Multiple Retrotransposon-mediated NF-YA Gene Duplication Events Recurred in Diverse Groups of Mammals at Different Ancestry Levels

NF-Y is a transcription factor trimer formed by Histone Fold subunits NF-YB/NF-YC and NF-YA, which confers sequence-specificity for the CCAAT box, an important cis regulatory element. The subunits are extremely conserved in all eukaryotes and in mammals they are typically encoded by single copy genes. We describe here the presence of a second NF-YA termed NF-YAr for retrogene in diverse groups of mammals (Cetacea, Ruminantia, Ursidae, Sciuridae, hippopotamus, and greater horseshoe bat). NF-YAr retrogenes are located on different chromosomes with respect to the parental gene; they are compact and intronless, or with few annotated introns. Phylogenetic and synteny analyses indicate multiple independent retrotransposition events in the different orders. Analysis of RNA-seq data of Bos taurus suggests expression confined to spermatozoa. Conservation of translation initiation signals around predicted start codons, and of 5'UTR sequences, are consistent with protein expression, suggesting that NF-YAr is a translated, retroposed NF-YA. 3D-informed structural considerations of the predicted protein sequences point at deleterious changes for CCAAT-binding and, potentially, for trimer formation. These findings indicate that multiple independent NF-YA retrotransposition events were fixed in selected orders of mammals, generating a second NF-YA with a strict tissue distribution.