Biology subjects

De, T.

Publications and source records attributed to De, T..

11 recordsLinked to original sources

bioRxiv2025

FeSBCP Analogue from Cyanobacteria: Insights from in vitro and in silico Studies

The blue light responsive Cryptochrome/Photolyase Family harbours two important photoactivatable proteins - cryptochromes and photolyases. While cryptochromes are essentially photoreceptors with diverse biological activities including circadian rhythm, photolyases repair UV damaged cyclobutane pyrimidine dimers (CPD) or (6-4) pyrimidine-pyrimidone photoadducts. Both cryptochromes and photolyases share a common Photolyase Homology Region (PHR) where they harbour a light harvesting antenna chromophore and redox-active flavin di-nucleotide (FAD). Even though photolyases do not possess an extension in the C-terminal region unlike cryptochromes, a recent discovery of FeS cluster containing bacterial cryptochrome-photolyase proteins (FeSBCPs) present an interesting retreat from the conventional photolyase architecture. They possess an additional modular redox center, [4Fe4S] iron-sulfur cluster connected by conserved cysteine residues. Herein, we characterize a cyanobacterial FeSBCP from Cyanobium sp. using tools from bioinformatics, biochemistry and biophysics. Sequence analysis reveals substitution in the well-conserved aromatic residues, meant for electron transfer. In silico modeling and docking supported by electrophoretic mobility shift assay as well as spectroscopic measurements do suggest efficient binding and repair of CyPhrB to damaged single/double-stranded substrates containing 6-4 photolesion. Considering FeS clusters established roles in DNA binding/repair activities, we speculate the role of FeS clusters in FeSBCPs and existence of FeS-FAD-DNA triangle towards efficient electron transfer.

biochemistry↗

bioRxiv2025

Segmental copy number amplifications are stable in the absence of selection

Copy number variants (CNVs) are DNA duplications and deletions that cause genetic variation, underlying rapid adaptive evolution. CNVs often confer selective advantages, but can also incur fitness costs. Evolution of Saccharomyces cerevisiae in nutrient-limited chemostats recurrently selects for amplifications of nutrient transporter genes. However, their fate upon return to a non-selective environment remains unknown. To investigate CNV fitness and stability upon removing the original selection pressure, we studied 15 CNV lineages (11 segmental, 4 whole-chromosomal amplifications) selected in nitrogen-limited chemostats. CNV stability was monitored using fluorescent reporters during propagation in nutrient-rich batch cultures for 110-220 generations. All aneuploid lineages showed rapid CNV loss and reversion to a single-copy genotype, whereas segmental amplifications were remarkably stable- one of 11 strains reverted. Pairwise fitness competitions in rich media revealed strong fitness defects associated solely with CNVs that reverted; reversion led to increased fitness. Using simulation-based inference to estimate reversion rates and fitness effects, we determined negative selection as the primary driver of CNV loss. Whole-genome sequencing revealed that reversion of aneuploids and a segmental amplification left no evidence of prior CNV existence, rendering revertant genomes indistinguishable from the single-copy ancestor. Detailed characterization of a partial revertant identified chromosomal translocation, suggesting that extant CNVs can undergo structural diversification. Our findings provide novel evidence that most segmental CNVs adapted to nitrogen limitation are stable upon removal of selection, but costly gene amplifications are readily reversible. Together, these highlight the importance of CNVs in both long-term genome evolution and rapid, reversible adaptation to transient selection.

evolutionary biology↗

bioRxiv2024

Combined analysis of somatic mutations and gene expression reveals nuclear speckles-associated enhanced stemness in gingivobuccal carcinoma under DNA damage response

