Biology subjects

Venu, V.

Publications and source records attributed to Venu, V..

7 recordsLinked to original sources

bioRxiv2026

Resolving in vitro heterogeneity of host functional responses to HCoV-229E via single-cell analyses

Understanding host-pathogen interactions at the molecular level is essential to elucidating the mechanisms that govern immunity and pathogenesis. While diverse responses to viral infection have been documented, it remains unclear if this variability arises from the complex host milieu or represents an intrinsic property of the infection itself. To investigate this, we performed single-cell (sc) RNA sequencing analysis of infected MRC-5 fibroblast cells with human coronavirus 229E (HCoV-229E), which revealed pronounced variation in viral load across time points and biological replicates. While viral sequences were higher at 24 hours post-infection (hpi), more host genes were differentially expressed at 48 hpi, indicating dynamic responses during infection progression. Cells with higher viral load upregulated expression of unfolded protein response genes and NF-{kappa}B regulators, and downregulated expression of fibroblast identity and cell cycle genes, reflecting a shift toward a stress-adaptive, antiviral state. Network analyses identified NF-{kappa}B signaling as a central regulatory axis, with negative regulators overexpressed in high-viral-load clusters. Additionally, ATAC-seq analysis showed that regions of increased chromatin accessibility were enriched for NF-{kappa}B subunits, further supporting its role in transcriptional control. These findings demonstrate that even within ostensibly uniform cell cultures, viral infection induces distinct heterogeneous transcriptional and regulatory responses.

microbiology↗

bioRxiv2024

Epigenomic manipulation reveals the relationship between locus specific chromatin dynamics and gene expression

Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states such as cancer. Therapies focused on epigenetic modulation alter gene expression to correct dysfunction, though the mechanisms and perpetuation of these states is unknown. Here, we use integrated epigenomics and three-dimensional chromatin structure-function analyses after acute histone deacetylase inhibitor cancer drug treatment (suberoylanilide hydroxamic acid in lung cancer cells). Treatment induced substantial (13%) genomic rearrangement that rebounds despite persistent gene expression changes and spreading of acetylation. The chromatin functional landscape (accessibility, active transcription modification, and gene expression) is controlled and locus-specific, while chromatin contacts are globally altered resulting in a moderate weakening of topologically associating domains. Chromatin states are more dynamic at transcriptionally active loci while genes with reduced expression are epigenetically stable suggesting chromatin architectural turnover and nucleosome remodeling is locus-specific and underlies the bidirectional expression changes. Thus, local 3D chromatin and genome structural dynamics is integral for loci regulation in response to epigenomic perturbation. The partial persistence of these altered features may have larger implications for efficacy of epigenetic drugs in amelioration of disease states.

cancer biology↗

bioRxiv2024

SLUR(M)-py: A SLURM Powered Pythonic Pipeline for Parallel Processing of 3D (Epi)genomic Profiles

Epigenomics has become multi-faceted, with researchers exploring chromatin structure, nucleosome states, and epigenetic modifications, producing large, complex multi-omic data sets. Given this shift, there is de-mand for bioinformatics that leverage high performance computing (HPC) and parallelization to quickly process data. As such, we developed SLUR(M)-py: a pythonic computational platform that leverages the Simple Linux Utility for Resource Management system (SLURM) to process sequencing data. SLUR(M)-py is multi-omic and automates calls to SLURM for processing paired-end sequences from chromatin charac-terization experiments, including whole-genome, ChIP-seq, ATAC-seq, and Hi-C, thereby eliminating the need for multiple analytics pipelines. To demonstrate SLUR(M)-pys utility, we employ ATAC-seq and Hi-C data from viral infection experiments and the ENCODE project, and illustrate its processing speed and completeness, which outpaces current HPC pipelines. We explore the effect of dropping duplicate se-quenced reads in ATAC-seq, demonstrate how SLUR(M)-py can be used for quality control, and how to detect artifacts in Hi-C from viral infection experiments. Finally, we show how features in SLUR(M)-py, like inter-chromosomal analysis, can be used to explore the dynamics of chromosomal contacts in mammalian cells. This multi-omic, system agnostic platform eases the computational burden for researchers and quickly produces accurate, reliable data analytics for the epigenomics community.

bioinformatics↗

bioRxiv2023

Vaccinia virus infection induces concurrent alterations in host chromatin architecture, accessibility, and gene expression

Genomic DNA folds into complex configurations that produce particular local and global structures thought to profoundly impact genome function. To understand the dynamic nature of this relationship, we investigated the extent of host chromatin structural and functional changes in response to a viral agent. We performed comprehensive assessments of host architecture (Hi-C), accessibility (ATAC-seq), and gene expression (RNA-seq) in a paired manner in response to attenuated vaccinia (smallpox) virus. Over time, infection significantly increased long-range intra-chromosomal interactions and decreased chromatin accessibility. Fine-scale accessibility changes were independent of broad-scale chromatin compartment exchange, which increased (up to 12% of the genome) over time, underscoring potential independent mechanisms for global and local chromatin reorganization. The majority of differentially expressed genes, including those downregulated in immune responses, had concurrent alterations in local accessibility and loop domain restructuring. Increased B compartmentalization, intra-chromosomal interactions, and decreased inter-chromosomal interactions and chromatin accessibility together indicate that infection converts the host genome into a more condensed state with nearly equal bidirectional differential gene expression. These changes in host chromatin features may have implications for developing efficacious anti-viral countermeasures. Overall, our empirical data provides evidence of orchestrated concurrent alterations in chromatin architecture, accessibility, and gene expression in response to infection, further reinforcing the notion of coordinated structure-function dynamics of the genome.

