Identification and cross-species comparison of canine osteoarthritic gene regulatory cis-elements

SummaryObjectiveTo better understand transcription regulation of osteoarthritis (OA) by examining common promoter motifs in canine osteoarthritic genes, to identify other genes containing these motifs and to assess the conservation of these motifs between canine, human, mouse and rat.
Design
Differentially expressed transcripts in canine OA were mapped to the human genome. We thus identified 20 orthologous human transcripts representing 19 up-regulated genes and 62 orthologous transcripts representing 60 down-regulated genes. The 5 kbp upstream regions of these transcripts were used to identify binding sites and build promoter models based on those sites. The human genome was subsequently searched for other transcripts likely to be regulated by the same promoter models. Orthologous transcripts were then identified in canine, rat and mouse for determination of potential cross-species conservation of binding sites comprising the promoter model.
Results
Four promoter models containing 5–6 transcripts and 5–8 common transcription factor binding sites were developed. They include binding sites for AP-4, AP-2α and γ, and E2F. Several hundred other human genes were found to contain these promoter motifs. Furthermore these motifs were significantly over represented in the orthologous genes in canine, rat and mouse genomes.
Conclusions
We have developed and applied a computational methodology to identify common promoter elements implicated in OA and shared amongst four higher vertebrates. The transcription factors associated with these binding sites and other genes driven by these promoter motifs have been implicated in OA, chondrocyte development and with other biological factors involved in the disease.