Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes

  • Dinucleotides are known as determinants for various structural and physiochemical properties of DNA and for binding affinities of proteins to DNA. These properties (e.g., stiffness) and bound proteins (e.g., transcription factors) are known to influence important biological functions, such as transcription regulation and 3D chromatin organization. Accordingly, the question arises of how the considerable variations in dinucleotide contents of eukaryotic chromosomes could still provide consistent DNA properties resulting in similar functions and 3D conformations. In this work, we investigate the hypothesis that coupled dinucleotide contents influence DNA properties in opposite directions to moderate each other’s influences. Analyzing all 2478 chromosomes of 155 eukaryotic species, considering bias from coding sequences and enhancers, we found sets of correlated and anti-correlated dinucleotide contents. Using computational models, we estimated changes of DNA properties resulting from this coupling. We found that especially pure A/T dinucleotides (AA, TT, AT, TA), known to influence histone positioning and AC/GT contents, are relevant moderators and that, e.g., the Roll property, which is known to influence histone affinity of DNA, is preferably moderated. We conclude that dinucleotide contents might indirectly influence transcription and chromatin 3D conformation, via regulation of histone occupancy and/or other mechanisms.

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Metadaten
Author:Aaron Sievers, Liane Sauer, Marc Bisch, Jan Sprengel, Michael HausmannORCiD, Georg HildenbrandORCiD
DOI:https://doi.org/https://doi.org/10.3390/genes14030755
ISSN:2073-4425
Parent Title (English):Genes
Publisher:MDPI AG
Document Type:Article
Language:English
Year of Completion:2023
Release Date:2024/11/14
GND Keyword:Genom
Volume:14
Issue:3
Article Number:755
Institutes:Fakultät Ingenieurwissenschaften und Informatik / Studiengänge / Medical Engineering and Data Science (Bachelor)
Research Focuses / Research Horizons:Intelligent Systems / Artifical Intelligence and Data Science
Materials / Material Testing & Sensor Technology
Reviewed:ja
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