Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation.
Identifieur interne : 000638 ( Main/Exploration ); précédent : 000637; suivant : 000639Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation.
Auteurs : Deborah Weighill [États-Unis] ; David Macaya-Sanz [États-Unis] ; Stephen Paul Difazio [États-Unis] ; Wayne Joubert [États-Unis] ; Manesh Shah [États-Unis] ; Jeremy Schmutz [États-Unis] ; Avinash Sreedasyam [États-Unis] ; Gerald Tuskan [États-Unis] ; Daniel Jacobson [États-Unis]Source :
- Frontiers in genetics [ 1664-8021 ] ; 2019.
Abstract
Various 'omics data types have been generated for Populus trichocarpa, each providing a layer of information which can be represented as a density signal across a chromosome. We make use of genome sequence data, variants data across a population as well as methylation data across 10 different tissues, combined with wavelet-based signal processing to perform a comprehensive analysis of the signature of the centromere in these different data signals, and successfully identify putative centromeric regions in P. trichocarpa from these signals. Furthermore, using SNP (single nucleotide polymorphism) correlations across a natural population of P. trichocarpa, we find evidence for the co-evolution of the centromeric histone CENH3 with the sequence of the newly identified centromeric regions, and identify a new CENH3 candidate in P. trichocarpa.
DOI: 10.3389/fgene.2019.00487
PubMed: 31214244
PubMed Central: PMC6554479
Affiliations:
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Wayne" sort="Joubert, Wayne" uniqKey="Joubert W" first="Wayne" last="Joubert">Wayne Joubert</name><affiliation wicri:level="2"><nlm:affiliation>Oak Ridge Leadership Computing Facility, Oak Ridge National Laboratory, Oak Ridge, TN, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Oak Ridge Leadership Computing Facility, Oak Ridge National Laboratory, Oak Ridge, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Shah, Manesh" sort="Shah, Manesh" uniqKey="Shah M" first="Manesh" last="Shah">Manesh Shah</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><affiliation wicri:level="2"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>HudsonAlpha Institute for Biotechnology, Huntsville, AL</wicri:regionArea><placeName><region type="state">Alabama</region></placeName></affiliation></author><author><name sortKey="Sreedasyam, Avinash" sort="Sreedasyam, Avinash" uniqKey="Sreedasyam A" first="Avinash" last="Sreedasyam">Avinash Sreedasyam</name><affiliation wicri:level="2"><nlm:affiliation>HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>HudsonAlpha Institute for Biotechnology, Huntsville, AL</wicri:regionArea><placeName><region type="state">Alabama</region></placeName></affiliation></author><author><name sortKey="Tuskan, Gerald" sort="Tuskan, Gerald" uniqKey="Tuskan G" first="Gerald" last="Tuskan">Gerald Tuskan</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Jacobson, Daniel" sort="Jacobson, Daniel" uniqKey="Jacobson D" first="Daniel" last="Jacobson">Daniel Jacobson</name><affiliation wicri:level="2"><nlm:affiliation>The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author></analytic><series><title level="j">Frontiers in genetics</title><idno type="ISSN">1664-8021</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Various 'omics data types have been generated for <i>Populus trichocarpa</i>, each providing a layer of information which can be represented as a density signal across a chromosome. We make use of genome sequence data, variants data across a population as well as methylation data across 10 different tissues, combined with wavelet-based signal processing to perform a comprehensive analysis of the signature of the centromere in these different data signals, and successfully identify putative centromeric regions in <i>P. trichocarpa</i> from these signals. Furthermore, using SNP (single nucleotide polymorphism) correlations across a natural population of <i>P. trichocarpa</i>, we find evidence for the co-evolution of the centromeric histone CENH3 with the sequence of the newly identified centromeric regions, and identify a new CENH3 candidate in <i>P. trichocarpa</i>.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">31214244</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>29</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-8021</ISSN><JournalIssue CitedMedium="Print"><Volume>10</Volume><PubDate><Year>2019</Year></PubDate></JournalIssue><Title>Frontiers in genetics</Title><ISOAbbreviation>Front Genet</ISOAbbreviation></Journal><ArticleTitle>Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation.