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Genomics Proteomics Bioinformatics. 2008 Dec;6(3-4):129-43. doi: 10.1016/S1672-0229(09)60001-2.

Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter.

Author information

1
Bovine Functional Genomics Laboratory, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA. george.liu@ars.usda.gov

Abstract

A systematic phylogenetic footprinting approach was performed to identify conserved transcription factor binding sites (TFBSs) in mammalian promoter regions using human, mouse and rat sequence alignments. We found that the score distributions of most binding site models did not follow the Gaussian distribution required by many statistical methods. Therefore, we performed an empirical test to establish the optimal threshold for each model. We gauged our computational predictions by comparing with previously known TFBSs in the PCK1 gene promoter of the cytosolic isoform of phosphoenolpyruvate carboxykinase, and achieved a sensitivity of 75% and a specificity of approximately 32%. Almost all known sites overlapped with predicted sites, and several new putative TFBSs were also identified. We validated a predicted SP1 binding site in the control of PCK1 transcription using gel shift and reporter assays. Finally, we applied our computational approach to the prediction of putative TFBSs within the promoter regions of all available RefSeq genes. Our full set of TFBS predictions is freely available at http://bfgl.anri.barc.usda.gov/tfbsConsSites.

PMID:
19329064
PMCID:
PMC5054123
DOI:
10.1016/S1672-0229(09)60001-2
[Indexed for MEDLINE]
Free PMC Article
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