ArticleScientific reports2024
Z-DNA formation in promoters conserved between human and mouse are associated with increased transcription reinitiation rates.
Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Z-DNA-induced genomic instability in the human pangenome.Research square · 2026Article
- Nonconsensus flanking sequence of hundreds of base pairs around in vivo binding sites: statistical beacons for transcription factor scanning.Nucleic acids research · 2026Article
- Structural basis of B-to-Z DNA transition mediated by an anti-Z-DNA antibody.Nucleic acids research · 2026Article
- Non-B DNA structures and their contributions to genetic diversity, aging, and disease.Nucleic acids research · 2026Review
- Formation and biological implications of Z-DNA.Trends in genetics : TIG · 2026Review
- Alternative nucleic acid structures in microbial biology: regulatory functions and antimicrobial opportunities.Frontiers in cellular and infection microbiology · 2026Review
- Characterization of Z-DNA dynamics across the tree of life.bioRxiv : the preprint server for biology · 2025Article
- Control of Gene Expression by Proteins That Bind Many Alternative Nucleic Acid Structures Through the Same Domain.International journal of molecular sciences · 2025Article
- Z-DNA Hunter tool for straightforward detection of Z-DNA forming regions and a case study inNAR genomics and bioinformatics · 2025Article
- Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes.bioRxiv : the preprint server for biology · 2025Article
- The evolutionary entanglement of flipons with zinc fingers and retroelements has engendered a large family of Z-DNA and G-quadruplex binding proteins.Open biology · 2025Article
- Deep learning deciphers the related role of master regulators and G-quadruplexes in tissue specification.Scientific reports · 2025Article
- Structural features of DNA and their potential contribution to blind mole rat (Nannospalax xanthodon) longevity.Biogerontology · 2025Article
- Zα and Zβ Localize ADAR1 to Flipons That Modulate Innate Immunity, Alternative Splicing, and Nonsynonymous RNA Editing.International journal of molecular sciences · 2025Review
- Flipons enable genomes to learn by intermediating the exchange of energy for information.Journal of the Royal Society, Interface · 2025Review
- A Compendium of G-Flipon Biological Functions That Have Experimental Validation.International journal of molecular sciences · 2024Review
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
A long-standing question concerns the role of Z-DNA in transcription. Here we use a deep learning approach DeepZ that predicts Z-flipons based on DNA sequence, structural properties of nucleotides and omics data. We examined Z-flipons that are conserved between human and mouse genomes after generating whole-genome Z-flipon maps and then validated them by orthogonal approaches based on high resolution chemical mapping of Z-DNA and the transformer algorithm Z-DNABERT. For human and mouse, we revealed similar pattern of transcription factors, chromatin remodelers, and histone marks associated with conserved Z-flipons. We found significant enrichment of Z-flipons in alternative and bidirectional promoters associated with neurogenesis genes. We show that conserved Z-flipons are associated with increased experimentally determined transcription reinitiation rates compared to promoters without Z-flipons, but without affecting elongation or pausing. Our findings support a model where Z-flipons engage Transcription Factor E and impact phenotype by enabling the reset of preinitiation complexes when active, and the suppression of gene expression when engaged by repressive chromatin complexes.
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