Comparative evolutionary analysis of the FoxG1 transcription factor from diverse vertebrates identifies conserved recognition sites for microRNA regulation

Comparative analysis of orthologues from diverse vertebrates can be used to identify molecular signatures that are important for gene function and which may predict novel regulatory mechanisms or explain morphological diversity. The forkhead box G1 (FoxG1) transcription factor is potentially a strong candidate gene for determining forebrain size in vertebrates due to its role in the development of the telencephalon, where it promotes progenitor proliferation and suppresses premature neurogenesis. To investigate the role of FoxG1 in forebrain evolution, we cloned and analyzed the cDNA sequences for nine new FoxG1 orthologues, including six mammals and three reptiles, and show that there is an extended proline and glutamine region in the N-terminal domain that is specific to mammals. In contrast to some previous studies of other potential determinants of brain size, we find no evidence that the coding sequence of FoxG1 has evolved under positive selection in vertebrates. Previously published work has indicated that FOXG1 was duplicated in humans, and two forms, FOXG1A and FOXG1B, are present in the Entrez Gene database. We report that FOXG1 has not been duplicated in humans and that FOXG1A is likely to be an artifact. Our comparative analysis of FOXG1B and its orthologues has revealed a very high level of conservation in the 3' untranslated region (UTR). Using available computational tools, we find evidence for conserved recognition sites for the miR-9 and miR-33 microRNAs in the FoxG1 3' UTR and hypothesize that these brain-expressed microRNAs may regulate FoxG1 post-transcriptionally during forebrain development.