Afanasyev, A. Y. | bioRxiv Science

bioRxiv2022

Stretching of long double-stranded DNA and RNA described by the same model.

We propose a bead-spring model that accurately reproduces a variety of experimental force-extension curves of long double-stranded DNA and RNA, including torsionally constrained and unconstrained DNA, and negatively supercoiled DNA. A key feature of the model is a specific non-convex energy function of the spring. We provide an algorithm for obtaining five required parameters of the model from experimental force-extension curves. In the plateau region of the force-extension curves, our molecular dynamics simulations show that the polymer separates into a mix of weakly and strongly stretched states without forming macroscopically distinct phases.

biophysics↗

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↗