The evolution of ultraconserved elements with different phylogenetic origins

Handle URI:
http://hdl.handle.net/10754/325238
Title:
The evolution of ultraconserved elements with different phylogenetic origins
Authors:
Ryu, Tae Woo; Seridi, Loqmane; Ravasi, Timothy ( 0000-0002-9950-465X )
Abstract:
Background: Ultraconserved elements of DNA have been identified in vertebrate and invertebrate genomes. These elements have been found to have diverse functions, including enhancer activities in developmental processes. The evolutionary origins and functional roles of these elements in cellular systems, however, have not yet been determined. Results: Here, we identified a wide range of ultraconserved elements common to distant species, from primitive aquatic organisms to terrestrial species with complicated body systems, including some novel elements conserved in fruit fly and human. In addition to a well-known association with developmental genes, these DNA elements have a strong association with genes implicated in essential cell functions, such as epigenetic regulation, apoptosis, detoxification, innate immunity, and sensory reception. Interestingly, we observed that ultraconserved elements clustered by sequence similarity. Furthermore, species composition and flanking genes of clusters showed lineage-specific patterns. Ultraconserved elements are highly enriched with binding sites to developmental transcription factors regardless of how they cluster. Conclusion: We identified large numbers of ultraconserved elements across distant species. Specific classes of these conserved elements seem to have been generated before the divergence of taxa and fixed during the process of evolution. Our findings indicate that these ultraconserved elements are not the exclusive property of higher modern eukaryotes, but rather transmitted from their metazoan ancestors. 2012 Ryu et al.; licensee BioMed Central Ltd.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Ryu T, Seridi L, Ravasi T (2012) The evolution of ultraconserved elements with different phylogenetic origins. BMC Evolutionary Biology 12: 236. doi:10.1186/1471-2148-12-236.
Publisher:
Springer Nature
Journal:
BMC Evolutionary Biology
Issue Date:
5-Dec-2012
DOI:
10.1186/1471-2148-12-236
PubMed ID:
23217155
PubMed Central ID:
PMC3556307
Type:
Article
ISSN:
14712148
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorRyu, Tae Wooen
dc.contributor.authorSeridi, Loqmaneen
dc.contributor.authorRavasi, Timothyen
dc.date.accessioned2014-08-27T09:41:32Z-
dc.date.available2014-08-27T09:41:32Z-
dc.date.issued2012-12-05en
dc.identifier.citationRyu T, Seridi L, Ravasi T (2012) The evolution of ultraconserved elements with different phylogenetic origins. BMC Evolutionary Biology 12: 236. doi:10.1186/1471-2148-12-236.en
dc.identifier.issn14712148en
dc.identifier.pmid23217155en
dc.identifier.doi10.1186/1471-2148-12-236en
dc.identifier.urihttp://hdl.handle.net/10754/325238en
dc.description.abstractBackground: Ultraconserved elements of DNA have been identified in vertebrate and invertebrate genomes. These elements have been found to have diverse functions, including enhancer activities in developmental processes. The evolutionary origins and functional roles of these elements in cellular systems, however, have not yet been determined. Results: Here, we identified a wide range of ultraconserved elements common to distant species, from primitive aquatic organisms to terrestrial species with complicated body systems, including some novel elements conserved in fruit fly and human. In addition to a well-known association with developmental genes, these DNA elements have a strong association with genes implicated in essential cell functions, such as epigenetic regulation, apoptosis, detoxification, innate immunity, and sensory reception. Interestingly, we observed that ultraconserved elements clustered by sequence similarity. Furthermore, species composition and flanking genes of clusters showed lineage-specific patterns. Ultraconserved elements are highly enriched with binding sites to developmental transcription factors regardless of how they cluster. Conclusion: We identified large numbers of ultraconserved elements across distant species. Specific classes of these conserved elements seem to have been generated before the divergence of taxa and fixed during the process of evolution. Our findings indicate that these ultraconserved elements are not the exclusive property of higher modern eukaryotes, but rather transmitted from their metazoan ancestors. 2012 Ryu et al.; licensee BioMed Central Ltd.en
dc.language.isoenen
dc.publisherSpringer Natureen
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en
dc.subjectDevelopmental enhancersen
dc.subjectGenome evolutionen
dc.subjectMarine biologyen
dc.subjectTranscriptional regulatory networksen
dc.subjectUltraconserved elementsen
dc.subjectapoptosisen
dc.subjectcommunity compositionen
dc.subjectDNAen
dc.subjectevolutionary biologyen
dc.subjectgeneen
dc.subjectgenomeen
dc.subjectphylogeneticsen
dc.subjectspecies diversityen
dc.subjectAnimaliaen
dc.subjectEukaryotaen
dc.subjectInvertebrataen
dc.subjectMetazoaen
dc.subjectVertebrataen
dc.subjectDNAen
dc.subjecttranscription factoren
dc.subjectbinding siteen
dc.subjectclassificationen
dc.subjectgenetic variabilityen
dc.subjectgeneticsen
dc.subjectgenomeen
dc.subjectmetabolismen
dc.subjectmolecular evolutionen
dc.subjectmolecular geneticsen
dc.subjectnucleotide sequenceen
dc.subjectphylogenyen
dc.subjectspecies differenceen
dc.subjectBase Sequenceen
dc.subjectBinding Sitesen
dc.subjectConserved Sequenceen
dc.subjectDNAen
dc.subjectEvolution, Molecularen
dc.subjectGenetic Variationen
dc.subjectGenomeen
dc.subjectMolecular Sequence Dataen
dc.subjectPhylogenyen
dc.subjectSpecies Specificityen
dc.subjectTranscription Factorsen
dc.titleThe evolution of ultraconserved elements with different phylogenetic originsen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalBMC Evolutionary Biologyen
dc.identifier.pmcidPMC3556307en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Medicine, Division of Medical Genetics, University of California, San Diego, 9500 Gilman Drive, San Diego, CA 92093-0688, United Statesen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorRyu, Tae Wooen
kaust.authorSeridi, Loqmaneen
kaust.authorRavasi, Timothyen

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