Biology subjects

Tolokh, I. S.

Publications and source records attributed to Tolokh, I. S..

4 recordsLinked to original sources

bioRxiv2026

Reversing aging-like 3D genome disorganization in a Drosophila interphase model

Recent experimental evidence suggests that aging may arise from the progressive deterioration of the epigenetic landscape, while reversing the trend can result in cell and tissue rejuvenation. A mechanistic understanding of how restoration of a key component of this landscape - the 3D structure of the genome - can be accomplished is lacking. Here we investigate lamina-dependent disruption and recovery of the 3D architecture of the Drosophila melanogaster genome at TAD resolution ([~] 100 kb), using a model of the entire nucleus; weakening of chromatin-lamina interactions mimics an aging-associated loss of chromatin organization. We characterize this loss using the Shannon entropy of appropriately normalized Hi-C contact matrices. Our main finding is that lamina-depletion-induced increases in Hi-C map disorder, deterioration of chromosome territories, and cell-to-cell conformational heterogeneity are largely reversible when WT-like LAD-nuclear-envelope interactions are restored. The original and recovered conformational states of chromatin are nearly indistinguishable by bulk Hi-C contact matrix; the corresponding Pearson correlation coefficient is 0.999902. The direct experimentally testable prediction is that restoration of functional LAD-lamina interactions will promote recovery of young/WT-like 3D chromatin architecture after lamina-dependent architectural disruption.

genomics↗

bioRxiv2025

Quantifying Conformational Heterogeneity of 3D Genome Organization in Fruit Fly

The three-dimensional (3D) organization of interphase chromatin in eukaryotes is complex; details of the corresponding genome structures vary stochastically from cell to cell. Here, we propose a metric to quantify the cell-to-cell heterogeneity of the 3D chromatin conformations in ensembles of single cells: Conformational Heterogeneity (C.H.) is defined as the standard deviation of the ensemble distribution of the per cell average Euclidean inter-loci distances [<]Rs[>], for a given genomic separation s between the loci. We have used the metric to examine and quantify in detail the cell-to-cell heterogeneity of conformations of the interphase X chromosome in fruit fly generated via three distinctly different modeling approaches, which take experimental Hi-C data as input. Two of the approaches use bulk Hi-C and lamina-DamID data, while the third relies on single-cell Hi-C maps. An algorithm is proposed to facilitate comparison of C.H. of models constructed at different resolutions, and to examine the behavior of conformational heterogeneity with increasing model resolution. Higher resolution models show a greater C.H., in general. The impact of the model resolution is strongest near the genomic distance s corresponding to the resolution limit of the model, and diminishes for larger genomic distances: extrapolating the resolution from approximately 14 kb to 2 kb has little effect on the C.H. beyond [~]100 kb. All chromatin models examined in this work show a very similar trend of monotonically increasing structural heterogeneity with s, up to the genomic TAD size; beyond that, significant differences arise, with the model based on single-cell Hi-C showing nearly opposite trend compared to the two models that use bulk Hi-C data. We attribute these major differences to relatively subtle differences in the modeling approaches, which we discuss. Based on the analysis, we propose to explore the possibility of inclusion of bulk Hi-C data into training of chromatin models that are based on necessarily limited single-cell Hi-C data. Within our computational approach, depletion of nuclear lamins leads to increased structural heterogeneity at nearly all genomic separations, with the potential implication that cell functions that depend on chromatin structure might be more variable within lamins depleted nuclei compared to the wild type.

genomics↗

bioRxiv2022

The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level.

Multiple studies have demonstrated a negative correlation between gene expression and the positioning of genes at the nuclear envelope (NE) lined by nuclear lamina. In this paper, we ask whether there is a causal, systematic relationship between the expression level of the groups of genes in topologically associating domains (TADs) of Drosophila nuclei and the probabilities of TADs to be found at the NE. To investigate the nature of this possible relationship, we combine a coarse-grained dynamic model of the entire Drosophila nucleus with genome-wide gene expression data; we analyze the TAD averaged transcription levels of genes against the probabilities of individual TADs to be near the NE in the control and lamins-depleted nuclei. Our findings demonstrate that, within the statistical error margin, the stochastic positioning of Drosophila melanogaster TADs at the NE does not, by itself, systematically affects the mean level of gene expression in these TADs, while the expected negative correlation is confirmed. The correlation is weak and disappears completely for TADs not containing lamina-associated domains (LADs) or TADs containing LADs, considered separately. Verifiable hypotheses of the underlying mechanism for the presence of correlation without causality are discussed.

cell biology↗

bioRxiv2022

Strong interactions between highly-dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin

BackgroundInteractions among topologically associating domains (TADs), and between the nuclear envelope (NE) and lamina-associated domains (LADs) are expected to shape various aspects of 3D chromatin structure and dynamics; however, relevant genome-wide experiments that may provide statistically significant conclusions remain difficult. ResultsWe have developed a coarse-grained dynamical model of the Drosophila melanogaster nuclei at TAD resolution that explicitly accounts for four distinct epigenetic classes of TADs and LAD-NE interactions. The model is parameterized to reproduce the experimental Hi-C map of the wild type (WT) nuclei; it describes time evolution of the chromatin over the G1 phase of the interphase. Best agreement with the experiment is achieved when the simulations include an ensemble of nuclei, corresponding to the experimentally observed set of several possible mutual arrangements of chromosomal arms. The model is validated against multiple structural features of chromatin from several different experiments not used in model development, including those that describe changes in chromatin induced by lamin depletion. Predicted positioning of all LADs at the NE is highly dynamic - the same LAD can attach, detach and move far away from the NE multiple times during interphase. The probabilities of LADs to be in contact with the NE vary by an order of magnitude, despite all having the same affinity to the NE in the model. These probabilities are mostly determined by a highly variable local linear density of LADs along the genome which also has a strong effect on the predicted radial positioning of individual TADs. Higher probability of a TAD to be near NE is largely determined by a higher linear density of LADs surrounding this TAD. The distribution of LADs along the chromosome chains plays a notable role in maintaining a non-random average global structure of chromatin. Relatively high affinity of LADs to the NE in the WT nuclei substantially reduces sensitivity of the global radial chromatin distribution to variations in the strength of TAD-TAD interactions compared to the lamin depleted nuclei, where a 0.5 kT increase of cross-type TAD-TAD interactions doubles the chromatin density in the central nucleus region. ConclusionsA dynamical model of the entire fruit fly genome makes multiple genome-wide predictions of biological interest. The distribution of LADs along the chromatin chains affects their probabilities to be in contact with the NE and radial positioning of highly mobile TADs, playing a notable role in creating a non-random average global structure of the chromatin. We conjecture that an important role of attractive LAD-NE interactions is to stabilize global chromatin structure against inevitable cell-to-cell variations in TAD-TAD interactions.

molecular biology↗