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

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dc.citation.articleNumber2387
dc.citation.firstpage2405
dc.citation.issueNumber8
dc.citation.journalTitleGenome Biology and Evolution
dc.citation.volumeNumber8
dc.contributor.authorYue, Jia-Xing
dc.contributor.authorKozmikova, Iryna
dc.contributor.authorOno, Hiroki
dc.contributor.authorNossa, Carlos W.
dc.contributor.authorKozmik, Zbynek
dc.contributor.authorPutnam, Nicholas H.
dc.contributor.authorYu, Jr-Kai
dc.contributor.authorHolland, Linda Z.
dc.date.accessioned2016-09-30T20:52:22Z
dc.date.available2016-09-30T20:52:22Z
dc.date.issued2016
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.
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.
dc.identifier.doihttp://dx.doi.org/10.1093/gbe/evw158
dc.identifier.urihttps://hdl.handle.net/1911/91640
dc.language.isoeng
dc.publisherOxford University Press
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.
dc.subject.keywordCNE
dc.subject.keywordregulatory element
dc.subject.keywordcephalochordate
dc.subject.keywordasymmetron
dc.subject.keywordamphioxus
dc.titleConserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
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