ArticleNucleic acids research2005
Large-scale structural analysis of the core promoter in mammalian and plant genomes.
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 43 papers.
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Who cites it
43 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
- iPro2L-DG: Hybrid network based on improved densenet and global attention mechanism for identifying promoter sequences.Heliyon · 2024Article
- Physical Peculiarity of Two Sites in Human Promoters: Universality and Diverse Usage in Gene Function.International journal of molecular sciences · 2024Article
- Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters.International journal of molecular sciences · 2022Article
- Article
- Intron exon boundary junctions in human genome have in-built unique structural and energetic signals.Nucleic acids research · 2021Article
- Toward a Universal Structural and Energetic Model for Prokaryotic Promoters.Biophysical journal · 2018Article
- Article
- Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA.BMC genomics · 2017Article
- DNA structural features of eukaryotic TATA-containing and TATA-less promoters.FEBS open bio · 2017Article
- Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Structural features of DNA that determine RNA polymerase II core promoter.BMC genomics · 2016Article
- Maximal Expression of the Evolutionarily Conserved Slit2 Gene Promoter Requires Sp1.Cellular and molecular neurobiology · 2016Article
- Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features.BMC bioinformatics · 2016Article
- The impact of sequence length and number of sequences on promoter prediction performance.BMC bioinformatics · 2015Article
- Genome-wide analysis of transcription factor binding sites and their characteristic DNA structures.BMC genomics · 2015Article
- Rule-based knowledge acquisition method for promoter prediction in human and Drosophila species.TheScientificWorldJournal · 2014Article
- Structural properties of prokaryotic promoter regions correlate with functional features.PloS one · 2014Article
- Gene promoters show chromosome-specificity and reveal chromosome territories in humans.BMC genomics · 2013Article
- Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots.PloS one · 2013Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA encodes at least two independent levels of functional information. The first level is for encoding proteins and sequence targets for DNA-binding factors, while the second one is contained in the physical and structural properties of the DNA molecule itself. Although the physical and structural properties are ultimately determined by the nucleotide sequence itself, the cell exploits these properties in a way in which the sequence itself plays no role other than to support or facilitate certain spatial structures. In this work, we focus on these structural properties, comparing them between different organisms and assessing their ability to describe the core promoter. We prove the existence of distinct types of core promoters, based on a clustering of their structural profiles. These results indicate that the structural profiles are much conserved within plants (Arabidopsis and rice) and animals (human and mouse), but differ considerably between plants and animals. Furthermore, we demonstrate that these structural profiles can be an alternative way of describing the core promoter, in addition to more classical motif or IUPAC-based approaches. Using the structural profiles as discriminatory elements to separate promoter regions from non-promoter regions, reliable models can be built to identify core-promoter regions using a strictly computational approach.
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