ArticleNucleic acids research2009
High DNA melting temperature predicts transcription start site location in human and mouse.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- SEQSIM: A novel bioinformatics tool for comparisons of promoter regions-a case study of calcium binding protein spermatid associated 1 (CABS1).BMC bioinformatics · 2025Article
- Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns.The EMBO journal · 2023Article
- Evaluating Plant Gene Models Using Machine Learning.Plants (Basel, Switzerland) · 2022Article
- Gene promoters show chromosome-specificity and reveal chromosome territories in humans.BMC genomics · 2013Article
- Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics.PLoS computational biology · 2013Article
- Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters.BMC genomics · 2012Article
- DNA-energetics-based analyses suggest additional genes in prokaryotes.Journal of biosciences · 2012Article
- A comparison study on feature selection of DNA structural properties for promoter prediction.BMC bioinformatics · 2012Article
- DNA structural properties in the classification of genomic transcription regulation elements.Bioinformatics and biology insights · 2012Article
- Ensemble approach combining multiple methods improves human transcription start site prediction.BMC genomics · 2010Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The accurate computational prediction of transcription start sites (TSS) in vertebrate genomes is a difficult problem. The physicochemical properties of DNA can be computed in various ways and a many combinations of DNA features have been tested in the past for use as predictors of transcription. We looked in detail at melting temperature, which measures the temperature, at which two strands of DNA separate, considering the cooperative nature of this process. We find that peaks in melting temperature correspond closely to experimentally determined transcription start sites in human and mouse chromosomes. Using melting temperature alone, and with simple thresholding, we can predict TSS with accuracy that is competitive with the most accurate state-of-the-art TSS prediction methods. Accuracy is measured using both experimentally and manually determined TSS. The method works especially well with CpG island containing promoters, but also works when CpG islands are absent. This result is clear evidence of the important role of the physical properties of DNA in the process of transcription. It also points to the importance for TSS prediction methods to include melting temperature as prior information.
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