Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus

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 analy...

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Bibliographic Details
Published in:Genome research 2011-06, Vol.21 (6), p.850-862
Main Authors: Horvath, Julie E, Sheedy, Christina B, Merrett, Stephanie L, Diallo, Abdoulaye Banire, Swofford, David L, NISC Comparative Sequencing Program, Green, Eric D, Willard, Huntington F
Format: Article
Language:English
Subjects:
Animals
Base Sequence
Chromosomes, Artificial, Bacterial
Computational Biology
DNA, Complementary - genetics
Evolution, Molecular
Genes, X-Linked - genetics
Humans
In Situ Hybridization, Fluorescence
Lemur
Lemur - genetics
Likelihood Functions
Models, Genetic
Molecular Sequence Data
Phylogeny
Polymerase Chain Reaction
Primates
RNA, Long Noncoding
RNA, Untranslated - genetics
Sequence Analysis, DNA
Species Specificity
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Summary: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.
ISSN:1088-9051
1549-5469
DOI:10.1101/gr.111849.110