Submitted to: Genomics, Proteomics and Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/19/2012
Publication Date: 2/1/2013
Citation: Bickhart, D.M., Liu, G. 2013. Identification of candidate transcription factor binding sites in the cattle genome. Genomics, Proteomics and Bioinformatics. 11(3):195-198. Interpretive Summary: A resource that provides candidate transcription factor binding sites within the genome does not currently exist for cattle. We generated over 379,000 putative Transition Factor Binding Sites predictions in the upstream promoters of all available (~8,000) Mammalian Gene Collection annotated genes based on sequence conservation across cattle, human and dog. Farmers, scientist, consumers and policy planners who need to improve beef quality and production will benefit from this research.
Technical Abstract: A resource that provides candidate transcription factor binding sites does not currently exist for cattle. Such data is necessary, as predicted sites may serve as excellent starting locations for future 'omics studies to develop transcriptional regulation hypotheses. In order to generate this resource, we employed a phylogenetic footprinting approach -- using sequence conservation across cattle, human and dog -- and position specific scoring matrices to identify 379,333 putative transcription factor binding sites upstream of near 8,000 MGC annotated genes within the cattle genome. Comparisons of our predictions to known binding site loci within the PCK1 promoter region revealed a 66.7% sensitivity and 50% specificity for our method of discovery. Additionally, we intersected our predictions with known cattle SNP variants in dbSNP and on the Illumina BovineHD 770k and Bos 1 SNP chips, finding 7,534, 444 and 346 overlaps, respectively. Due to our stringent filtering criteria, these results represent high quality predictions of putative transcription factor binding sites within the cattle genome. All binding site predictions are freely available at the following website: http://bfgl.anri.barc.usda.gov/cattleTFBS.