Moderation of structural DNA properties by coupled dinucleotide contents in eukaryotes

• Verfasst von: Sievers, Aaron [VerfasserIn]
• Verfasst von: Sauer, Liane [VerfasserIn]
• Verfasst von: Bisch, Marc [VerfasserIn]
• Verfasst von: Sprengel, Jan [VerfasserIn]
• Verfasst von: Hausmann, Michael [VerfasserIn]
• Verfasst von: Hildenbrand, Georg Lars [VerfasserIn]
• Titel: Moderation of structural DNA properties by coupled dinucleotide contents in eukaryotes
• Verf.angabe: Aaron Sievers, Liane Sauer, Marc Bisch, Jan Sprengel, Michael Hausmann and Georg Hildenbrand
• E-Jahr: 2023
• Jahr: 20 March 2023
• Umfang: 18 S.
• Fussnoten: Gesehen am 20.04.2023
• Titel Quelle: Enthalten in: Genes
• Ort Quelle: Basel : MDPI, 2009
• Jahr Quelle: 2023
• Band/Heft Quelle: 14(2023), 3 vom: März, Artikel-ID 755, Seite 1-18
• ISSN Quelle: 2073-4425
• DOI: doi:10.3390/genes14030755
• Datenträger: Online-Ressource
• Sprache: eng
• Sach-SW: k-mer
• Sach-SW: 3D conformation
• Sach-SW: dinucleotides
• Sach-SW: DNA
• Sach-SW: sequence analysis
• Sach-SW: structural DNA properties
• K10plus-PPN: 1843259419

Abstract

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.