ArticleNucleic acids research2012
DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 47 citations in OpenAlex.
- Review
- Mechanistic insights into PCBP1-driven unfolding of selected i-motif DNA at GNature communications · 2026Article
- DNA breathing and shape encode distinct mechanisms of transcription factor binding.Bioinformatics advances · 2026Article
- Contribution of DNA breathing to physical interactions with transcription factors.bioRxiv : the preprint server for biology · 2025Article
- DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors.Nucleic acids research · 2024Article
- Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention.bioRxiv : the preprint server for biology · 2024Article
- Non-canonical DNA structures in the human ribosomal DNA.Histochemistry and cell biology · 2023Review
- Examining DNA breathing with pyDNA-EPBD.Bioinformatics (Oxford, England) · 2023Article
- Creation and resolution of non-B-DNA structural impediments during replication.Critical reviews in biochemistry and molecular biology · 2022Article
- Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy.Frontiers in molecular biosciences · 2021Review
- Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data.BMC genomics · 2019Article
- High-Performance Image-Based Measurements of Biological Forces and Interactions in a Dual Optical Trap.ACS nano · 2018Article
- Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization.Scientific reports · 2017Article
- Enhancement of RecA-mediated self-assembly in DNA nanostructures through basepair mismatches and single-strand nicks.Scientific reports · 2017Article
- The role of structural parameters in DNA cyclization.BMC bioinformatics · 2016Article
- Analysis of the leakage of gene repression by an artificial TetR-regulated promoter in cyanobacteria.BMC research notes · 2015Article
- A rare functional noncoding variant at the GWAS-implicated MIR137/MIR2682 locus might confer risk to schizophrenia and bipolar disorder.American journal of human genetics · 2014Article
- Mesoscopic model and free energy landscape for protein-DNA binding sites: analysis of cyanobacterial promoters.PLoS computational biology · 2014Article
- Modeling DNA thermodynamics under torsional stress.Biophysical journal · 2014Article
- A new paradigm for transcription factor TFIIB functionality.Scientific reports · 2014Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
Abstract
The genome-wide mapping of the major gene expression regulators, the transcription factors (TFs) and their DNA binding sites, is of great importance for describing cellular behavior and phenotypic diversity. Presently, the methods for prediction of genomic TF binding produce a large number of false positives, most likely due to insufficient description of the physiochemical mechanisms of protein-DNA binding. Growing evidence suggests that, in the cell, the double-stranded DNA (dsDNA) is subject to local transient strands separations (breathing) that contribute to genomic functions. By using site-specific chromatin immunopecipitations, gel shifts, BIOBASE data, and our model that accurately describes the melting behavior and breathing dynamics of dsDNA we report a specific DNA breathing profile found at YY1 binding sites in cells. We find that the genomic flanking sequence variations and SNPs, may exert long-range effects on DNA dynamics and predetermine YY1 binding. The ubiquitous TF YY1 has a fundamental role in essential biological processes by activating, initiating or repressing transcription depending upon the sequence context it binds. We anticipate that consensus binding sequences together with the related DNA dynamics profile may significantly improve the accuracy of genomic TF binding sites and TF binding-related functional SNPs.
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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.