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 transc...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-03-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/3/755 |
| _version_ | 1797611514516996096 |
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| author | Aaron Sievers Liane Sauer Marc Bisch Jan Sprengel Michael Hausmann Georg Hildenbrand |
| author_facet | Aaron Sievers Liane Sauer Marc Bisch Jan Sprengel Michael Hausmann Georg Hildenbrand |
| author_sort | Aaron Sievers |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-11T06:28:47Z |
| format | Article |
| id | doaj.art-1e530d1a89e240f182c3cd02a54299d2 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T06:28:47Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-1e530d1a89e240f182c3cd02a54299d22023-11-17T11:18:59ZengMDPI AGGenes2073-44252023-03-0114375510.3390/genes14030755Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in EukaryotesAaron Sievers0Liane Sauer1Marc Bisch2Jan Sprengel3Michael Hausmann4Georg Hildenbrand5Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, GermanyKirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, GermanyKirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, GermanyKirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, GermanyKirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, GermanyKirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, GermanyDinucleotides 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.https://www.mdpi.com/2073-4425/14/3/755DNAdinucleotides<i>k</i>-merstructural DNA properties3D conformationsequence analysis |
| spellingShingle | Aaron Sievers Liane Sauer Marc Bisch Jan Sprengel Michael Hausmann Georg Hildenbrand Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes Genes DNA dinucleotides <i>k</i>-mer structural DNA properties 3D conformation sequence analysis |
| title | Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes |
| title_full | Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes |
| title_fullStr | Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes |
| title_full_unstemmed | Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes |
| title_short | Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes |
| title_sort | moderation of structural dna properties by coupled dinucleotide contents in eukaryotes |
| topic | DNA dinucleotides <i>k</i>-mer structural DNA properties 3D conformation sequence analysis |
| url | https://www.mdpi.com/2073-4425/14/3/755 |
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