Biology subjects

Vasudevan, M.

Publications and source records attributed to Vasudevan, M..

8 recordsLinked to original sources

bioRxiv2025

T13F2.2 of C. elegans is Critical for Chromatin Organization, Autophagy, and Longevity

Intricately modulated by a spectrum of proteins, Chromatin structure governs gene expression and cellular homeostasis. In Caenorhabditis elegans, critical components like the TATA-binding protein tbp-1 play pivotal roles in orchestrating chromatin dynamics. While the function of many of the interacting partners of tbp-1 is well-understood, our study brings into focus a lesser-known entity, T13F2.2, an unexplored tbp-1 interacting protein and a putative RNA polymerase II transcriptional coactivator. Employing reverse genetics, we found that RNAi-induced depletion of T13F2.2 resulted in pronounced disruptions to nuclear architecture, evidenced by nuclear staining and transmission electron microscopy. Accompanying these structural anomalies, we observed increased autophagy, pointing to cellular stress and a hyperacetylation of the core histones, suggesting potential chromatin decompaction. Notably, multifaceted functional alterations, upon the partial knockdown of the T13F2.2, culminated in a substantial reduction in the worms lifespan. Intriguingly, interventions such as administering ROS scavengers and autophagy modulators offered a reprieve from this life-shortening effect. Transcriptomic analysis upon T13F2.2 knockdown revealed upregulation of genes related to autophagy and chromatin remodelling, alongside downregulation of genes involved in longevity pathways and oxidative stress response. This study, thus, not only puts forward the functional implication of an uncharacterized gene in C. elegans biology, but also further emphasizes the role of chromatin organization in aging at the organismal level.

genetics↗

bioRxiv2024

GENOMIC PROFILING OF SARS-COV-2 STRAINS CIRCULATING IN SOUTH EASTERN REGION OF INDIA DURING THREE WAVES OF PANDEMIC

Continuous bio-surveillance of SARS-CoV-2 is an ongoing task at local, national and global levels since the pandemic onset for understanding genetic evolution and vaccine efficacy. Present study was designed to track the emergence of new variants along the duration of three peaks of infection in the city of Puducherry, India. A total of 128 samples were subjected to Illumina deep RNA sequencing. The results showed predominance of uncommon, delta and omicron variants in first, second and third waves respectively. The most common pangolin lineage was B.1.560 and B.1.617.2. The study observed a total of 3133 common and 11 new mutations. The most common is in the Spike_D614G. A new set of mutations was observed in key viral factors such as NS16 that are implicated to be involved in immune evasion. This may have impact on enhanced disease virulence, vaccine efficiency and possible tolerance to current antivirals. This warrants further in vitro studies to understand the significance of the mutations. While the results presented would also augment the ongoing research on evolutionary and the genetic epidemiology of SARS-CoV-2, it also emphasizes the need for continuous genetic monitoring to predict the forthcoming threats due to the emergence of new or existing variants.

molecular biology↗

bioRxiv2024

Epigenetic Modulation to perturb the SYNGAP1 Intellectual Disability (ID) that ameliorates synaptic and behavioural deficits

Sporadic heterozygous mutations in SYNGAP1 affects social and emotional behaviour that are often observed in intellectual disability (ID) and autism spectrum disorder (ASD). Although neurophysiological deficits have been extensively studied, the epigenetic landscape of SYNGAP1 mutation-mediated intellectual disability is unexplored. Here, we have surprisingly found that the p300/CBP specific acetylation marks of histones are significantly repressed in the adolescent hippocampus of Syngap1+/- mouse. To establish the causal relationship of Syngap1+/- phenotype and the altered histone acetylation signature we have treated 2-4 months old Syngap1+/- mouse with glucose-derived carbon nanosphere (CSP) conjugated potent small molecule activator (TTK21) of p300/CBP lysine acetyltransferase (CSP-TTK21). The enhancement of the p300/CBP specific acetylation marks of histones by CSP-TTK21 restored deficits in spine density, synaptic function, and social preferences of Syngap1+/- mouse that is very closely comparable to wild type littermates. The hippocampal RNA-Seq analysis of the treated mice revealed that the expression of many critical genes related to the ID/ASD reversed due to the treatment of the specific small molecule activator. This study could be the first demonstration of the reversal of autistic behaviour and neural wiring upon the modulation of altered epigenetic modification (s).

neuroscience↗

bioRxiv2023

ACSL4 activity drives TNBC metastasis by positively regulating Histone H3 Acetylation mediated SNAIL expression

