ArticleNucleic acids research2002
Definition and prediction of the full range of transcription factor binding sites--the hepatocyte nuclear factor 1 dimeric site.
Article in Nucleic acids research, 2002. 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, 26 citations in OpenAlex.
- Novel Genetic Rearrangements in Hepatitis B Virus: Complex Structural Variations and Structural Variation Polymorphisms.Viruses · 2021Review
- Novel Mechanisms for IGF-I Regulation by Glucagon in Carp Hepatocytes: Up-Regulation of HNF1α and CREB Expression via Signaling Crosstalk for IGF-I Gene Transcription.Frontiers in endocrinology · 2019Article
- Regulation of hepatocyte identity and quiescence.Cellular and molecular life sciences : CMLS · 2015Review
- Characterization of an apparently novel β-cell line-enriched 80-88 kDa transcriptional activator of the MafA and Pdx1 genes.The Journal of biological chemistry · 2013Article
- Genetics is a major determinant of expression of the human hepatic uptake transporter OATP1B1, but not of OATP1B3 and OATP2B1.Genome medicine · 2013Article
- The -14010*C variant associated with lactase persistence is located between an Oct-1 and HNF1α binding site and increases lactase promoter activity.Human genetics · 2011Article
- Hnf1α (MODY3) regulates β-cell-enriched MafA transcription factor expression.Molecular endocrinology (Baltimore, Md.) · 2011Article
- Genomic promoter analysis predicts functional transcription factor binding.Advances in bioinformatics · 2008Article
- The GCN4 bZIP targets noncognate gene regulatory sequences: quantitative investigation of binding at full and half sites.Biochemistry · 2007Article
- The GCN4 bZIP can bind to noncognate gene regulatory sequences.Biochimica et biophysica acta · 2006Article
- A comprehensive software suite for the analysis of cDNAs.Genomics, proteomics & bioinformatics · 2005Article
- Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites.Nucleic acids research · 2005Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
In animals, transcription factor binding sites are hard to recognize because of their extensive variation. We therefore characterized the general relationship between a specific protein-binding site and its DNA sequence and used this relationship to generate a predictive algorithm for searching other DNA sequences. The experimental process was defined by studying hepatocyte nuclear factor 1 (HNF1), which binds DNA as a dimer on two inverted-repeat 7-bp half sites separated by one base. The binding model was based on the equivalence of the two half sites, which was confirmed in examples where specific modified sites were compared. Binding competition analysis was used to determine the effects of substitution of all four bases at each position in the half site. From these data, a weighted half-site matrix was generated and the full site was evaluated as the sum of two half-site scores. This process accurately predicted even weak binding sites that were significantly different from the consensus sequence. The predictions also showed a direct correlation with measured protein binding.
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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.