Smokeless tobacco chewing habits in India lead to a high prevalence of Gingivobuccal oral squamous cell carcinoma (OSCC-GB). Cancer stem cells (CSCs) are a sub-population of cancer cells within a tumor with stem-like properties and are believed to contribute to tumor initiation, progression, increased resistance to drug therapy, and promote post-therapeutic cancer relapse. An RNA-seq data-based integrative analysis of somatic mutation and gene expression was performed to explore the role of CSCs in disease progression using the novel Indian-origin OSCC-GB cell line IIOC019 from a patient with tobacco-chewing habit. The identified DNA damage-related known mutational signature (ID1, SBS5) indicates the impact of smokeless tobacco-related carcinogens in the IIOC019 cell line. The differentially expressed somatic variants, functional impact predictions, and survival analysis reveal the role of DNA damage response (DDR)-related genes in OSCC-GB, with the SON gene as a significant player. The study suggests that the loss of function in a somatic variant of the SON gene is associated with enhanced stemness and increased risk of disease progression in OSCC-GB under DDR conditions. The newly identified CSC-associated somatic variants appear to promote cancer spread, local recurrence, and resistance to chemotherapy or radiotherapy, contributing to the high mortality rates among Indian OSCC-GB patients.

genomics↗

bioRxiv2024

PyPlaque: an Open-source Python Package for Phenotypic Analysis of Virus Plaque Assays

Virological plaque assays are the primary method for quantifying infectious particles in a suspension, achieved by incubating a serial dilution of the virus with a monolayer of indicator cells. Existing software tools for quantification of plaque assay images lack modularity, show measurements disagreements or are closed-source - a common hurdle in BioImage analysis. We introduce PyPlaque, an open-source Python package focusing on flexibility and modularity rather than a bulky graphic user interface. Unlike previous methods, an abstracted architecture using object-oriented programming allows accommodation of various experimental containers and specimen carriers as data structures while focusing on phenotype-specific information. Aligned with the logical flow of experimental design and desired quantifications, it delivers insights at multiple granularity levels, facilitating detailed analysis. We demonstrate how this approach allows to focus on alleviating the disagreement in measurements. Furthermore, similar design is generalisable to diverse datasets in various biological contexts that fit our structural paradigm.

bioinformatics↗

bioRxiv2024

DNA replication errors are a major source of adaptive gene amplification

Copy number variants (CNVs)--gains and losses of genomic sequences--are an important source of genetic variation underlying rapid adaptation and genome evolution. However, despite their central role in evolution little is known about the factors that contribute to the structure, size, formation rate, and fitness effects of adaptive CNVs. Local genomic sequences are likely to be an important determinant of these properties. Whereas it is known that point mutation rates vary with genomic location and local DNA sequence features, the role of genome architecture in the formation, selection, and the resulting evolutionary dynamics of CNVs is poorly understood. Previously, we have found that the GAP1 gene in Saccharomyces cerevisiae undergoes frequent and repeated amplification and selection under long-term experimental evolution in glutamine-limiting conditions. The GAP1 gene has a unique genomic architecture consisting of two flanking long terminal repeats (LTRs) and a proximate origin of DNA replication (autonomously replicating sequence, ARS), which are likely to promote rapid GAP1 CNV formation. To test the role of these genomic elements on CNV-mediated adaptive evolution, we performed experimental evolution in glutamine-limited chemostats using engineered strains lacking either the adjacent LTRs, ARS, or all elements. Using a CNV reporter system and neural network simulation-based inference (nnSBI) we quantified the formation rate and fitness effect of CNVs for each strain. We find that although GAP1 CNVs repeatedly form and sweep to high frequency in strains with modified genome architecture, removal of local DNA elements significantly impacts the rate and fitness effect of CNVs and the rate of adaptation. We performed genome sequence analysis to define the molecular mechanisms of CNV formation for 177 CNV lineages. We find that across all four strain backgrounds, between 26% and 80% of all GAP1 CNVs are mediated by Origin Dependent Inverted Repeat Amplification (ODIRA) which results from template switching between the leading and lagging strand during DNA synthesis. In the absence of the local ARS, a distal ARS can mediate CNV formation via ODIRA. In the absence of local LTRs, homologous recombination mechanisms still mediate gene amplification following de novo insertion of retrotransposon elements at the locus. Our study demonstrates the remarkable plasticity of the genome and reveals that template switching during DNA replication is a frequent source of adaptive CNVs.

evolutionary biology↗

bioRxiv2023

Post-transcriptional mechanisms modulate the consequences of adaptive copy number variation

