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

Abstract

Multiple studies have shown a correlation between gene expression and positioning of genes at nuclear envelope (NE) lined by nuclear lamina. Here, we ask whether there is a causal, systematic connection between the expression level of the groups of genes in topologically associating domains (TADs) of Drosophila nuclei and the probability of TADs to be found at the NE. To investigate the connection, we combine a coarse-grained dynamic model of the entire Drosophila nucleus with the genome-wide gene expression data for both the control and lamins depleted (LD) nuclei. We analyze the TAD averaged transcription levels of genes against the probabilities of individual TADs to be near the NE. Our findings suggest that, within statistical error margin, positioning of Drosophila TADs at the nuclear envelope does not, by itself, systematically affect the average gene expression in these TADs, while the expected negative correlation is confirmed. Verifiable hypotheses of the underlying mechanism for the presence of correlation without causality are discussed. We introduce a TAD length normalized metric for the average transcription activity of genes in a TAD: number of Reads mapped to all genes in a TAD Per Kilobase of TAD length per Million reads mapped to all TADs (RPKMT).

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

“…The dynamical model of the 3D chromatin organization in fruit fly proposed in this study offers a number of novel genome-wide insights, both biological and methodological, while also reinforcing robustness of some of the conclusions about chromatin organization previously made using models of mammalian nuclei. Combined with appropriate experimental data, our model can be used to make structurefunction predictions on genome-wide level [104].…”