Triple-Negative Breast Cancer (TNBC) has profound unmet medical need globally for its devastating clinical outcome associated with rapid metastasis and lack of targeted therapies. Recently, lipid metabolic reprogramming has emerged as a major driver of breast cancer metastasis. Here, we unveil a strong association between the heightened expression of fatty acid metabolic enzyme, acyl-CoA synthetase 4 (ACSL4) and TNBC, which is primarily attributed by the selective absence of progesterone receptor (PR). Loss of ACSL4 function, either through genetic ablation or pharmacological inhibition significantly reduces metastatic potential of TNBC. Global transcriptome analysis reveals that ACSL4 activity markedly influences the gene expression pattern associated with TNBC migration. Mechanistically, ACSL4 alters fatty acid oxidation (FAO) and cellular acetyl-CoA levels, leading to the hyper-acetylation of particularly H3K27Ac and H3K9Ac marks resulting in overexpression of SNAIL during the course of TNBC metastatic spread to lymph node and lungs. Further, human TNBC metastasis exhibits positive correlation between ACSL4 and SNAIL expression. Altogether, our findings provide new molecular insights regarding the intricate interplay between metabolic alterations and epigenetic modifications, intertwined to orchestrate TNBC metastasis and posit a rational understanding for the development of ACSL4 inhibitors as a targeted therapy against TNBC.

cancer biology↗

bioRxiv2022

Differential structural organization and gene expression regulatory networks of lamin A Ig fold domain mutants of muscular dystrophy.

In metazoan cells, lamins form a proteinaceous meshwork as a major structural component of the nucleus and also play a role in regulating essential cellular processes. Lamins, along with their interactors, act as determinants for chromatin organization throughout the nucleus. The major dominant missense mutations responsible for autosomal dominant forms of muscular dystrophies reside in the Ig fold domain of lamin A. However, how lamin A contributes to the distribution of heterochromatin and balances euchromatin, and how it relocates epigenetic marks to shape chromatin states, remains poorly defined, making it difficult to draw conclusions about the prognosis of lamin A-mediated muscular dystrophies.In the first part of this report, we identified the in-vitro organization of full-length lamin A proteins due to two well-documented Ig LMNA mutations, R453W and W514R, through biophysical and electron microscopy observations. We further demonstrated that both lamin A/C mutant cells predominantly expressed nucleoplasmic aggregates with reduced amounts at the nuclear envelope. Labeling specific markers of epigenetics, such as H3K9me3, H3K27me3, H3K36me3, and HP1, allowed correlation of lamin A mutations with epigenetic mechanisms. Immunofluorescence and biochemical analyses indicated transcriptional upregulation. In addition to manipulating epigenetic mechanisms, our proteomic studies traced diverse expressions of transcription regulators, RNA synthesis and processing proteins, protein translation components, and posttranslational modifications. These data suggest severe perturbations in targeting other proteins to the nucleus.Our study also predicts specific structural configurations of lamin A determined by its interacting partners patterns. SignificanceO_LIThis study investigates the effects of two severe mutations in the LMNA gene associated with muscular dystrophies: R453W and W514R. C_LIO_LIThis research aims to provide new insights into the structural environment of full-length lamin A protein due to single-point mutations. C_LIO_LIOur study employs proteomics to map expression levels of regulators involved in epigenetic states, RNA synthesis and processing, and protein synthesis and processing. C_LIO_LIIt assesses potential effects on binding affinity and transcription, as well as alterations in heterochromatin protein distribution and RNA polymerase II functionality due to mutations affecting lamin A. C_LIO_LIA systematic investigation of lamin A interactors is conducted to explore their associations with other proteins. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=67 SRC="FIGDIR/small/493956v2_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@10ac33dorg.highwire.dtl.DTLVardef@197fa20org.highwire.dtl.DTLVardef@a679daorg.highwire.dtl.DTLVardef@18a03a7_HPS_FORMAT_FIGEXP M_FIG Figure: Schematic diagram representing the results. Mutations in lamin A protein evicts the nucleosome from nuclear periphery and consequently promotes aberrant gene expression. C_FIG

biochemistry↗

bioRxiv2022

Interconnection between molecular regulators in LMNA related muscular dystrophy

Nuclear lamina is composed of different A-type and B-type lamin proteins and acts as major regulator of DNA replication, transcription, heterochromatin-euchromatin machinery. The majority of mutations in A type lamin are associated with some forms of muscular dystrophies,that majorly distinguishable by a common clinical feature : progressive skeletal muscle wasting. This speculates impaired skeletal muscle differentiation during development and after injury with the influence of myriad of signalling pathways. The molecular mechanism behind phenotypes of lamin A associated muscular dystrophies are still elusive . Here, we used genome wide expression analysis platform during the differentiation of murine C2C12 skeletal muscle cells to investigate the factors have been attributed to the disease. We compared the expression levels of the components of pathways that indicates important role of skeletal muscle as well as identified gene regulatory networks at two different time points of muscle differentiation in wild type and mutant cells. We also report significant perturbations in the expression and activation of Wnt signalling pathway in mutant cells among 40 dysregulated signalling pathways , presenting pronounced regulation of normal downstream myogenic signalling . Finally, with this largest data sets we evaluate in depth characterization of molecular effectors for myogenic differentiation, which could allow greater insight into development of therapeutic strategies for the remission of patients with LMNA linked muscle - related pathologies.

cell biology↗

bioRxiv2022

Evaluation of lamin A/C mechanotransduction under different surface topography in LMNA related muscular dystrophy.

