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Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses

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dc.contributor.author Hurle, Belen
dc.contributor.author Marquès i Bonet, Tomàs, 1975-
dc.contributor.author Antonacci, Francesca
dc.contributor.author Hughes, Inna
dc.contributor.author Ryan, Joseph F.
dc.contributor.author NISC Comparative Sequencing Program
dc.contributor.author Eichler, Evan E.
dc.contributor.author Ornitz, David M.
dc.contributor.author Green, Eric D.
dc.date.accessioned 2015-04-13T07:30:17Z
dc.date.available 2015-04-13T07:30:17Z
dc.date.issued 2011
dc.identifier.citation Hurle B, Marques-Bonet T, Antonacci F, Hughes I, Ryan JF, Blakesley R et al. Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses. BMC Evolutionary Biology. 2011; 11: 23. DOI 10.1186/1471-2148-11-23
dc.identifier.issn 1471-2148
dc.identifier.uri http://hdl.handle.net/10230/23398
dc.description.abstract Background: Mutations in the Otopetrin 1 gene (Otop1) in mice and fish produce an unusual bilateral vestibular pathology that involves the absence of otoconia without hearing impairment. The encoded protein, Otop1, is the only functionally characterized member of the Otopetrin Domain Protein (ODP) family; the extended sequence and structural preservation of ODP proteins in metazoans suggest a conserved functional role. Here, we use the tools of sequence- and cytogenetic-based comparative genomics to study the Otop1 and the Otop2-Otop3 genes and to establish their genomic context in 25 vertebrates. We extend our evolutionary study to include the gene mutated in Usher syndrome (USH) subtype 1G (Ush1g), both because of the head-to-tail clustering of Ush1g with Otop2 and because Otop1 and Ush1g mutations result in inner ear phenotypes. Results: We established that OTOP1 is the boundary gene of an inversion polymorphism on human chromosome 4p16 that originated in the common human-chimpanzee lineage more than 6 million years ago. Other lineage-specific evolutionary events included a three-fold expansion of the Otop genes in Xenopus tropicalis and of Ush1g in teleostei fish. The tight physical linkage between Otop2 and Ush1g is conserved in all vertebrates. To further understand the functional organization of the Ushg1-Otop2 locus, we deduced a putative map of binding sites for CCCTC-binding factor (CTCF), a mammalian insulator transcription factor, from genome-wide chromatin immunoprecipitation-sequencing (ChIP-seq) data in mouse and human embryonic stem (ES) cells combined with detection of CTCF-binding motifs. Conclusions: The results presented here clarify the evolutionary history of the vertebrate Otop and Ush1g families, and establish a framework for studying the possible interaction(s) of Ush1g and Otop in developmental pathways.
dc.description.sponsorship This work was supported by the NHGRI Intramural Research Program, NIDCD grant DC02236 (DMO); and NHGRI grants HG002385 and HG0058815 (EEE). EEE is an investigator of the Howard Hughes Medical Institute.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof BMC Evolutionary Biology. 2011; 11: 23
dc.rights © Hurle B, Marques-Bonet T, Antonacci F, Hughes I, Ryan JF, Blakesley R et al. Creative Commons Attribution License http://creativecommons.org/licenses/by/2.0/
dc.rights.uri http://creativecommons.org/licenses/by/2.0
dc.subject.other Genètica animal
dc.subject.other Vertebrats
dc.subject.other Genètica molecular
dc.title Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/1471-2148-11-23
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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