ArticleNucleic acids research2010
DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It carries an expression of concern. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Efficient High-Throughput DNA Breathing Features Generation Using Jax-EPBD.bioRxiv : the preprint server for biology · 2024Article
- DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors.Nucleic acids research · 2024Article
- Predicting Transcription Factor Binding Sites with Deep Learning.International journal of molecular sciences · 2024Article
- Article
- 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
- Bubble Relaxation Dynamics in Homopolymer DNA Sequences.Molecules (Basel, Switzerland) · 2023Article
- Nonlinear physics opens a new paradigm for accurate transcription start site prediction.BMC bioinformatics · 2022Article
- MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network.Briefings in bioinformatics · 2022Article
- Ideas and methods of nonlinear mathematics and theoretical physics in DNA science: the McLaughlin-Scott equation and its application to study the DNA open state dynamics.Biophysical reviews · 2021Review
- 0.1 THz exposure affects primary hippocampus neuron gene expression via alternating transcription factor binding.Biomedical optics express · 2021Article
- Article
- DNA Supercoiling: an Ancestral Regulator of Gene Expression in Pathogenic Bacteria?Computational and structural biotechnology journal · 2019Review
- DNA structure at the plasmid origin-of-transfer indicates its potential transfer range.Scientific reports · 2018Article
- Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization.Scientific reports · 2017Article
- Focused transcription from the human CR2/CD21 core promoter is regulated by synergistic activity of TATA and Initiator elements in mature B cells.Cellular & molecular immunology · 2016Article
- Analysis of the leakage of gene repression by an artificial TetR-regulated promoter in cyanobacteria.BMC research notes · 2015Article
- Unravelling the Role of the F55 Regulator in the Transition from Lysogeny to UV Induction of Sulfolobus Spindle-Shaped Virus 1.Journal of virology · 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
Corrections and comments
- Expression of concern
Authors and funding
8 authors.
Funding
Abstract
We assess the role of DNA breathing dynamics as a determinant of promoter strength and transcription start site (TSS) location. We compare DNA Langevin dynamic profiles of representative gene promoters, calculated with the extended non-linear PBD model of DNA with experimental data on transcription factor binding and transcriptional activity. Our results demonstrate that DNA dynamic activity at the TSS can be suppressed by mutations that do not affect basal transcription factor binding-DNA contacts. We use this effect to establish the separate contributions of transcription factor binding and DNA dynamics to transcriptional activity. Our results argue against a purely 'transcription factor-centric' view of transcription initiation, suggesting that both DNA dynamics and transcription factor binding are necessary conditions for transcription initiation.
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Registered trials
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.