Copy-number variants (CNVs) are an important class of recurrent variants that mediate adaptive evolution. While CNVs can increase the relative fitness of the organism, they can also incur a cost. We previously evolved populations of Saccharomyces cerevisiae over hundreds of generations in glutamine-limited (Gln-) chemostats and observed the recurrent evolution of CNVs at the GAP1 locus. To understand the role that expression plays in adaptation, both in relation to the adaptation of the organism to the selective condition, and as a consequence of the CNV, we measured the transcriptome, translatome, and proteome of 4 strains of evolved yeast, each with a unique CNV, and their ancestor in Gln-conditions. We find CNV-amplified genes correlate with higher RNA abundance; however, this effect is reduced at the level of the proteome, consistent with post-transcriptional dosage compensation. By normalizing each level of expression by the abundance of the preceding step we were able to identify widespread divergence in the efficiency of each step in the gene in the efficiency of each step in gene expression. Genes with significantly different translational efficiency were enriched for potential regulatory mechanisms including either upstream open reading frames, RNA binding sites for SSD1, or both. Genes with lower protein expression efficiency were enriched for genes encoding proteins in protein complexes. Taken together, our study reveals widespread changes in gene expression at multiple regulatory levels in lineages containing adaptive CNVs highlighting the diverse ways in which adaptive evolution shapes gene expression.

genomics↗

bioRxiv2022

Leverage drug perturbation to reveal genetic regulators of hepatic gene expression in African Americans

BackgroundExpression quantitative loci (eQTL) studies have paved the way in identifying genetic variation impacting gene expression levels. African Americans (AAs) are disproportionately underrepresented in eQTL studies, resulting in a lack of power to identify population-specific regulatory variations especially related to drug response. Specific drugs are known to affect the biosynthesis of drug metabolism enzymes as well as other genes. We used drug perturbation in cultured primary hepatocytes derived from AAs to determine the effect of drug treatment on eQTL mapping and to identify the drug response eQTLs (reQTLs) that show altered effect size following drug treatment. MethodsWhole-genome genotyping (Illumina MEGA array) and RNA-sequencing were performed on 60 primary hepatocyte cultures after treatment with 6 drugs (Rifampin, Phenytoin, Carbamazepine, Dexamethasone, Phenobarbital, and Omeprazole) and at baseline (no treatment). eQTLs were mapped by treatment and jointly using Meta Tissue. ResultsWe found varying transcriptional changes across different drug treatments and identified Nrf2 as a potential general transcriptional regulator. We jointly mapped eQTL with gene expression data for across all drug treatments and baseline which increased our power to detect eQTLs by 2.7-fold. We also identified 2,988 reQTLs (eQTLs with altered effect size after drug treatment), which were more likely to overlap transcription factor binding sites and uncovered a novel reQTL, rs61017966 that increases CYP3A5 gene expression, a major drug metabolizing enzyme responsible for both drug response and adverse events across several drug classes. ConclusionsOur results provide novel insights into the genetic regulation of gene expression in hepatocytes through drug perturbation and provide insight into SNPs that effect the livers ability to respond to transcription upregulation.

genomics↗

bioRxiv2021

The genetic origin and architecture of sex determination

Here, I demonstrate that sex determination and sexual dimorphism across tree of life are deeply related to polyamine biochemistry in cells, especially to the synteny of genes: [SAT1-NR0B1], [SAT2-SHBG] and DMRT1. This synteny was found to be most distinct in mammals. Further, the common protein domain of SAT1 and SAT2 - PF00583 was shown to be present in the genome of the last universal common ancestor (LUCA). Protein domain-domain interaction analysis of LUCAs genes suggests the possibility that LUCA had developed an immune defence against viruses. This domain-domain interaction analysis is the first scientific evidence indicating that viruses existed at least 3.5 billions years ago and probably co-existed with LUCA on early Hadean Earth.

genomics↗

bioRxiv2020

Signatures Of TSPAN8 Variants Associated With Human Metabolic Regulation And Diseases

Here, with the example of common copy number variation (CNV) in the TSPAN8 gene, we present an important piece of work in the field of CNV detection, CNV association with complex human traits such as 1H NMR metabolomic phenotypes and an example of functional characterization of CNVs among human induced pluripotent stem cells (HipSci). We report TSPAN8 exon 11 as a new locus associated with metabolomic regulation and show that its biology is associated with several metabolic diseases such as type 2 diabetes (T2D), obesity and cancer. Our results further demonstrate the power of multivariate association models over univariate methods and define new metabolomic signatures for several new genomic loci, which can act as a catalyst for new diagnostics and therapeutic approaches.

genomics↗

bioRxiv2020

Incorporation of DNA methylation into eQTL mapping in African Americans.

