Loss of heterozygosity by SCRaMbLEing.
Identifieur interne : 000316 ( Main/Corpus ); précédent : 000315; suivant : 000317Loss of heterozygosity by SCRaMbLEing.
Auteurs : Yunxiang Li ; Yi Wu ; Lu Ma ; Zhou Guo ; Wenhai Xiao ; Yingjin YuanSource :
- Science China. Life sciences [ 1869-1889 ] ; 2019.
English descriptors
- KwdEn :
- Aneuploidy (MeSH), Chromosomes, Fungal (genetics), Drug Resistance, Microbial (drug effects), Drug Resistance, Microbial (genetics), Evolution, Molecular (MeSH), Genetic Techniques (MeSH), Genetic Variation (MeSH), Genome, Fungal (genetics), Genomic Instability (MeSH), Heterozygote (MeSH), Humans (MeSH), Loss of Heterozygosity (genetics), Phenotype (MeSH), Saccharomyces cerevisiae (genetics), Saccharomyces cerevisiae Proteins (genetics), Sirolimus (pharmacology), Transcription Factors (genetics).
- MESH :
- chemical , genetics : Saccharomyces cerevisiae Proteins, Transcription Factors.
- drug effects : Drug Resistance, Microbial.
- genetics : Chromosomes, Fungal, Drug Resistance, Microbial, Genome, Fungal, Loss of Heterozygosity, Saccharomyces cerevisiae.
- chemical , pharmacology : Sirolimus.
- Aneuploidy, Evolution, Molecular, Genetic Techniques, Genetic Variation, Genomic Instability, Heterozygote, Humans, Phenotype.
Abstract
Genetic variation drives phenotypic evolution within populations. Genetic variation can be divided into different forms according to the size of genomic changes. However, study of large-scale genomic variation such as structural variation and aneuploidy is still limited and mainly based on the static, predetermined feature of individual genomes. Here, using SCRaMbLE, different levels of loss of heterozygosity (LOH) events including short-range LOH, long-range LOH and whole chromosome LOH were detected in evolved strains. By contrast, using rapid adaptive evolution, aneuploidy was detected in the adaptive strains. It was further found that deletion of gene GLN3, long-range LOH in the left arm of synthetic chromosome X, whole chromosome LOH of synthetic chromosome X, and duplication of chromosome VIII (trisomy) lead to increased rapamycin resistance in synthetic yeast. Comparative analysis of genome stability of evolved strains indicates that the aneuploid strain has a higher frequency of degeneration than the SCRaMbLEd strain. These findings enrich our understanding of genetic mechanism of rapamycin resistance in yeast, and provide valuable insights into yeast genome architecture and function.
DOI: 10.1007/s11427-019-9504-5
PubMed: 30900161
Links to Exploration step
pubmed:30900161Le document en format XML
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China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation></author><author><name sortKey="Ma, Lu" sort="Ma, Lu" uniqKey="Ma L" first="Lu" last="Ma">Lu Ma</name><affiliation><nlm:affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation></author><author><name sortKey="Guo, Zhou" sort="Guo, Zhou" uniqKey="Guo Z" first="Zhou" last="Guo">Zhou Guo</name><affiliation><nlm:affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation></author><author><name sortKey="Xiao, Wenhai" sort="Xiao, Wenhai" uniqKey="Xiao W" first="Wenhai" last="Xiao">Wenhai Xiao</name><affiliation><nlm:affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation></author><author><name sortKey="Yuan, Yingjin" sort="Yuan, Yingjin" uniqKey="Yuan Y" first="Yingjin" last="Yuan">Yingjin Yuan</name><affiliation><nlm:affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China. yjyuan@tju.edu.cn.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China. yjyuan@tju.edu.cn.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:30900161</idno><idno type="pmid">30900161</idno><idno type="doi">10.1007/s11427-019-9504-5</idno><idno type="wicri:Area/Main/Corpus">000316</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000316</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Loss of heterozygosity by SCRaMbLEing.</title><author><name sortKey="Li, Yunxiang" sort="Li, Yunxiang" uniqKey="Li Y" first="Yunxiang" last="Li">Yunxiang Li</name><affiliation><nlm:affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wu, Yi" sort="Wu, Yi" uniqKey="Wu Y" first="Yi" last="Wu">Yi Wu</name><affiliation><nlm:affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation></author><author><name sortKey="Ma, Lu" sort="Ma, Lu" uniqKey="Ma L" first="Lu" last="Ma">Lu Ma</name><affiliation><nlm:affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation></author><author><name sortKey="Guo, Zhou" sort="Guo, Zhou" uniqKey="Guo Z" first="Zhou" last="Guo">Zhou Guo</name><affiliation><nlm:affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation></author><author><name sortKey="Xiao, Wenhai" sort="Xiao, Wenhai" uniqKey="Xiao W" first="Wenhai" last="Xiao">Wenhai Xiao</name><affiliation><nlm:affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.</nlm:affiliation></affiliation></author><author><name sortKey="Yuan, Yingjin" sort="Yuan, Yingjin" uniqKey="Yuan Y" first="Yingjin" last="Yuan">Yingjin Yuan</name><affiliation><nlm:affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China. yjyuan@tju.edu.cn.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China. yjyuan@tju.edu.cn.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Science China. Life sciences</title><idno type="eISSN">1869-1889</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Aneuploidy (MeSH)</term><term>Chromosomes, Fungal (genetics)</term><term>Drug Resistance, Microbial (drug effects)</term><term>Drug Resistance, Microbial (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Genetic Techniques (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genome, Fungal (genetics)</term><term>Genomic Instability (MeSH)</term><term>Heterozygote (MeSH)</term><term>Humans (MeSH)</term><term>Loss of Heterozygosity (genetics)</term><term>Phenotype (MeSH)</term><term>Saccharomyces cerevisiae (genetics)</term><term>Saccharomyces cerevisiae Proteins (genetics)</term><term>Sirolimus (pharmacology)</term><term>Transcription Factors (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Saccharomyces cerevisiae Proteins</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Drug Resistance, Microbial</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosomes, Fungal</term><term>Drug Resistance, Microbial</term><term>Genome, Fungal</term><term>Loss of