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dc.contributor.authorSeridi, Loqmane
dc.contributor.authorRyu, Tae Woo
dc.contributor.authorRavasi, Timothy
dc.date.accessioned2014-11-06T07:03:13Z
dc.date.available2014-11-06T07:03:13Z
dc.date.issued2014-10-07
dc.identifier.citationSeridi L, Ryu T, Ravasi T (2014) Dynamic Epigenetic Control of Highly Conserved Noncoding Elements. PLoS ONE 9(10): e109326. doi:10.1371/journal.pone.0109326
dc.identifier.issn1932-6203
dc.identifier.pmid25289637
dc.identifier.doi10.1371/journal.pone.0109326
dc.identifier.urihttp://hdl.handle.net/10754/333746
dc.description.abstractBackground Many noncoding genomic loci have remained constant over long evolutionary periods, suggesting that they are exposed to strong selective pressures. The molecular functions of these elements have been partially elucidated, but the fundamental reason for their extreme conservation is still unknown. Results To gain new insights into the extreme selection of highly conserved noncoding elements (HCNEs), we used a systematic analysis of multi-omic data to study the epigenetic regulation of such elements during the development of Drosophila melanogaster. At the sequence level, HCNEs are GC-rich and have a characteristic oligomeric composition. They have higher levels of stable nucleosome occupancy than their flanking regions, and lower levels of mononucleosomes and H3.3, suggesting that these regions reside in compact chromatin. Furthermore, these regions showed remarkable modulations in histone modification and the expression levels of adjacent genes during development. Although HCNEs are primarily initiated late in replication, about 10% were related to early replication origins. Finally, HCNEs showed strong enrichment within lamina-associated domains. Conclusion HCNEs have distinct and protective sequence properties, undergo dynamic epigenetic regulation, and appear to be associated with the structural components of the chromatin, replication origins, and nuclear matrix. These observations indicate that such elements are likely to have essential cellular functions, and offer insights into their epigenetic properties.
dc.language.isoen
dc.publisherPublic Library of Science (PLoS)
dc.relation.urlhttp://dx.plos.org/10.1371/journal.pone.0109326
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectChromatin
dc.subjectDNA replication
dc.subjectGene regulation
dc.subjectGenome evolution
dc.subjectHistone modification
dc.subjectInvertebrate genomics
dc.subjectNucleosomes
dc.subjectSequence motif analysis
dc.titleDynamic Epigenetic Control of Highly Conserved Noncoding Elements
dc.typeArticle
dc.contributor.departmentApplied Mathematics and Computational Science Program
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentComputer Science Program
dc.contributor.departmentIntegrative Systems Biology Lab
dc.identifier.journalPLoS ONE
dc.identifier.pmcidPMC4188601
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionDepartment of Medicine, Division of Genetics, University of California San Diego, La Jolla, California, United States of America
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personSeridi, Loqmane
kaust.personRyu, Tae Woo
kaust.personRavasi, Timothy
refterms.dateFOA2018-06-13T15:34:45Z


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This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Except where otherwise noted, this item's license is described as This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.