Epigenetics is a reversible molecular mechanism that plays a critical role in many developmental, adaptive, and disease processes. DNA methylation has been shown to regulate gene expression and the advent of high throughput technologies has made genome-wide DNA methylation analysis possible. We investigated the effect of DNA methylation in eQTL mapping (methylation-adjusted eQTLs), by incorporating DNA methylation as a SNP-based covariate in eQTL mapping in African American derived hepatocytes. We found that the addition of DNA methylation uncovered new eQTLs and eGenes. Previously discovered eQTLs were significantly altered by the addition of DNA methylation data suggesting that methylation may modulate the association of SNPs to gene expression. We found that methylation-adjusted eQTLs which were less significant compared to PC-adjusted eQTLs were enriched in lipoprotein measurements (FDR = 0.0040), immune system disorders (FDR = 0.0042), and liver enzyme measurements (FDR = 0.047), suggesting a role of DNA methylation in regulating the genetic basis of these phenotypes. Our methylation-adjusted eQTL analysis also uncovered novel SNP-gene pairs. For example, our study found the SNP, rs11546996, was associated to PNKP. In a previous GWAS, this SNP was associated with primary biliary cirrhosis although the causal gene was thought to be SPIB. Our methylation-adjusted method potentially adds new understanding to the genetic basis of complex diseases that disproportionally affect African Americans.

genomics↗

bioRxiv2018

Uncovering the role admixture in health disparity: characterization of hepatocyte gene expression and DNA methylation in African-Americans

BackgroundAfrican Americans (AAs) are an admixed population with portions of their genome derived from West Africans and Europeans. In AAs, the proportion of West African ancestry (WAA) can vary widely and may explain the genetic drivers of disease, specifically those that disproportionately affect this understudied population. To examine the relationship between the proportion of WAA and gene expression, we used high dimensional data obtained from AA primary hepatocytes, a tissue important in disease and drug response. MethodsRNA sequencing (Illumina HiSeq Platform) was conducted on 60 AA-derived primary hepatocytes, with methylation profiling (Illumina MethylationEPIC BeadChip) of 44 overlapping samples. WAA for each sample was calculated using fastSTRUCTURE and correlated to both gene expression and DNA methylation. The GTEx consortium (n = 15) was used for replication and a second cohort (n = 206) was using used for validation using differential gene expression between AAs and European-Americans. ResultsWe identified 131 genes associated with WAA (FDR< 0.1), of which 28 gene expression traits were replicated (FDR<0.1) and enriched in angiogenesis and inflammatory pathways (FDR<0.1). These 28 replicated gene expression traits represented 257 GWAS catalog phenotypes. Among the PharmGKB pharmacogenes, VDR, PTGIS, ALDH1A1, CYP2C19 and P2RY1 were associated with WAA (p < 0.05) with replication of CYP2C19 and VDR in GTEx. Association of DNA methylation with WAA identified 1037 differentially methylated regions (FDR<0.05), with hypomethylated genes enriched in drug response pathways. Overlapping of differentially methylated regions with the 131 significantly correlated gene expression traits identified 5 genes with concordant directions of effect: COL26A1, HIC1, MKNK2, RNF135, SNAI1 and TRIM39. ConclusionsWe conclude that WAA contributes to variability in hepatic gene expression and DNA methylation with identified genes indicative of diseases disproportionately affecting AAs. Specifically, WAA-associated genes were linked to previously identified loci in cardiovascular disease (PTGIS, PLAT), renal disease (APOL1) and drug response (CYP2C19).

genomics↗