Biology subjects

Sethuraman, S.

Publications and source records attributed to Sethuraman, S..

4 recordsLinked to original sources

bioRxiv2026

Non-canonical histone H3.3 and its chaperones HIRA and DAXX participate in the regulation of KSHV latency

Kaposis sarcoma-associated herpesvirus (KSHV), also named HHV-8, is the etiological agent of Kaposi sarcoma (KS), Primary effusion lymphoma (PEL), and Multicentric Castlemans disease. After de novo infection, KSHV genomes rapidly circularize and acquire a chromatin state that favors latency. During latency, the KSHV episome is decorated with distinct epigenetic marks that segregate the viral genome into transcriptionally active and repressed domains, enabling persistent silencing of lytic genes while retaining the capacity for reactivation. Transcription activity of chromatin is regulated at multiple levels, including the incorporation of histone variants such as H3.3, by a specific set of histone chaperones such as HIRA and DAXX. The interaction between LANA and these interphase active chaperones suggests that H3.3 deposition is a critical driver of early chromatinization and the long-term stability of KSHV latency. We detected rapid H3.3 deposition on KSHV episomes and on episomes within long-term infected cells. Moreover, we demonstrated that genetically disrupting the host H3.3 chaperone HIRA pathway by CRISPR/Cas9-mediated knockout impacted the regulation of LANA and maintenance of viral latency that was not altered in DAXX knockout cells. Collectively, these results support a role for HIRA-mediated H3.3 deposition in the regulation of KSHV latency.

molecular biology↗

bioRxiv2025

Deep learning-driven morphology analysis enables label-free classification of therapeutic agent- naive versus resistant cancer cells

Therapeutic drug treatments of solid tumors are often undermined by various resistance mechanisms. Identification of drug-resistance phenotypes at the single cell level is challenging because conventional molecular methods are cell-destructive, labor-intensive, and cost-prohibitive. To overcome these challenges, we developed an orthogonal approach to drug-resistance phenotyping, through the use of deep-learning-driven morphology analysis of single, high resolution cell images. Specifically, we trained deep learning-based drug resistance classifiers using cell images from 5 different cell lines that were rendered resistant to 5 different therapeutic agents, using a foundation model framework. With high accuracy, the classifier correctly predicted naive or resistance phenotypes across all cancer types and across all the therapeutic agent types (chemotherapeutic, targeted) tested. These results showed that morphology can capture complex phenotype information in the context of drug treatment. To demonstrate the potential clinical utility of the drug resistance classifier, it was applied to a dissociated tumor biopsy and the resulting phenotype predictions were in close concordance with scRNASeq analysis of the biopsy. Our study highlights the potential of deep-learning-driven morphology analysis to provide complex phenotype information, and ultimately shape oncology drug treatment strategies at the patient-level in a clinical context.

cancer biology↗

bioRxiv2021

Invivo and systematic analysis of random multigenic deletions associated with human diseases during epithelial morphogenesis using Drosophila

Random loss of multigenic loci on chromosomes, a crucial drive for evolution, occurs frequently in all living organisms. Analysis of such chromosomal disruption and understanding the consequences of their impact on the growth and development of multicellular organisms is challenging. In this report, we have addressed this issue using invivo mosaic analysis of deficiency lines in Drosophila. Genes on fly deficiency lines were compared with human orthologs for their implications in disease development during cytoskeletal processes and epithelial morphogenesis. The cytoskeletal phenotypes from the fly has been utilized to predict the function of human orthologs. In addition, as these Drosophila deficiency lines are equivalent to human microdeletions, based on the clonal behaviour and phenotypes generated, a systematic analysis has been carried out to establish the critical loci that correspond to Microdeletion Syndromes and Mendelian Disorders in humans. Further we have drawn the synteny that exists between these chromosomes and have identified critical region corresponding to defects. A few potential candidates that might have an implication in epithelial morphogenesis are also identified.

genetics↗

bioRxiv2020

DNA methylation directs nucleosome positioning in RNA-mediated transcriptional silencing

Repressive chromatin modifications are instrumental in regulation of gene expression and transposon silencing. In Arabidopsis thaliana, transcriptional silencing is performed by the RNA-directed DNA methylation (RdDM) pathway. In this process, two specialized RNA polymerases, Pol IV and Pol V, produce non-coding RNAs, which recruit several RNA-binding proteins and lead to the establishment of repressive chromatin marks. An important feature of chromatin is nucleosome positioning, which has also been implicated in RdDM. We show that RdDM affects nucleosomes via the SWI/SNF chromatin remodeling complex. This leads to the establishment of nucleosomes on methylated regions, which counteracts the general depletion of DNA methylation on nucleosomal regions. Nucleosome placement by RdDM has no detectable effects on the pattern of DNA methylation. Instead, DNA methylation by RdDM and other pathways affects nucleosome positioning. We propose a model where DNA methylation serves as one of the determinants of nucleosome positioning.

plant biology↗