Abstract
This paper presents ChroTeMo, a tool for chromosome territory modelling, accompanied by ChroTeVi–a chromosome territory visualisation software that uses the data obtained by ChroTeMo. These tools have been developed in order to complement the molecular cytogenetic research of interphase nucleus structure in a model grass Brachypodium distachyon. Although the modelling tool has been initially created for one particular species, it has universal application. The proposed version of ChroTeMo allows for generating a model of chromosome territory distribution in any given plant or animal species after setting the initial, species-specific parameters. ChroTeMo has been developed as a fully probabilistic modeller. Due to this feature, the comparison between the experimental data on the structure of a nucleus and the results obtained from ChroTeMo can indicate whether the distribution of chromosomes inside a nucleus is also fully probabilistic or is subjected to certain non-random patterns. The presented tools have been written in Python, so they are multiplatform, portable and easy to read. Moreover, if necessary they can be further developed by users writing their portions of code. The source code, documentation, and wiki, as well as the issue tracker and the list of related articles that use ChroTeMo and ChroTeVi, are accessible in a public repository at Github under GPL 3.0 license.
Highlights
Almost every living eukaryotic cell contains genetic material in the form of chromatin consisting of linear DNA molecules and DNA-associated proteins, enclosed inside the cell nucleus
In the case of third configuration set, in general, the computing times were less diversified than for the set 2, but two outliers appeared. These results show that the modeller is capable to simulate chromosome territories (CTs) distribution for different species in a reasonable amount of time and that the average time of a single simulation depends strongly on the input parameters for modelling a given species
The Chromosome Territory Modeller and Viewer have been created in order to simulate the chromosome decondensation processes after nucleus division and to analyse the distribution pattern of the resulting chromosome territories
Summary
Almost every living eukaryotic cell contains genetic material in the form of chromatin consisting of linear DNA molecules and DNA-associated proteins, enclosed inside the cell nucleus. Chromatin fibres condense into rod-like structures called chromosomes, which enables balanced and efficient segregation of genetic material into two daughter cells. During the period between two subsequent divisions, called interphase, chromosomes decondense and occupy distinct 3-D areas within the nucleus, known as chromosome territories (CTs) [1]. Chromosome territories can be experimentally identified using cytomolecular approach of in situ hybridisation with fluorescently labelled DNA probes (FISH) that enables specific discrimination and visualisation of individual chromosomes.
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