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Home >Foods and Raw Materials > Archive > Volume 13, Issue 2, 2025 > Spatial genomic codes
ISSN 2308-4057 (Print),
ISSN 2310-9599 (Online)

Spatial genomic codes

Glazko Tatiana a
,
Kosovsky Gleb a
,
Glazko Valeriy a
Affiliation
a Scientific Research Institute of Fur-Bearing Animal Breeding and Rabbit Breeding named after V.A. Afanas`ev, Rodniki
Copyright ©Glazko et al. This is an open access article distributed under the terms of the Creative Commons Attribution 4.0. (http://creativecommons.org/licenses/by/4.0/), allowing third parties to copy and redistribute the material in any medium or format and to remix, transform, and build upon the material for any purpose, even commercially, provided the original work is properly cited and states its license.
Received 24 April, 2024 | Accepted in revised form 03 September, 2024 | Published 20 November, 2024
DOI: http://doi.org/10.21603/2308-4057-2025-2-653
Abstract
The increasing variability of phenotypic traits in agricultural animal species makes it necessary to search for reliable DNA markers. Due to the poor efficiency of using clustered single-nucleotide polymorphisms (SNP) and individual genomic elements, the hierarchy of gene regulatory networks has become a relevant research area. We summarized available information on different levels of epigenetic regulation, from the linear DNA sequence and its secondary and tertiary structures to the factors outside the cell nucleus, i.e., intercellular contacts and interactions with the extracellular matrix. We also discussed the features of genomic distribution and the role of topologically associated domains (TADs), and architectural protein CTCF in chromatin loop formation. CTCF mediates protein-protein interactions and interacts with various RNA variants. It also involved in epigenetic modifications of the DNA nucleotide sequence, a target of CTCF binding. Such targeted sites are located in transposable elements (TEs). As a result of the evolutionary conservation, they are also to be found in TAD, regardless of the fact that they are delivered by species-specific TEs. CTCF and its binding sites are known to affect the structure of the mitotic spindle. They also have a certain impact on cholesterol biosynthesis, which affects the plasma membrane and cell migration. CTCF indirectly participates in the variability of intercellular contacts and interactions with the extracellular matrix. In animals, CTCF and its binding targets are involved in all levels of gene regulatory networks that maintain or change genomic expression.
Keywords
G4 quadruplexes, DNA-RNA hybrids, CTCF, chromatin loops, topologically associated domains (TAD), extranuclear factors, neoplastic transformation
FUNDING
The study is supported by the Ministry of Science and Higher Education of the Russian Federation (state agreement No. 075-00503-24-01).
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Glazko TT, Kosovsky GYu, Glazko VI. Spatial genomic codes. Foods and Raw Materials. 2025;13(2):409–422. https://doi.org/10.21603/2308-4057-2025-2-653 
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