Identification of Conserved Regulatory Elements in Mammalian Promoter Regions:A Case Study Using the PCK1 Promoter

摘要

A systematic phylogenetic footprinting approach was performed to identify con-served transcription factor binding sites (TFBSs) in mammalian promoter regions using human,mouse and rat sequence alignments. We found that the score dis-tributions 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 pro-moter 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 tran-scription 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.