Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome - PubMed (original) (raw)
. 1997 Feb 21;266(2):231-45.
doi: 10.1006/jmbi.1996.0760.
Affiliations
- PMID: 9047360
- DOI: 10.1006/jmbi.1996.0760
Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome
F Tronche et al. J Mol Biol. 1997.
Abstract
Hepatocyte nuclear factor 1 (HNF1) is a dimeric homeoprotein expressed in hepatocytes and in a few other epithelial cells where it helps regulate the expression of a specific subset of genes. In an attempt to identify novel target genes for HNF1 and to assess the distribution of its target sites within the vertebrate genome, we performed a computer-assisted search within the available databases using a weighted matrix. Several hundred potential target sequences were identified within the GenBank and EMBL data banks. DNA binding assays demonstrated that more than 95%, of the new sites tested (52 sites among 54) bound HNF1. Surprisingly many HNF1 target sites were found in genes that are transcribed in cell types that do not contain the protein. On the other hand these sites are 2.5 to five times more frequent in hepatic genes than expected. It seems that the presence of HNF1 sites in liver-specific genes was favoured, but that no counter-selection occurred within the rest of the genome. HNF1 binding sites in liver genes are more often associated in clusters with sites for other transcription factors and the enrichment is more pronounced in promoter regions. We identified more than 100 liver specific genes that are potentially regulated by HNF1.
Similar articles
- HNF1, a homeoprotein member of the hepatic transcription regulatory network.
Tronche F, Yaniv M. Tronche F, et al. Bioessays. 1992 Sep;14(9):579-87. doi: 10.1002/bies.950140902. Bioessays. 1992. PMID: 1365913 Review. - Interplay between a new HNF3 and the HNF1 transcriptional factors in the duck hepatitis B virus enhancer.
Crescenzo-Chaigne B, Pillot J, Lilienbaum A. Crescenzo-Chaigne B, et al. Virology. 1995 Oct 20;213(1):231-40. doi: 10.1006/viro.1995.1563. Virology. 1995. PMID: 7483267 - Salmon HNF1: cDNA sequence, evolution, tissue specificity and binding to the salmon serum albumin promoter.
Deryckere F, Byrnes L, Wagner A, McMorrow T, Gannon F. Deryckere F, et al. J Mol Biol. 1995 Mar 17;247(1):1-10. doi: 10.1006/jmbi.1994.0115. J Mol Biol. 1995. PMID: 7897653 - Hepatocyte nuclear factor 1, a transcription factor at the crossroads of glucose homeostasis.
Pontoglio M. Pontoglio M. J Am Soc Nephrol. 2000 Nov;11 Suppl 16:S140-3. J Am Soc Nephrol. 2000. PMID: 11065346 Review.
Cited by
- Genetic evidence that HNF-1alpha-dependent transcriptional control of HNF-4alpha is essential for human pancreatic beta cell function.
Hansen SK, Párrizas M, Jensen ML, Pruhova S, Ek J, Boj SF, Johansen A, Maestro MA, Rivera F, Eiberg H, Andel M, Lebl J, Pedersen O, Ferrer J, Hansen T. Hansen SK, et al. J Clin Invest. 2002 Sep;110(6):827-33. doi: 10.1172/JCI15085. J Clin Invest. 2002. PMID: 12235114 Free PMC article. - Association of Common Variants in HNF1A Gene with Serum AFP Level in Healthy Chinese Individuals and HCC Patients.
Li XJ, Shao DH, He ML, Liang GW. Li XJ, et al. Dis Markers. 2019 Nov 7;2019:6273497. doi: 10.1155/2019/6273497. eCollection 2019. Dis Markers. 2019. PMID: 31915469 Free PMC article. - In silico detection of sequence variations modifying transcriptional regulation.
Andersen MC, Engström PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW, Odeberg J. Andersen MC, et al. PLoS Comput Biol. 2008 Jan;4(1):e5. doi: 10.1371/journal.pcbi.0040005. Epub 2007 Nov 27. PLoS Comput Biol. 2008. PMID: 18208319 Free PMC article. - A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery.
Wang X, Gao H, Shen Y, Weinstock GM, Zhou J, Palzkill T. Wang X, et al. Nucleic Acids Res. 2008 Sep;36(15):4863-71. doi: 10.1093/nar/gkn477. Epub 2008 Jul 24. Nucleic Acids Res. 2008. PMID: 18653527 Free PMC article.