ArticlePLoS genetics2008
Functional characterization of variations on regulatory motifs.
Article in PLoS genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 16 papers.
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The trial behind it
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
16 citing papers in PubMed, 23 citations in OpenAlex.
- Genome-wide characterization and seasonal modulation of Hsp60 expression in juvenile Hilsa Shad across distinct upstream habitats.Journal, genetic engineering & biotechnology · 2025Article
- Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants.Human mutation · 2016Article
- Methodology for single nucleotide polymorphism selection in promoter regions for clinical use. An example of its applicability.International journal of molecular epidemiology and genetics · 2016Article
- Functional implications of local DNA structures in regulatory motifs.TheScientificWorldJournal · 2013Article
- CDX1 confers intestinal phenotype on gastric epithelial cells via induction of stemness-associated reprogramming factors SALL4 and KLF5.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast.PloS one · 2012Article
- Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA.Gene regulation and systems biology · 2012Article
- The impact of cis-acting polymorphisms on the human phenotype.The HUGO journal · 2011Article
- Prediction of functional regulatory SNPs in monogenic and complex disease.Human mutation · 2011Article
- Selective genomic targeting by FRA-2/FOSL2 transcription factor: regulation of the Rgs4 gene is mediated by a variant activator protein 1 (AP-1) promoter sequence/CREB-binding protein (CBP) mechanism.The Journal of biological chemistry · 2011Article
- Functional dissection of IME1 transcription using quantitative promoter-reporter screening.Genetics · 2010Article
- Human variation in short regions predisposed to deep evolutionary conservation.Molecular biology and evolution · 2010Article
- Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae.Genome biology and evolution · 2010Article
- Impact of DNA-binding position variants on yeast gene expression.Nucleic acids research · 2009Article
- Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.Microbiology and molecular biology reviews : MMBR · 2009Review
- Predicting functional regulatory polymorphisms.Bioinformatics (Oxford, England) · 2008Article
Corrections and comments
- Erratum issuedMichal, Lapidot [corrected to Lapidot, Michal]
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors (TFs) regulate gene expression through specific interactions with short promoter elements. The same regulatory protein may recognize a variety of related sequences. Moreover, once they are detected it is hard to predict whether highly similar sequence motifs will be recognized by the same TF and regulate similar gene expression patterns, or serve as binding sites for distinct regulatory factors. We developed computational measures to assess the functional implications of variations on regulatory motifs and to compare the functions of related sites. We have developed computational means for estimating the functional outcome of substituting a single position within a binding site and applied them to a collection of putative regulatory motifs. We predict the effects of nucleotide variations within motifs on gene expression patterns. In cases where such predictions could be compared to suitable published experimental evidence, we found very good agreement. We further accumulated statistics from multiple substitutions across various binding sites in an attempt to deduce general properties that characterize nucleotide substitutions that are more likely to alter expression. We found that substitutions involving Adenine are more likely to retain the expression pattern and that substitutions involving Guanine are more likely to alter expression compared to the rest of the substitutions. Our results should facilitate the prediction of the expression outcomes of binding site variations. One typical important implication is expected to be the ability to predict the phenotypic effect of variation in regulatory motifs in promoters.
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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.