ArticleNucleic acids research2022
DNAcycP: a deep learning tool for DNA cyclizability prediction.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 45 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
- Differential nucleosome organization in human interphase and metaphase chromosomes.Molecular systems biology · 2026Article
- Contributions of DNA mechanics and trans-regulation to nucleosome positioning in Schizosaccharomyces pombe and its role in co-transcriptional splicing.Epigenetics & chromatin · 2026Article
- Mlh1-Pms1 couples ATP-driven DNA compaction with nick-dependent endonuclease activation.Nucleic acids research · 2025Article
- Differential nucleosome organization in human interphase and metaphase chromosomes.bioRxiv : the preprint server for biology · 2025Article
- DNA bendability regulates transcription factor binding to nucleosomes.Nature structural & molecular biology · 2025Article
- CTCF binding landscape is shaped by the epigenetic state of the N-terminal nucleosome in relation to CTCF motif orientation.Nucleic acids research · 2025Article
- FACT weakens the nucleosomal barrier to transcription and preserves its integrity by forming a hexasome-like intermediate.Molecular cell · 2025Article
- Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes.iScience · 2025Article
- Article
- 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
- Interpretable deep residual network uncovers nucleosome positioning and associated features.Nucleic acids research · 2024Article
- A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization.Molecular systems biology · 2024Article
- Long extrachromosomal circular DNA identification by fusing sequence-derived features of physicochemical properties and nucleotide distribution patterns.Scientific reports · 2024Article
- Employing bimodal representations to predict DNA bendability within a self-supervised pre-trained framework.Nucleic acids research · 2024Article
- Time series-based hybrid ensemble learning model with multivariate multidimensional feature coding for DNA methylation prediction.BMC genomics · 2023Article
- Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA flexibility.NAR genomics and bioinformatics · 2023Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA mechanical properties play a critical role in every aspect of DNA-dependent biological processes. Recently a high throughput assay named loop-seq has been developed to quantify the intrinsic bendability of a massive number of DNA fragments simultaneously. Using the loop-seq data, we develop a software tool, DNAcycP, based on a deep-learning approach for intrinsic DNA cyclizability prediction. We demonstrate DNAcycP predicts intrinsic DNA cyclizability with high fidelity compared to the experimental data. Using an independent dataset from in vitro selection for enrichment of loopable sequences, we further verified the predicted cyclizability score, termed C-score, can well distinguish DNA fragments with different loopability. We applied DNAcycP to multiple species and compared the C-scores with available high-resolution chemical nucleosome maps. Our analyses showed that both yeast and mouse genomes share a conserved feature of high DNA bendability spanning nucleosome dyads. Additionally, we extended our analysis to transcription factor binding sites and surprisingly found that the cyclizability is substantially elevated at CTCF binding sites in the mouse genome. We further demonstrate this distinct mechanical property is conserved across mammalian species and is inherent to CTCF binding DNA motif.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.