The evolution of genomic imprinting : a comparative analysis of the DLK1/DIO3 domain in extant vertebrates

Functional data indicates that genomic imprinting arose alongside placentation in therian mammals. This theory predicts that oviparous monotremes will not imprint but viviparous marsupials will. The DLK1/DIO3 cluster (approximately 1 million base pairs long) is ideal for investigating the evolution of imprinting as all of the protein coding genes within the cluster are expressed in the placenta. The DLK1/DIO3 imprinted domain was mapped and sequenced in a marsupial (tammar wallaby) and monotreme (platypus). DLK1 and DIO3 genes were identified in both species and found to be biallelically expressed. Imprinted expression of genes within this region is therefore restricted to the eutherian lineage. A seven way comparative sequence analysis of the entire DLK1/DIO3 region in chicken, platypus, wallaby, opossum, dog, mouse and human was performed. Results indicate that genomic signatures previously associated with imprinting clusters i.e. SINE depletion and increased GC content, were only associated with the imprinted eutherian DLK1/DIO3 region, suggesting these features evolved in the region alongside the acquisition of imprinting. The IG-DMR, the imprinting control region for the domain, is not present in non-eutherian species. Comparative expression and epigenetic analysis in platypus and wallaby suggest the paternal chromosome in eutherians is most similar to the ancestral DLK1/DIO3 region. The snoRNA and microRNA clusters in the domain were shown to be eutherian specific, causing a region of relative expansion in these species, whereas one specific eutherian region was resistant to expansion. A region orthologous to the retrotransposon like gene, RTL1, was identified in both marsupials, but not in platypus or chicken. In marsupials the RTL1region lacks an open reading frame and is not expressed. This indicates that, in marsupials, RTL1 did not gain a function (or lost it) and the sequence diverged. In eutherians RTL1 acquired a function in placentation, an event which may have driven the evolution of imprinted expression within the region.EThOS - Electronic Theses Online ServiceGBUnited Kingdo