Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle

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dc.citation.articleNumber2387en_US
dc.citation.firstpage2405en_US
dc.citation.issueNumber8en_US
dc.citation.journalTitleGenome Biology and Evolutionen_US
dc.citation.volumeNumber8en_US
dc.contributor.authorYue, Jia-Xingen_US
dc.contributor.authorKozmikova, Irynaen_US
dc.contributor.authorOno, Hirokien_US
dc.contributor.authorNossa, Carlos W.en_US
dc.contributor.authorKozmik, Zbyneken_US
dc.contributor.authorPutnam, Nicholas H.en_US
dc.contributor.authorYu, Jr-Kaien_US
dc.contributor.authorHolland, Linda Z.en_US
dc.date.accessioned2016-09-30T20:52:22Zen_US
dc.date.available2016-09-30T20:52:22Zen_US
dc.date.issued2016en_US
dc.description.abstractCephalochordates, the sister group of vertebrates + tunicates, are evolving particularly slowly. Therefore, genome comparisons between two congeners of Branchiostoma revealed so many conserved noncoding elements (CNEs), that it was not clear how many are functional regulatory elements. To more effectively identify CNEs with potential regulatory functions, we compared noncoding sequences of genomes of the most phylogenetically distant cephalochordate genera, Asymmetron andBranchiostoma, which diverged approximately 120–160 million years ago. We found 113,070 noncoding elements conserved between the two species, amounting to 3.3% of the genome. The genomic distribution, target gene ontology, and enriched motifs of these CNEs all suggest that many of them are probably cis-regulatory elements. More than 90% of previously verified amphioxus regulatory elements were re-captured in this study. A search of the cephalochordate CNEs around 50 developmental genes in several vertebrate genomes revealed eight CNEs conserved between cephalochordates and vertebrates, indicating sequence conservation over >500 million years of divergence. The function of five CNEs was tested in reporter assays in zebrafish, and one was also tested in amphioxus. All five CNEs proved to be tissue-specific enhancers. Taken together, these findings indicate that even though Branchiostoma andAsymmetron are distantly related, as they are evolving slowly, comparisons between them are likely optimal for identifying most of their tissue-specific cis-regulatory elements laying the foundation for functional characterizations and a better understanding of the evolution of developmental regulation in cephalochordates.en_US
dc.identifier.citationYue, Jia-Xing, Kozmikova, Iryna, Ono, Hiroki, et al.. "Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle." <i>Genome Biology and Evolution,</i> 8, no. 8 (2016) Oxford University Press: 2405. http://dx.doi.org/10.1093/gbe/evw158.en_US
dc.identifier.doihttp://dx.doi.org/10.1093/gbe/evw158en_US
dc.identifier.urihttps://hdl.handle.net/1911/91640en_US
dc.language.isoengen_US
dc.publisherOxford University Pressen_US
dc.rightsArticle is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.en_US
dc.subject.keywordCNEen_US
dc.subject.keywordregulatory elementen_US
dc.subject.keywordcephalochordateen_US
dc.subject.keywordasymmetronen_US
dc.subject.keywordamphioxusen_US
dc.titleConserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principleen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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