Chromosome Territory Modeller and Viewer

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.

Brachypodium distachyon – A Useful Model in the Qualification of Mutagen-Induced Micronuclei Using Multicolor FISH

“…Although the mFISH approach that enabled the simultaneous application of four different probes is by itself quite novel in plant mutagenesis, it can be anticipated that the real potential of Brachypodium as a model in such studies using single-locus chromosomes specific BAC clones [49] and/or their sequence-ordered painting pools [50] will be developed in the near future. These BAC-FISH-based ‘chromosome barcoding’ and ‘chromosome painting’ approaches have proven to be effective in revealing the structure and evolution of Brachypodium karyotypes [51–53] and interphase nucleus organization [54, 55]. They are also very likely to provide a plethora of useful information about the exact mechanisms that govern micronuclei formation in plants after mutagenic treatment.…”

The arrangement of Brachypodium distachyon chromosomes in interphase nuclei

“…In this study, we present the results of 3-D FISH with pools of chromosome arm-specific bacterial artificial chromosome (BAC) clones in the root nuclei of B. distachyon with the aim of analysing the arrangement of homologous chromosomes during interphase. Additionally, in order to assess whether their distribution is random or is subject to some defined patterns, the experimental data were compared with the results of a computer simulation (ChroTeMo) that assumes a fully probabilistic distribution of interphase chromosomes ( Tkacz et al ., 2016 ).…”

Distance-Profile Chart: a Novel Visual Representation of Mutual Location of 3D Objects

“…When we started to work on chromosome territory (CT) [2] modeling algorithm and application for model visualization [3] we did not assume that it will result in further methodological and algorithmic problems (others that concerns only model itself). But, when finishing Chromosome Territory Modeler (ChroTeMo) and Chromosome Territory Viewer (ChroTeVi) [3] subsequent question appears: OK, so we have a probabilistic 3D model of chromosome territory for certain species.…”

“…But, when finishing Chromosome Territory Modeler (ChroTeMo) and Chromosome Territory Viewer (ChroTeVi) [3] subsequent question appears: OK, so we have a probabilistic 3D model of chromosome territory for certain species. Such a model can be visually analyzed and compared by the human to the photos from FISH microscopy using chromosome paintings method, but .…”

“…Data for this DPC charts was taken from Brachypodium Distachyon chromosome territory model, generated with ChroTeMo [3]. This certain DPC shows a mutual location of CTs of the other chromosome arms for the first arm of the fifth chromosome as an object of reference.…”