Most of the single point mutations of the LMNA gene are associated with distinct muscular dystrophies, marked by heterogenous phenotypes but primarily the loss and symmetric weakness of skeletal muscle tissue. The molecular mechanism and phenotype-genotype relationships in these muscular dystrophies are poorly understood. An effort has been here to delineating the adaptation of mechanical inputs into biological response by mutant cells of lamin A associated muscular dystrophy. In this study we implement engineered smooth and pattern surfaces of particular young modulus to mimic muscle physiological range. Using fluorescence and atomic force microscopy we present distinct architecture of the actin filament along with abnormally distorted cell and nuclear shape in mutants, which showed a tendency to deviate from wild type cells. Topographic features of pattern surface antagonizes the binding of the cell with it. Correspondingly, from the analysis of genome wide expression data in wild type and mutant cells, we report differential expression of the gene products of the structural components of cell adhesion as well as LINC (linkers of nucleoskeleton and cytoskeleton) protein complexes. This study also reveals mis expressed downstream signaling processes in mutant cells, which could potentially lead to onset of the disease upon the application of engineered materials to substitute the role of conventional cues in instilling cellular behaviors in muscular dystrophies. Collectively, these data support the notion that lamin A is essential for proper cellular mechanotransduction from extracellular environment to the genome and impairment of the muscle cell differentiation in the pathogenic mechanism for lamin A associated muscular dystrophy.

cell biology↗

bioRxiv2021

EP300 (p300) mediated histone butyrylation is critical for adipogenesis

ObjectiveThe master epigenetic enzyme EP300 (p300) besides having lysine acetyltransferase activity can also catalyse other acylation modifications (propionylation, butyrylation, crotonylation etc.), the physiological implications of which are yet to be established fully. We hypothesized that p300 catalysed histone butyrylation may have a causal relationship with adipogenesis and the consequent obesity. MethodsHistone butyrylation pattern was investigated in 3T3L1 cells upon adipogenesis by immunoblotting and chromatin immunoprecipitation experiments. A small molecule modulator that could specifically inhibit p300 catalysed butyrylation without affecting its canonical acetyltransferase activity was screened from a series of compounds and then administered in differentiating 3T3L1 adipocytes as well as high fat diet-induced and genetically obese mice to validate the importance of butyrylation in adipogenesis. ResultsHistone butyrylation was increased upon adipogenesis both globally and locally in the promoters of pro-adipogenic genes along with an upregulation in the expression of acyl CoA generating enzyme Acss2, knockdown of which led to reduced butyrylation. Treatment of differentiating 3T3L1 cells with the p300 specific butyrylation inhibitor LTK-14A led to abrogation of adipogenesis with reduced expression of pro-adipogenic genes and inhibition of H4K5 butyrylation. LTK-14A administration could also attenuate weight gain in both mice models of obesity by preventing adipocyte hypertrophy via H4K5 butyrylation inhibition. ConclusionOur results indicate that p300 catalysed histone butyrylation may have a causal relationship with the process of adipogenesis. Site specific inhibition of butyrylation could lead to adipogenesis repression and hence this epigenetic modification could be targeted for obesity treatment. HighlightsO_LIHistone butyrylation has been established as a new epigenetic signature in the context of adipogenesis. C_LIO_LITo the best of our knowledge, this is the first report of a selective inhibitor of p300 catalysed histone acylation (butyrylation) without affecting its canonical acetyltransferase activity. C_LIO_LISpecific inhibition of H4K5 butyrylation could be a possible mechanism for inhibiting adipogenesis and hepatic steatosis leading to better control of obesity. C_LIO_LILTK-14A class of molecule could be developed as anti-obesity therapeutics. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/454641v3_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1f29b35org.highwire.dtl.DTLVardef@abc5fcorg.highwire.dtl.DTLVardef@1534388org.highwire.dtl.DTLVardef@176d706_HPS_FORMAT_FIGEXP M_FIG Proposed model for the role of p300-mediated histone butyrylation in adipogenesis: In pre-adipocytes, there exists a basal level of histone acetylation while butyrylation is present to a much lesser extent owing to low stoichiometric levels of butyryl CoA. Induction of adipogenesis causes a simultaneous upregulation of histone acetylation and butyrylation marks leading to increased rate of adipogenesis and concomitant transcriptional activation of pro-adipogeneic genes. Onset of obesity in mice, either due to excess energy intake through high fat diet consumption or increased de novo synthesis of fatty acids due to leptin receptor gene mutation leading to hyperphagic behavior, is accompanied by adipocyte hyperplasia and hypertrophy. Both the organs of adipose tissue and liver were found to have enhanced levels of H4K5 butyrylation during obesity. LTK-14A, a butyrylation specific inhibitor could efficiently prevent the processes of adipogenesis and adipocyte hypertrophy due to inhibition of H4K5 butyrylation in these organs. Thus the compound could attenuate weight gain by selective inhibition of butyrylation without affecting acetylation, thereby highlighting the importance of histone butyrylation in adipogenesis and obesity. C_FIG

molecular biology↗