title: A case-by-case evolutionary analysis of four imprinted retrogenes.
abstract: Retroposition is a widespread phenomenon resulting in the generation of new genes that are initially related to a parent gene via very high coding sequence similarity. We examine the evolutionary fate of four retrogenes generated by such an event; mouse Inpp5f_v2, Mcts2, Nap1l5, and U2af1-rs1. These genes are all subject to the epigenetic phenomenon of parental imprinting. We first provide new data on the age of these retrogene insertions. Using codon-based models of sequence evolution, we show these retrogenes have diverse evolutionary trajectories, including divergence from the parent coding sequence under positive selection pressure, purifying selection pressure maintaining parent-retrogene similarity, and neutral evolution. Examination of the expression pattern of retrogenes shows an atypical, broad pattern across multiple tissues. Protein 3D structure modeling reveals that a positively selected residue in U2af1-rs1, not shared by its parent, may influence protein conformation. Our case-by-case analysis of the evolution of four imprinted retrogenes reveals that this interesting class of imprinted genes, while similar in regulation and sequence characteristics, follow very varied evolutionary paths.
authors.affiliation: Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, United Kingdom. ruth.mccole@genetics.harvard.edu
authors.forename: Ruth B
authors.initials: RB
authors.lastname: McCole
authors.forename: Noeleen B
authors.initials: NB
authors.lastname: Loughran
authors.forename: Mandeep
authors.initials: M
authors.lastname: Chahal
authors.forename: Luis P
authors.initials: LP
authors.lastname: Fernandes
authors.forename: Roland G
authors.initials: RG
authors.lastname: Roberts
authors.forename: Franca
authors.initials: F
authors.lastname: Fraternali
authors.forename: Mary J
authors.initials: MJ
authors.lastname: O'Connell
authors.forename: Rebecca J
authors.initials: RJ
authors.lastname: Oakey
mesh_terms: D000818:Animals; D004843:Epistasis, Genetic; D019143:Evolution, Molecular; D018392:Genomic Imprinting; D000072181:Inositol Polyphosphate 5-Phosphatases; D051379:Mice; D008957:Models, Genetic; D008961:Models, Structural; D027501:Monocarboxylic Acid Transporters / Q000235:genetics; D009419:Nerve Tissue Proteins / Q000235:genetics; D009687:Nuclear Proteins / Q000235:genetics; D010744:Phosphoric Monoester Hydrolases / Q000235:genetics; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D012261:Ribonucleoproteins / Q000235:genetics; D000072668:Splicing Factor U2AF
chemical_list: D027501:Monocarboxylic Acid Transporters; C496209:Nap1l5 protein, mouse; D009419:Nerve Tissue Proteins; D009687:Nuclear Proteins; D018626:Retroelements; D012261:Ribonucleoproteins; C490426:Slc16a7 protein, mouse; D000072668:Splicing Factor U2AF; C000607495:Zrsr1 protein, mouse; D010744:Phosphoric Monoester Hydrolases; D000072181:Inositol Polyphosphate 5-Phosphatases