</ArticleTitle><Pagination><MedlinePgn>487</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fgene.2019.00487</ELocationID><Abstract><AbstractText>Various 'omics data types have been generated for <i>Populus trichocarpa</i>, each providing a layer of information which can be represented as a density signal across a chromosome. We make use of genome sequence data, variants data across a population as well as methylation data across 10 different tissues, combined with wavelet-based signal processing to perform a comprehensive analysis of the signature of the centromere in these different data signals, and successfully identify putative centromeric regions in <i>P. trichocarpa</i> from these signals. Furthermore, using SNP (single nucleotide polymorphism) correlations across a natural population of <i>P. trichocarpa</i>, we find evidence for the co-evolution of the centromeric histone CENH3 with the sequence of the newly identified centromeric regions, and identify a new CENH3 candidate in <i>P. trichocarpa</i>.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Weighill</LastName><ForeName>Deborah</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Macaya-Sanz</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>DiFazio</LastName><ForeName>Stephen Paul</ForeName><Initials>SP</Initials><AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Joubert</LastName><ForeName>Wayne</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Oak Ridge Leadership Computing Facility, Oak Ridge National Laboratory, Oak Ridge, TN, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shah</LastName><ForeName>Manesh</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schmutz</LastName><ForeName>Jeremy</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek, CA, United States.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sreedasyam</LastName><ForeName>Avinash</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tuskan</LastName><ForeName>Gerald</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jacobson</LastName><ForeName>Daniel</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>05</Month><Day>31</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Genet</MedlineTA><NlmUniqueID>101560621</NlmUniqueID><ISSNLinking>1664-8021</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">CENH3</Keyword><Keyword MajorTopicYN="N">DNA methylation</Keyword><Keyword MajorTopicYN="N">Populus trichocarpa centromeres</Keyword><Keyword MajorTopicYN="N">SNP density</Keyword><Keyword MajorTopicYN="N">co-evolution</Keyword><Keyword MajorTopicYN="N">data integration</Keyword><Keyword MajorTopicYN="N">wavelet transform</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>11</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>05</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>6</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>6</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>6</Month><Day>20</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31214244</ArticleId><ArticleId IdType="doi">10.3389/fgene.2019.00487</ArticleId><ArticleId IdType="pmc">PMC6554479</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Science. 1999 Dec 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Weighill</name></region><name sortKey="Difazio, Stephen Paul" sort="Difazio, Stephen Paul" uniqKey="Difazio S" first="Stephen Paul" last="Difazio">Stephen Paul Difazio</name><name sortKey="Jacobson, Daniel" sort="Jacobson, Daniel" uniqKey="Jacobson D" first="Daniel" last="Jacobson">Daniel Jacobson</name><name sortKey="Jacobson, Daniel" sort="Jacobson, Daniel" uniqKey="Jacobson D" first="Daniel" last="Jacobson">Daniel Jacobson</name><name sortKey="Joubert, Wayne" sort="Joubert, Wayne" uniqKey="Joubert W" first="Wayne" last="Joubert">Wayne Joubert</name><name sortKey="Macaya Sanz, David" sort="Macaya Sanz, David" uniqKey="Macaya Sanz D" first="David" last="Macaya-Sanz">David Macaya-Sanz</name><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><name sortKey="Shah, Manesh" sort="Shah, Manesh" uniqKey="Shah M" first="Manesh" last="Shah">Manesh Shah</name><name sortKey="Sreedasyam, Avinash" sort="Sreedasyam, Avinash" uniqKey="Sreedasyam A" first="Avinash" last="Sreedasyam">Avinash Sreedasyam</name><name sortKey="Tuskan, Gerald" sort="Tuskan, Gerald" uniqKey="Tuskan G" first="Gerald" last="Tuskan">Gerald Tuskan</name><name sortKey="Weighill, Deborah" sort="Weighill, Deborah" uniqKey="Weighill D" first="Deborah" last="Weighill">Deborah Weighill</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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