Biology subjects

Basir, R.

Publications and source records attributed to Basir, R..

3 recordsLinked to original sources

bioRxiv2024

Polymer Model Integrates Super-Resolution Imaging and Epigenomic Sequencing to Elucidate the Role of Epigenetic Reactions in Shaping 4D Chromatin Organization

Chromatin, with its complex spatial and temporal organization, plays a crucial role in regulating gene expression. Recent advancements in super-resolution microscopy have revealed that nanoscale domains of heterochromatin (repressed segments) embedded within a euchromatin (active segments) background are fundamental units of 3D chromatin organization. In tissue-resident cells, the size of these heterochromatin domains varies with the microenvironment, particularly its stiffness, and chromatin organization is also influenced by pharmacological and epigenetic drugs. However, the mechanisms governing heterochromatin domain size under various conditions and their impact on gene expression remain unclear. To address this knowledge gap, we have developed a dynamic, next-generation sequencing informed chromatin copolymer model. Our model simulates the spatiotemporal evolution of chromatin, driven by passive diffusion and active epigenetic reactions, which interconvert euchromatin and heterochromatin. By integrating chromatin-chromatin interaction energetics and diffusion-reaction dynamics, we predict the formation of nanoscale heterochromatin-rich domains and establish a scaling relationship between their size and the modulation of epigenetic reaction rates. Additionally, our model predicts that epigenetic and chromatin compaction changes in response to changes in global reaction rates occur predominantly at domain boundaries. We validated these predictions via Hi-C contact map analysis and super-resolution imaging of hyperacetylated melanoma cells. Subsequent RNA-seq analysis suggested a pivotal role of these epigenetic shifts in influencing the metastatic potential of these cells. We further validated our mesoscale findings against chromatin rearrangement in hMSCs, which exhibit sensitivity of epigenetic reaction rates to changes in microenvironmental stiffness. Finally, we evaluated the effects of cycling of epigenetic reaction rates in silico, mimicking the cellular transition to different extracellular conditions, and back again. This finding reveals a cell-type invariant mechanism driven by domain boundaries, whereby chromatin organization guides epigenetic memory formation. Our findings show that chromatin reorganization in response to changes in epigenetic reaction rates resulting from alterations in the microenvironment, drug exposure and disease progression impacts both immediate cellular responses and long-term epigenetic memory.

biophysics↗

bioRxiv2024

Revealing the Biophysics of Lamina-Associated Domain Formation by Integrating Theoretical Modeling and High-Resolution Imaging

The interactions between chromatin and the nuclear lamina orchestrate cell type-specific gene activity by forming lamina-associated domains (LADs) which preserve cellular characteristics through gene repression. However, unlike the interactions between chromatin segments, the strength of chromatin-lamina interactions and their dependence on cellular environment are not well understood. Here, we develop a theory to predict the size and shape of peripheral heterochromatin domains by considering the energetics of chromatin-chromatin interactions, the affinity between chromatin and the nuclear lamina and the kinetics of methylation and acetylation9in human mesenchymal stem cells (hMSCs). Through the analysis of super-resolution images of peripheral heterochromatin domains using this theoretical framework, we determine the nuclear lamina-wide distribution of chromatin-lamina affinities. We find that the extracted affinity is highly spatially heterogeneous and shows a bimodal distribution, indicating regions along the lamina with strong chromatin binding and those exhibiting vanishing chromatin affinity interspersed with some regions exhibiting a relatively diminished chromatin interactions, in line with the presence of structures such as nuclear pores. Exploring the role of environmental cues on peripheral chromatin, we find that LAD thickness increases when hMSCs are cultured on a softer substrate, in correlation with contractility-dependent translocation of histone deacetylase 3 (HDAC3) from the cytosol to the nucleus. In soft microenvironments, chromatin becomes sequestered at the nuclear lamina, likely due to the interactions of HDAC3 with the chromatin anchoring protein LAP2{beta} ,increasing chromatin-lamina affinity, as well as elevated levels of the intranuclear histone methylation. Our findings are further corroborated by pharmacological interventions that inhibit contractility, as well as by manipulating methylation levels using epigenetic drugs. Notably, in the context of tendinosis, a chronic condition characterized by collagen degeneration, we observed a similar increase in the thickness of peripheral chromatin akin to that of cells cultured on soft substrates consistent with theoretical predictions. Our findings underscore the pivotal role of the microenvironment in shaping genome organization and highlight its relevance in pathological conditions.

biophysics↗

bioRxiv2020

Effects of Malaysian strains of Toxoplasma gondii on behaviours and their possible risk in schizophrenia-like rat model

Toxoplasma gondii (T. gondii) is a protozoan parasite that reside majorly in the brain of its intermediate host. T. gondii infected rodents shows some degree of behaviour deficits, while T. gondii infection in humans is associated with psychiatric problems such as schizophrenia. The present study aimed to evaluate the effects of Malaysian strains of T. gondii on rats. Forty five, four weeks old, male Wistar rats were used. The rats were assigned into five groups: two control groups (CG1 and CG2) and three experimental groups (EG1, EG2, EG3). CG1 rats received phosphate buffered saline (PBS), CG2 received MK-801 (as a model for schizophrenia), EG1, EG2, EG3 received orally 5 x 103 single T. gondii oocysts strain of type I, type II and type III respectively. After infection, all the five groups of rats were tested for T. gondii antibodies at two weeks post-infection (PI). Behavioural tests of exploratory activity (open field) and spatial learning and memory retention (Morris water maze) were performed on the ninth and tenth weeks PI followed by histological staining of rat brain. T. gondii IgM antibodies were detected in EG1, EG2 and EG3, but not in CG1 and CG2. The behaviour results demonstrated that rats from CG2, EG1, EG2 and EG3 had increased in their locomotor activities and memory deficits compared to control, while learning remain intact. Moreover, tissue cysts were found widely distributed exclusively in the whole brain of EG1, EG2 and EG3 without tropism. These findings taken together, implies that Malaysian strains of T. gondii are implicated in some causes of behaviour changes that are responsible for schizophrenia-like conditions if humans were infected.

animal behavior and cognition↗