ArticlePLoS computational biology2009
Toward a detailed description of the thermally induced dynamics of the core promoter.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed, 44 citations in OpenAlex.
- DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors.Nucleic acids research · 2024Article
- The Avoidance of Purine Stretches by Cancer Mutations.International journal of molecular sciences · 2024Article
- Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention.bioRxiv : the preprint server for biology · 2024Article
- Examining DNA breathing with pyDNA-EPBD.Bioinformatics (Oxford, England) · 2023Article
- Bubble Relaxation Dynamics in Homopolymer DNA Sequences.Molecules (Basel, Switzerland) · 2023Article
- 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
- Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics.PLoS computational biology · 2013Article
- Promoter polymorphisms in two overlapping 6p25 genes implicate mitochondrial proteins in cognitive deficit in schizophrenia.Molecular psychiatry · 2012Article
- DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells.Nucleic acids research · 2012Article
- Non-thermal effects of terahertz radiation on gene expression in mouse stem cells.Biomedical optics express · 2011Article
- DNA dynamics is likely to be a factor in the genomic nucleotide repeats expansions related to diseases.PloS one · 2011Article
- Article
- Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites.BMC bioinformatics · 2010Article
- DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation.Nucleic acids research · 2010Article
- DNA Breathing Dynamics in the Presence of a Terahertz Field.Physics letters. A · 2010Article
- High DNA melting temperature predicts transcription start site location in human and mouse.Nucleic acids research · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Establishing the general and promoter-specific mechanistic features of gene transcription initiation requires improved understanding of the sequence-dependent structural/dynamic features of promoter DNA. Experimental data suggest that a spontaneous dsDNA strand separation at the transcriptional start site is likely to be a requirement for transcription initiation in several promoters. Here, we use Langevin molecular dynamic simulations based on the Peyrard-Bishop-Dauxois nonlinear model of DNA (PBD LMD) to analyze the strand separation (bubble) dynamics of 80-bp-long promoter DNA sequences. We derive three dynamic criteria, bubble probability, bubble lifetime, and average strand separation, to characterize bubble formation at the transcriptional start sites of eight mammalian gene promoters. We observe that the most stable dsDNA openings do not necessarily coincide with the most probable openings and the highest average strand displacement, underscoring the advantages of proper molecular dynamic simulations. The dynamic profiles of the tested mammalian promoters differ significantly in overall profile and bubble probability, but the transcriptional start site is often distinguished by large (longer than 10 bp) and long-lived transient openings in the double helix. In support of these results are our experimental transcription data demonstrating that an artificial bubble-containing DNA template is transcribed bidirectionally by human RNA polymerase alone in the absence of any other transcription factors.
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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.