. Additionally, the study underscores the central role of abscisic acid (ABA) in mediating stress responses through hormonal regulation, with transgenic plants displaying increased ABA levels due to the upregulation of biosynthesis genes and downregulation of catabolism genes. This hormonal adjustment is critical for stomatal closure, reducing water loss, and enhancing tolerance to abiotic stresses. Our findings elucidate the complex genetic and molecular pathways that underpin abiotic stress tolerance in plants, offering valuable insights for future research aimed at improving crop resilience through genetic engineering, thereby addressing the challenges of climate change and environmental stressors.

plant biology↗
bioRxiv2022

A comprehensive study of mRNA and long noncoding RNAs in Indian Breast cancer patients using transcriptomics approach

BackgroundBreast cancer (BC) is one of the leading causes of cancer-associated death in women. Despite the progress in therapeutic regimen, resistance and recurrence of Breast cancer have impacted Overall Survival. Transcriptomic profiling of tumour samples has led to identifying subtype-specific differences, identifying biomarkers, and designing therapeutic strategies. Although there are multiple transcriptomic studies on breast cancer patients from different geographical regions, a comprehensive study on long noncoding RNA (lncRNA) and mRNA in Indian Breast cancer patients in multiple subtypes are very limited. This study aims to understand the subtype-specific alterations and mRNA-lncRNA gene sets. MethodWe have performed transcriptome analysis of 17 Indian breast cancer patients and matched normal belonging to 6 different subtypes, i.e., four patients in triple positive, three patients in estrogen receptor-positive (ER+ve), three patients in estrogen and progesterone receptor-positive (ER+ve, PR+ve), two patients in Human epidermal growth factor receptor (Her2+ve), three patients in triple-negative and one patient in ER+ve and Her2 +ve subtypes. Hierarchical clustering and principal component analysis were performed using R packages to derive gene sets. Univariate and multivariate Cox analyses were performed for survival analysis. ResultsmRNA and lncRNA expression profiles segregated Indian Breast cancer subtypes with minimum overlap. We have identified a 25mRNA-27 lncRNA gene set, which displayed proper segregation of the subtypes in our data. The same gene set also segregated premenopausal women samples in The Cancer Genome Atlas (TCGA) data. Pathway analysis of the differentially expressed genes revealed unique pathways for premenopausal and postmenopausal women. Kaplan-Meier survival analysis revealed menopausal status, grade of the tumour, and hormonal status displayed statistically significant effects (p < 0.05) on the risk of mortality due to breast cancer. Her2+ve patients showed low overall survival ConclusionThis is the first study describing subtype-specific mRNA and lncRNA gene expression in Indian Breast Cancer patients with unique pathway signatures for premenopausal and postmenopausal breast cancer patients. Additionally, our data identified an mRNA-lncRNA gene set that could segregate pre and postmenopausal women with Breast Cancer. Although the sample size is small, results from this study could be a foundation that could be validated further in a larger dataset to establish an mRNA-lncRNA signature specific to the Indian population which might, in turn, improve therapeutic decisions.

bioinformatics↗
bioRxiv2021

The genome trilogy of Anopheles stephensi, an urban malaria vector, reveals structure of a locus associated with adaptation to environmental heterogeneity

BackgroundAnopheles stephensi is the most menacing malaria vector to watch for in newly urbanizing parts of the world. The fitness is reported to be a direct consequence of the vector adapting to laying eggs in over-head water tanks with street-side water puddles polluted by oil and sewage. Large frequent inversions of malaria vectors are implicated in adaptation. ResultsWe report the assembly of a strain of An. stephensi of the type-form, collected from a construction site from Chennai (IndCh) in 2016. The genome completes the trilogy with respect to a 16 Mbp inversion (2Rb) in An. stephensi associated with adaptation to environmental heterogeneity. Comparative genome analysis revealed breakpoint structure and allowed extraction of 22,650 segregating SNPs for typing this inversion. Using whole genome sequencing of 82 individual mosquitoes, we conclude that one third of both wild and laboratory populations maintain heterozygous genotype of 2Rb. The large number of SNPs are tailored to assign inversion genotype directly from 1740 exonic SNPs 80% of which are expressed in various developmental stages. ConclusionsThe genome trilogy approach accelerates study of fine structure and typing of important inversions in malaria vectors putting the genome resources for the much understudied An. stephensi, on par with the extensively studied malaria vector, Anopheles gambiae. We argue that the IndCh genome is relevant for field translation work compared to those reported earlier by showing that individuals from diverse populations cluster with IndCh pointing to significant commerce between cities, perhaps, allowing for survival of the fittest strain.

genomics↗
bioRxiv2021

Unleashing a Novel Function of Endonuclease G in Mitochondrial Genome Instability

