ArticleNAR genomics and bioinformatics2023
Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA flexibility.
Article in NAR genomics and bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 8 citations in OpenAlex.
- Searching for sequence features that control DNA cyclizability.PNAS nexus · 2026Article
- cgNA+min: computation of sequence-dependent dsDNA energy-minimizing minicircles.Nucleic acids research · 2026Article
- DNAcycP2: improved estimation of intrinsic DNA cyclizability through data augmentation.Nucleic acids research · 2025Article
- Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics.bioRxiv : the preprint server for biology · 2024Article
- Depletion of CpG dinucleotides in bacterial genomes may represent an adaptation to high temperatures.NAR genomics and bioinformatics · 2024Article
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Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mechanical properties of DNA have been implied to influence many of its biological functions. Recently, a new high-throughput method, called loop-seq, which allows measuring the intrinsic bendability of DNA fragments, has been developed. Using loop-seq data, we created a deep learning model to explore the biological significance of local DNA flexibility in a range of different species from different kingdoms. Consistently, we observed a characteristic and largely dinucleotide-composition-driven change of local flexibility near transcription start sites. In the presence of a TATA-box, a pronounced peak of high flexibility can be observed. Furthermore, depending on the transcription factor investigated, flanking-sequence-dependent DNA flexibility was identified as a potential factor influencing DNA binding. Compared to randomized genomic sequences, depending on species and taxa, actual genomic sequences were observed both with increased and lowered flexibility. Furthermore, in
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Registered trials
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