ArticleGene2008
DNA sequence and structural properties as predictors of human and mouse promoters.
Article in Gene, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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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
23 citing papers in PubMed, 48 citations in OpenAlex.
- Segzoo: a turnkey system that summarizes genome annotations.Bioinformatics (Oxford, England) · 2026Article
- Physical Peculiarity of Two Sites in Human Promoters: Universality and Diverse Usage in Gene Function.International journal of molecular sciences · 2024Article
- Effects of DNA Methylation on Gene Expression and Phenotypic Traits in Cattle: A Review.International journal of molecular sciences · 2023Review
- Article
- Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters.International journal of molecular sciences · 2022Article
- Anchor-based bisulfite sequencing determines genome-wide DNA methylation.Communications biology · 2022Article
- Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.Briefings in bioinformatics · 2022Article
- The Role of Thymine DNA Glycosylase in Transcription, Active DNA Demethylation, and Cancer.Cancers · 2022Review
- Mononucleotide A-repeats may Play a Regulatory Role in Endothermic Housekeeping Genes.Evolutionary bioinformatics online · 2022Article
- Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species.Epigenetics & chromatin · 2018Article
- Recent Advances on the Machine Learning Methods in Identifying DNA Replication Origins in Eukaryotic Genomics.Frontiers in genetics · 2018Review
- Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.Scientific reports · 2017Article
- Alternative TSSs are co-regulated in single cells in the mouse brain.Molecular systems biology · 2017Article
- DNA structural features of eukaryotic TATA-containing and TATA-less promoters.FEBS open bio · 2017Article
- Abundance, arrangement, and function of sequence motifs in the chicken promoters.BMC genomics · 2014Article
- Aberrant repair initiated by mismatch-specific thymine-DNA glycosylases provides a mechanism for the mutational bias observed in CpG islands.Nucleic acids research · 2014Article
- Genetic and epigenetic determinants mediate proneness of oncogene breakpoint sites for involvement in TCR translocations.Genes and immunity · 2014Article
- Upstream mononucleotide A-repeats play a cis-regulatory role in mammals through the DICER1 and Ago proteins.Nucleic acids research · 2013Article
- MicroRNA 339 down-regulates μ-opioid receptor at the post-transcriptional level in response to opioid treatment.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2013Article
- Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics.PLoS computational biology · 2013Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Promoters play a central role in gene regulation, yet our power to discriminate them from non-promoter sequences in higher eukaryotes is mainly restricted to those associated with CpG islands. Here, we examined in silico the promoters of 30,954 human and 18,083 mouse transcripts in the DBTSS database, to assess the impact of particular sequence and structural features (propeller twist, bendability and nucleosome positioning preference) on promoter classification and prediction. Our analysis showed that a stricter-than-traditional definition of CpG islands captures low and high CpG count promoter classes more accurately than the traditional one. We observed that both human and mouse promoter sequences are flexible with the exception of the TATA box and TSS, which are rigid regions irrespective of association with a CpG island. Therefore varying levels of structural flexibility in promoters may affect their accessibility to proteins, and hence their specificity. For all features investigated, averaged values across core promoters discriminated CpG island associated promoters from background, whereas the same did not hold for promoters without a CpG island. However, local changes around - 34 to - 23 (expected position of TATA box) and the TSS were informative in discriminating promoters (both classes) from non-promoter sequences. Additionally, we investigated ATG deserts and observed that they occur in all promoter sets except those with a TATA-box and without a CpG island in human. Interestingly, all mouse promoter sets showed ATG codon depletion irrespective of the presence of a TATA-box, possibly reflecting a weaker contribution to TSS specificity in mouse.
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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.