genomics↗

bioRxiv2023

Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish

Despite deep evolutionary conservation, recombination varies greatly across the genome, among individuals, sexes, and populations and can be a major evolutionary force in the wild. Yet this variation in recombination and its impact on adaptively diverging populations is not well understood. To elucidate the nature and potential consequences of recombination rate variation, we characterized fine-scale recombination landscapes by combining pedigrees, functional genomics and field fitness measurements in an adaptively divergent pair of marine and freshwater threespine stickleback populations from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic location of almost 50,000 crossovers and built recombination maps for 36 marine, freshwater, and hybrid individuals at 3.8 kilobase resolution. Using these maps, we quantified the factors driving variation in recombination rate: we find strong heterochiasmy between sexes (68% of the variation) but also differences among ecotypes (21.8%). Hybrids show evidence of significant recombination suppression, both in overall map length and in individual loci. We further tested and found reduced recombination rates both within single marine-freshwater adaptive loci and between loci on the same chromosome, suggestive of selection on linked cassettes . We tested theory supporting the evolution of linked selection using temporal sampling along a natural hybrid zone, and found that recombinants with shuffled alleles across loci show traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers whose mechanisms are disrupted in hybrids, may have an important role to play in the maintenance of differences among adaptively diverging populations.

evolutionary biology↗

bioRxiv2023

Improved Quality Metrics for Association and Reproducibility in Chromatin Accessibility Data Using Mutual Information

BackgroundCorrelation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when comparing values between replicated sequencing experiments that probe chromatin accessibility, such as assays for transposase-accessible chromatin via sequencing (ATAC-seq). Such data can possess several regions across the human genome with little to no sequencing depth and are thus non-normal with a large portion of zero values. Despite distributed use in the epigenomics field, few studies have evaluated and benchmarked how correlation and association statistics behave across ATAC-seq experiments with known differences or the effects of removing specific outliers from the data. Here, we developed a computational simulation of ATAC-seq data to elucidate the behavior of correlation statistics and to compare their accuracy under set conditions of reproducibility. ResultsUsing these simulations, we monitored the behavior of several correlation statistics, including the Pearsons R and Spearmans{rho} coefficients as well as Kendalls{tau} and Top-Down correlation. We also test the behavior of association measures, including the coefficient of determination R2, Kendalls W, and normalized mutual information. Our experiments reveal an insensitivity of most statistics, including Spearmans{rho} , Kendalls{tau} , and Kendalls W, to increasing differences between simulated ATAC-seq replicates. The removal of co-zeros (regions lacking mapped sequenced reads) between simulated experiments greatly improves the estimates of correlation and association. After removing co-zeros, the R2 coefficient and normalized mutual information display the best performance, having a closer one-to-one relationship with the known portion of shared, enhanced loci between simulated replicates. When comparing values between experimental ATAC-seq data using a random forest model, mutual information best predicts ATAC-seq replicate relationships. ConclusionsCollectively, this study demonstrates how measures of correlation and association can behave in epigenomics experiments. We provide improved strategies for quantifying relationships in these increasingly prevalent and important chromatin accessibility assays.

bioinformatics↗

bioRxiv2018

Genome-wide recombination map construction from single individuals using linked-read sequencing

Meiotic recombination is a major molecular mechanism generating genomic diversity. Recombination rates vary across the genome, often involving localized crossover \"hotspots\" and \"coldspots\". Studying the molecular basis and mechanism underlying this variation within and among individuals has been challenging due to the high cost and effort required to construct individualized genome-wide maps of recombination crossovers. In this study we introduce a new method to detect recombination crossovers across the genome from sperm DNA using Illumina sequencing of linked-read libraries produced using 10X Genomics technology. We leverage the long range information provided by the linked short reads to phase and assign haplotype states to each DNA molecule. When applied to DNA from gametes of a diploid organism, the majority of linked-read molecules can be used to faithfully reconstruct an individuals two haplotypes present at each location in the genome. A valuable rare fraction of molecules that span meiotic crossovers between the two chromosome haplotypes can then be isolated from the broader population of nonrecombinant molecules. Our pipeline, called ReMIX, allows us to characterize the genomic location and intensity of meiotic crossovers in a single individual and faithfully detects previously described recombination hotspots discovered by studies using mapping panels in mice. With a median crossover resolution of the mouse and stickleback being 15kb and 23kb respectively, ReMIX provides a powerful, high-throughput, low-cost approach to quantify recombination variation across the genome opening up numerous opportunities to study recombination variation with high genomic resolution in multiple individuals. ReMIX source code is available at at https://github.com/adreau/ReMIX.

genomics↗