title: Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus.
abstract: Here we provide a detailed comparative analysis across the candidate X-Inactivation Center (XIC) region and the XIST locus in the genomes of six primates and three mammalian outgroup species. Since lemurs and other strepsirrhine primates represent the sister lineage to all other primates, this analysis focuses on lemurs to reconstruct the ancestral primate sequences and to gain insight into the evolution of this region and the genes within it. This comparative evolutionary genomics approach reveals significant expansion in genomic size across the XIC region in higher primates, with minimal size alterations across the XIST locus itself. Reconstructed primate ancestral XIC sequences show that the most dramatic changes during the past 80 million years occurred between the ancestral primate and the lineage leading to Old World monkeys. In contrast, the XIST locus compared between human and the primate ancestor does not indicate any dramatic changes to exons or XIST-specific repeats; rather, evolution of this locus reflects small incremental changes in overall sequence identity and short repeat insertions. While this comparative analysis reinforces that the region around XIST has been subject to significant genomic change, even among primates, our data suggest that evolution of the XIST sequences themselves represents only small lineage-specific changes across the past 80 million years.
authors.affiliation: Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA. juliann.horvath@duke.edu
authors.forename: Julie E
authors.initials: JE
authors.lastname: Horvath
authors.forename: Christina B
authors.initials: CB
authors.lastname: Sheedy
authors.forename: Stephanie L
authors.initials: SL
authors.lastname: Merrett
authors.forename: Abdoulaye Banire
authors.initials: AB
authors.lastname: Diallo
authors.forename: David L
authors.initials: DL
authors.lastname: Swofford
authors.lastname: NISC Comparative Sequencing Program
authors.forename: Eric D
authors.initials: ED
authors.lastname: Green
authors.forename: Huntington F
authors.initials: HF
authors.lastname: Willard
mesh_terms: D000818:Animals; D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial; D019295:Computational Biology; D018076:DNA, Complementary / Q000235:genetics; D019143:Evolution, Molecular; D050172:Genes, X-Linked / Q000235:genetics*; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D007900:Lemur / Q000235:genetics*; D016013:Likelihood Functions; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018076:DNA, Complementary; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated; C077885:XIST non-coding RNA