ArticleBMC genomics2008
Links between core promoter and basic gene features influence gene expression.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Time is ticking faster for long genes in aging.Trends in genetics : TIG · 2024Review
- On the Role of TATA Boxes and TATA-Binding Protein inPlants (Basel, Switzerland) · 2023Review
- So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes.EMBO reports · 2020Review
- Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy.Scientific reports · 2018Article
- DNA structural features of eukaryotic TATA-containing and TATA-less promoters.FEBS open bio · 2017Article
- DTIE, a novel core promoter element that directs start site selection in TATA-less genes.Nucleic acids research · 2016Article
- Co-occurrence of transcription and translation gene regulatory features underlies coordinated mRNA and protein synthesis.BMC genomics · 2014Article
- The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes.Genes & development · 2011Article
- Characteristics of core promoter types with respect to gene structure and expression in Arabidopsis thaliana.DNA research : an international journal for rapid publication of reports on genes and genomes · 2011Article
- GC3 biology in corn, rice, sorghum and other grasses.BMC genomics · 2010Article
- TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation.BMC genomics · 2010Article
- TAF4/4b x TAF12 displays a unique mode of DNA binding and is required for core promoter function of a subset of genes.The Journal of biological chemistry · 2009Article
- Characterization of sINR, a strict version of the Initiator core promoter element.Nucleic acids research · 2009Article
- Unique genes in plants: specificities and conserved features throughout evolution.BMC evolutionary biology · 2008Article
- Article
- A translation initiation element specific to mRNAs with very short 5'UTR that also regulates transcription.PloS one · 2008Article
- Review
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDiversity in rates of gene expression is essential for basic cell functions and is controlled by a variety of intricate mechanisms. Revealing general mechanisms that control gene expression is important for understanding normal and pathological cell functions and for improving the design of expression systems. Here we analyzed the relationship between general features of genes and their contribution to expression levels.
resultsGenes were divided into four groups according to their core promoter type and their characteristics analyzed statistically. Surprisingly we found that small variations in the TATA box are linked to large differences in gene length. Genes containing canonical TATA are generally short whereas long genes are associated with either non-canonical TATA or TATA-less promoters. These differences in gene length are primarily determined by the size and number of introns. Generally, gene expression was found to be tightly correlated with the strength of the TATA-box. However significant reduction in gene expression levels were linked with long TATA-containing genes (canonical and non-canonical) whereas intron length hardly affected the expression of TATA-less genes. Interestingly, features associated with high translation are prevalent in TATA-containing genes suggesting that their protein production is also more efficient.
conclusionOur results suggest that interplay between core promoter type and gene size can generate significant diversity in gene expression.
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