ArticleNucleic acids research2005
A highly distinctive mechanical property found in the majority of human promoters and its transcriptional relevance.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Distinctive physical properties of DNA shared by RNA polymerase II gene promoters and 5'-flanking regions of tRNA genes.Journal of biochemistry · 2024Article
- Physical Peculiarity of Two Sites in Human Promoters: Universality and Diverse Usage in Gene Function.International journal of molecular sciences · 2024Article
- iterb-PPse: Identification of transcriptional terminators in bacterial by incorporating nucleotide properties into PseKNC.PloS one · 2020Article
- A strong structural correlation between short inverted repeat sequences and the polyadenylation signal in yeast and nucleosome exclusion by these inverted repeats.Current genetics · 2019Article
- MicroRNA Promoter Identification in Arabidopsis Using Multiple Histone Markers.BioMed research international · 2015Article
- Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots.PloS one · 2013Article
- DNA structural properties in the classification of genomic transcription regulation elements.Bioinformatics and biology insights · 2012Article
- SP transcription factor paralogs and DNA-binding sites coevolve and adaptively converge in mammals and birds.Genome biology and evolution · 2012Article
- Compatible solute influence on nucleic acids: many questions but few answers.Saline systems · 2008Article
- Article
- Generic eukaryotic core promoter prediction using structural features of DNA.Genome research · 2008Article
- Boosting with stumps for predicting transcription start sites.Genome biology · 2007Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A recent study revealed that TATA boxes and initiator sequences have a common anomalous mechanical property, i.e. they comprise distinctive flexible and rigid sequences when compared with the other parts of the promoter region. In the present study, using the flexibility parameters from two different models, we calculated the average flexibility profiles of 1004 human promoters that do not contain canonical promoter elements, such as a TATA box, initiator (Inr) sequence, downstream promoter element or a GC box, and those of 382 human promoters that contain the GC box only. Here, we show that they have a common characteristic mechanical property that is strikingly similar to those of the TATA box-containing or Inr-containing promoters. Their most interesting feature is that the TATA- or Inr-corresponding region lies in the several nucleotides around the transcription start site. We have also found that a dinucleotide step from -1 to +1 (transcription start site) has a slight tendency to adopt CA that is known to be flexible. We also demonstrate that certain synthetic DNA fragments designed to mimic the average mechanical property of these 1386 promoters can drive transcription. This distinctive mechanical property may be the hallmark of a promoter.
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