Heterozygosity</term><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Sirolimus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Aneuploidy</term><term>Evolution, Molecular</term><term>Genetic Techniques</term><term>Genetic Variation</term><term>Genomic Instability</term><term>Heterozygote</term><term>Humans</term><term>Phenotype</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Genetic variation drives phenotypic evolution within populations. Genetic variation can be divided into different forms according to the size of genomic changes. However, study of large-scale genomic variation such as structural variation and aneuploidy is still limited and mainly based on the static, predetermined feature of individual genomes. Here, using SCRaMbLE, different levels of loss of heterozygosity (LOH) events including short-range LOH, long-range LOH and whole chromosome LOH were detected in evolved strains. By contrast, using rapid adaptive evolution, aneuploidy was detected in the adaptive strains. It was further found that deletion of gene GLN3, long-range LOH in the left arm of synthetic chromosome X, whole chromosome LOH of synthetic chromosome X, and duplication of chromosome VIII (trisomy) lead to increased rapamycin resistance in synthetic yeast. Comparative analysis of genome stability of evolved strains indicates that the aneuploid strain has a higher frequency of degeneration than the SCRaMbLEd strain. These findings enrich our understanding of genetic mechanism of rapamycin resistance in yeast, and provide valuable insights into yeast genome architecture and function.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30900161</PMID><DateCompleted><Year>2020</Year><Month>03</Month><Day>09</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>09</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1869-1889</ISSN><JournalIssue CitedMedium="Internet"><Volume>62</Volume><Issue>3</Issue><PubDate><Year>2019</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Science China. Life sciences</Title><ISOAbbreviation>Sci China Life Sci</ISOAbbreviation></Journal><ArticleTitle>Loss of heterozygosity by SCRaMbLEing.</ArticleTitle><Pagination><MedlinePgn>381-393</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s11427-019-9504-5</ELocationID><Abstract><AbstractText>Genetic variation drives phenotypic evolution within populations. Genetic variation can be divided into different forms according to the size of genomic changes. However, study of large-scale genomic variation such as structural variation and aneuploidy is still limited and mainly based on the static, predetermined feature of individual genomes. Here, using SCRaMbLE, different levels of loss of heterozygosity (LOH) events including short-range LOH, long-range LOH and whole chromosome LOH were detected in evolved strains. By contrast, using rapid adaptive evolution, aneuploidy was detected in the adaptive strains. It was further found that deletion of gene GLN3, long-range LOH in the left arm of synthetic chromosome X, whole chromosome LOH of synthetic chromosome X, and duplication of chromosome VIII (trisomy) lead to increased rapamycin resistance in synthetic yeast. Comparative analysis of genome stability of evolved strains indicates that the aneuploid strain has a higher frequency of degeneration than the SCRaMbLEd strain. These findings enrich our understanding of genetic mechanism of rapamycin resistance in yeast, and provide valuable insights into yeast genome architecture and function.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Yunxiang</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Yi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Lu</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Zhou</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xiao</LastName><ForeName>Wenhai</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yuan</LastName><ForeName>Yingjin</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China. yjyuan@tju.edu.cn.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China. yjyuan@tju.edu.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>03</Month><Day>01</Day></ArticleDate></Article><MedlineJournalInfo><Country>China</Country><MedlineTA>Sci China Life Sci</MedlineTA><NlmUniqueID>101529880</NlmUniqueID><ISSNLinking>1674-7305</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C071664">GLN3 protein, S cerevisiae</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D029701">Saccharomyces cerevisiae Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical><Chemical><RegistryNumber>W36ZG6FT64</RegistryNumber><NameOfSubstance UI="D020123">Sirolimus</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="CommentIn"><RefSource>Sci China Life Sci. 2019 Jun;62(6):868-869</RefSource><PMID Version="1">30927172</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D000782" MajorTopicYN="Y">Aneuploidy</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015825" MajorTopicYN="N">Chromosomes, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004352" MajorTopicYN="N">Drug Resistance, Microbial</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005821" MajorTopicYN="Y">Genetic Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016681" MajorTopicYN="N">Genome, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D042822" MajorTopicYN="N">Genomic Instability</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006579" MajorTopicYN="N">Heterozygote</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019656" MajorTopicYN="N">Loss of Heterozygosity</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010641" MajorTopicYN="N">Phenotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012441" MajorTopicYN="N">Saccharomyces cerevisiae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D029701" MajorTopicYN="N">Saccharomyces cerevisiae Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020123" MajorTopicYN="N">Sirolimus</DescriptorName><QualifierName UI="Q000494" MajorTopicYN="N">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">SCRaMbLE</Keyword><Keyword MajorTopicYN="N">aneuploidy</Keyword><Keyword MajorTopicYN="N">loss of heterozygosity (LOH)</Keyword><Keyword MajorTopicYN="N">rapid adaptive evolution</Keyword><Keyword MajorTopicYN="N">structural variation</Keyword><Keyword MajorTopicYN="N">synthetic yeast genome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>01</Month><Day>15</Day></PubMedPubDate><PubMedPubDate 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