Having its own genome makes mitochondria a unique and semiautonomous organelle within cells. Mammalian mitochondrial DNA (mtDNA) is double-stranded closed circular molecule of about 16 kb coding 37 genes. Mutations, including deletions in the mitochondrial genome can culminate in different human diseases. Mapping of the deletion junctions suggests that the breakpoints are generally seen at hotspots. 9-bp deletion (8271-8281), seen in the intergenic region of cytochrome c oxidase II/tRNALys, is the most common mitochondrial deletion. While it is associated with several diseases like myopathy, dystonia, and hepatocellular carcinoma, it has also been used as an evolutionary marker. However, the mechanism responsible for its fragility is unclear. In the current study, we show that Endonuclease G, a mitochondrial nuclease responsible for nonspecific cleavage of nuclear DNA during apoptosis, can induce breaks at sequences associated with 9-bp deletion, when it is present on a plasmid or in the mitochondrial genome. Through a series of in vitro and intracellular studies, we show that Endonuclease G binds to G-quadruplex structures formed at the hotspot and induces DNA breaks. Besides, we reconstitute the whole process of 9-bp deletion using purified Endonuclease G to induce breaks in mtDNA, followed by mitochondrial extract-mediated DSB repair and establish that microhomology-mediated end joining is responsible for the generation of mtDNA deletion. Finally, we show that the whole process is regulated by different stress conditions, which may modulate release of Endonuclease G to the mitochondrial matrix. Therefore, we uncover a new role for Endonuclease G in generating deletions, which is dependent on the formation of G4 DNA within the mitochondrial genome. Thus, in this study we identify a novel property of Endonuclease G, besides its role in apoptosis, and the recently described elimination of paternal mitochondria during fertilization.

molecular biology↗
bioRxiv2020

Classification of grain amaranths using chromosome-level genome assembly of ramdana, A. hypochondriacus

In the age of genomics-based crop improvement, a high-quality genome of a local landrace adapted to the local environmental conditions is critically important. Grain amaranths produce highly nutritional grains with a multitude of desirable properties including C4 photosynthesis highly sought-after in other crops. For improving the agronomic traits of grain amaranth and for the transfer of desirable traits to dicot crops, a reference genome of a local landrace is necessary. Towards this end, our lab had initiated sequencing the genome of Amaranthus (A.) hypochondriacus (A.hyp_K_white) and had reported a draft genome in 2014. We selected this landrace because it is well adapted for cultivation in India during the last century and is currently a candidate for TILLING-based crop improvement. More recently, a high-quality chromosome-level assembly of A. hypochondriacus (PI558499, Plainsman) was reported. Here, we report a chromosome-level assembly of A.hyp_K_white (AhKP) using low-coverage PacBio reads, contigs from the reported draft genome of A.hyp_K_white, raw HiC data and reference genome of Plainsman. The placement of A.hyp_K_white on the phylogenetic tree of grain amaranths of known accessions clearly suggests that A.hyp_K_white is genetically distal from Plainsman and is most closely related to the accession PI619259 from Nepal (Ramdana). Furthermore, the classification of another accession, Suvarna, adapted to the local environment and selected for yield and other desirable traits, is clearly A. cruentus. A classification based on hundreds of thousands of SNPs validated taxonomy-based classification for a majority of the accessions providing the opportunity for reclassification of a few.

genomics↗
bioRxiv2020

A near-chromosome level genome assembly of Anopheles stephensi

Malaria remains a major healthcare risk to growing economies like India and a chromosome-level reference genome of Anopheles stephensi is critical for successful vector management and an understanding of vector evolution. We report a chromosome-level assembly of an Indian strain from draft genomes of two strains using a homology-based iterative approach. The resulting assembly with an L50 of 9 had long enough scaffolds for building 90% of the three chromosomes using physical markers. The sequencing of individuals reveals a genetic diversity ten times higher than what is reported. Based on the developmental transcriptome and orthology of the 54 olfactory receptors (ORs) to those of other Anopheles species, we identify olfactory receptors with the potential for host recognition in the genus Anopheles. A comparative analysis of the genomes suggests limited inter-chromosomal gene flow and chromosomal arm switching with a potential role in adaptive radiation within the genus Anopheles.

genomics↗
bioRxiv2019

Cyanobacteria is uniquely enriched in the roots of grain amaranths

Plants and microbes have coexisted for millions of years and some have evolved mechanisms to achieve symbiosis driving positive selection. The bartering of chemicals produced by soil microbes and plants favour enrichment of certain types of bacteria near the roots that offers selective advantage to the plant under a given environment. Grain amaranths display certain important agronomic characteristics like C4 dicot, high protein and high lysine grains, resistance to biotic and abiotic stress, which can be translated to other crops. Considering an unusual collection of desirable traits shown by grain amaranths, it is worth pondering if symbiosis with bacteria has played any role in these traits. The objective of this study is to identify bacterial root microflora unique to grain amaranths. Here, by comparing rhizospheric and endophytic composition of 16S rRNA from various sections of roots from selected species under major plant orders including the three varieties of grain amaranths, we report that Cyanobacteria are uniquely enriched by grain amaranths. The diversity in OTUs among the Cyanobacteria also significantly increased among samples from amaranth species compared to negative control. This finding is also validated using root transcriptome of Amaranthus hypochondriacus, where we observe relative increase in Cyanobacterial population between day 15 to day 30 compared to other abundant phylum during this period.

plant biology↗