Size and functional state distribution of chromatin loop domains and its reorganization upon cell activation: Hi-C data analysis
DOI:
https://doi.org/10.15587/2519-8025.2018.143734Keywords:
chromatin, loop domains, chromatin compartments, Hi-C method, cell activation, bioinformaticsAbstract
Chromatin structure at high levels of its organization, which remains not to be completely understood, attracts much attention because it is the basis of regulation of functional processes in nuclei of eukaryotic cells. An important aspect of this organization is the existence of relatively autonomic structural elements, the chromatin loop domains. Hi-C is one of the most effective methods to study the three-dimensional structure of chromatin. The bioinformatic databases contain much Hi-C data that have not been examined completely. In particular, a detailed analysis of the loop sizes and regularities of their location in defined chromatin regions (transcriptionally active or inactive) has not been performed, it remains to be seen how the loop density and sizes change, if there is any change, depending on the functional activity of chromatin regions.
The aim of the study was to figure out the peculiarities of the size and functional state distribution of the chromatin loop domains in cells with different functional activity.
Materials and methods: bioinformatic analysis of the Hi-C data deposited in databases of open access.
Results: the size distributions of the chromatin loop domains in cells of different types, the distribution of the loop domains among different chromatin compartments in lymphoblastoid GM12878 cells and the size distributions within these compartments have been obtained, the changes in the loop size distribution under mouse lymphocyte activation have been analyzed.
Conclusions: the contour length of the loop domains is distributed exponentially, the distribution parameters are cell-specific, the majority of the loops are located in euchromatin regions, and the cell activation is accompanied by an increase in both the number of loops and their contour length
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Copyright (c) 2018 Katerina Afanasieva, Andrei Sivolob
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