Dynamic Epigenetic Control of Highly Conserved Noncoding Elements

Handle URI:
http://hdl.handle.net/10754/333746
Title:
Dynamic Epigenetic Control of Highly Conserved Noncoding Elements
Authors:
Seridi, Loqmane ( 0000-0001-7028-3024 ) ; Ryu, Tae Woo; Ravasi, Timothy ( 0000-0002-9950-465X )
Abstract:
Background 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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Applied Mathematics and Computational Science Program; Computer Science Program
Citation:
Seridi 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
Publisher:
Public Library of Science (PLoS)
Journal:
PLoS ONE
Issue Date:
7-Oct-2014
DOI:
10.1371/journal.pone.0109326
PubMed ID:
25289637
PubMed Central ID:
PMC4188601
Type:
Article
ISSN:
1932-6203
Additional Links:
http://dx.plos.org/10.1371/journal.pone.0109326
Appears in Collections:
Articles; Applied Mathematics and Computational Science Program; Computer Science Program; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorSeridi, Loqmaneen
dc.contributor.authorRyu, Tae Wooen
dc.contributor.authorRavasi, Timothyen
dc.date.accessioned2014-11-06T07:03:13Z-
dc.date.available2014-11-06T07:03:13Z-
dc.date.issued2014-10-07en
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.0109326en
dc.identifier.issn1932-6203en
dc.identifier.pmid25289637en
dc.identifier.doi10.1371/journal.pone.0109326en
dc.identifier.urihttp://hdl.handle.net/10754/333746en
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.en
dc.language.isoenen
dc.publisherPublic Library of Science (PLoS)en
dc.relation.urlhttp://dx.plos.org/10.1371/journal.pone.0109326en
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.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectChromatinen
dc.subjectDNA replicationen
dc.subjectGene regulationen
dc.subjectGenome evolutionen
dc.subjectHistone modificationen
dc.subjectInvertebrate genomicsen
dc.subjectNucleosomesen
dc.subjectSequence motif analysisen
dc.titleDynamic Epigenetic Control of Highly Conserved Noncoding Elementsen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentApplied Mathematics and Computational Science Programen
dc.contributor.departmentComputer Science Programen
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC4188601en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Medicine, Division of Genetics, University of California San Diego, La Jolla, California, United States of Americaen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorSeridi, Loqmaneen
kaust.authorRyu, Tae Wooen
kaust.authorRavasi, Timothyen

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