Prediction and Analysis of CpG Islands and Transcription Factor Binding Elements in Putative Imprinted Gene Cluster in Bovine Chromosome 29

Imprinted genes are expressed from one parental allele, and have been implicated in a host of biological processes and functions. Although dozens of genes have been identified and confirmed in mouse and human, very few are known in other mammalian species. Bovine chromosome 29 is the bovine equivalent of human chromosome 11 and mouse chromosome 7 containing the highest densities of imprinted genes. We selected 14 imprinted genes from a cluster in human chromosome 11 and mouse chromosome 7 and carried out computational analysis of CpG islands (CpGs) and transcription factor binding elements to better understand structural genomic features that may be predictive for identifying imprinted genes in the bovine genome. CpGs in promoter sequences were found in TSPAN32 and KCNQ1 in cattle, IGF2 and SLC22A18 in humans, and in CD81, OSBPL5 and TSSC4 in mouse. CpGs in the promoter regions may act as centers for methylation control and differential gene expression. No CpGs were found for INS in cattle, human and mouse orthologs. Binding sites for E2F, NANOG, OCT4 and SOX2 transcription factors (TFs) were predicted in 9 of the putative imprinted genes. The TFs appear to form clusters around the conserved regions found upstream of the transcription start sites with likely implications for gene silencing and regulation of gene expression through their DNA binding domains. Our results further strengthen the possible role of structural features to predict the molecular behavior of imprinted genes that can subsequently be explored experimentally.