Epigenetic Analysis through MSAP-NGS Coupled Technology: The Case Study of White Poplar Monoclonal Populations/Stands.
Identifieur interne : 000423 ( Main/Exploration ); précédent : 000422; suivant : 000424Epigenetic Analysis through MSAP-NGS Coupled Technology: The Case Study of White Poplar Monoclonal Populations/Stands.
Auteurs : Francesco Guarino [Italie] ; Berthold Heinze [Autriche] ; Stefano Castiglione [Italie] ; Angela Cicatelli [Italie]Source :
- International journal of molecular sciences [ 1422-0067 ] ; 2020.
Abstract
Over the last several decades, several lines of evidence have shown that epigenetic modifications modulate phenotype and mediate an organism's response to environmental stimuli. Plant DNA is normally highly methylated, although notable differences exist between species. Many biomolecular techniques based on PCR have been developed to analyse DNA methylation status, however a qualitative leap was made with the advent of next-generation sequencing (NGS). In the case of large, repetitive, or not-yet-sequenced genomes characterised by a high level of DNA methylation, the NGS analysis of bisulphite pre-treated DNA is expensive and time consuming, and moreover, in some cases data analysis is a major challenge. Methylation-sensitive amplification polymorphism (MSAP) analysis is a highly effective method to study DNA methylation. The method is based on the comparison of double DNA digestion profiles (EcoRI-HpaII and EcoRI-MspI) to reveal methylation pattern variations. These are often attributable to pedoclimatic and stress conditions which affect all organisms during their lifetime. In our study, five white poplar (Populus alba L.) specimens were collected from different monoclonal stands in the Maltese archipelago, and their DNA was processed by means of an innovative approach where MSAP analysis was followed by NGS. This allowed us to identify genes that were differentially methylated among the different specimens and link them to specific biochemical pathways. Many differentially methylated genes were found to encode transfer RNAs (tRNAs) related to photosynthesis or light reaction pathways. Our results clearly demonstrate that this combinatorial method is suitable for epigenetic studies of unsequenced genomes like P. alba (at the time of study), and to identify epigenetic variations related to stress, probably caused by different and changing pedoclimatic conditions, to which the poplar stands have been exposed.
DOI: 10.3390/ijms21197393
PubMed: 33036388
PubMed Central: PMC7582538
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Zambelli", University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA)</wicri:regionArea><wicri:noRegion>84084 Fisciano (SA)</wicri:noRegion></affiliation></author><author><name sortKey="Heinze, Berthold" sort="Heinze, Berthold" uniqKey="Heinze B" first="Berthold" last="Heinze">Berthold Heinze</name><affiliation wicri:level="3"><nlm:affiliation>Department of Forest Genetics, Austrian Federal Research Centre for Forests, 1131 Vienna, Austria.</nlm:affiliation><country xml:lang="fr">Autriche</country><wicri:regionArea>Department of Forest Genetics, Austrian Federal Research Centre for Forests, 1131 Vienna</wicri:regionArea><placeName><region type="land" nuts="2">Vienne (Autriche)</region><settlement type="city">Vienne (Autriche)</settlement></placeName></affiliation></author><author><name sortKey="Castiglione, Stefano" sort="Castiglione, Stefano" uniqKey="Castiglione S" first="Stefano" last="Castiglione">Stefano Castiglione</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA)</wicri:regionArea><wicri:noRegion>84084 Fisciano (SA)</wicri:noRegion></affiliation></author><author><name sortKey="Cicatelli, Angela" sort="Cicatelli, Angela" uniqKey="Cicatelli A" first="Angela" last="Cicatelli">Angela Cicatelli</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA)</wicri:regionArea><wicri:noRegion>84084 Fisciano (SA)</wicri:noRegion></affiliation></author></analytic><series><title level="j">International journal of molecular sciences</title><idno type="eISSN">1422-0067</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Over the last several decades, several lines of evidence have shown that epigenetic modifications modulate phenotype and mediate an organism's response to environmental stimuli. Plant DNA is normally highly methylated, although notable differences exist between species. Many biomolecular techniques based on PCR have been developed to analyse DNA methylation status, however a qualitative leap was made with the advent of next-generation sequencing (NGS). In the case of large, repetitive, or not-yet-sequenced genomes characterised by a high level of DNA methylation, the NGS analysis of bisulphite pre-treated DNA is expensive and time consuming, and moreover, in some cases data analysis is a major challenge. Methylation-sensitive amplification polymorphism (MSAP) analysis is a highly effective method to study DNA methylation. The method is based on the comparison of double DNA digestion profiles (<i>Eco</i>RI-<i>Hpa</i>II and <i>Eco</i>RI-<i>Msp</i>I) to reveal methylation pattern variations. These are often attributable to pedoclimatic and stress conditions which affect all organisms during their lifetime. In our study, five white poplar (<i>Populus alba</i> L.) specimens were collected from different monoclonal stands in the Maltese archipelago, and their DNA was processed by means of an innovative approach where MSAP analysis was followed by NGS. This allowed us to identify genes that were differentially methylated among the different specimens and link them to specific biochemical pathways. Many differentially methylated genes were found to encode transfer RNAs (tRNAs) related to photosynthesis or light reaction pathways. Our results clearly demonstrate that this combinatorial method is suitable for epigenetic studies of unsequenced genomes like <i>P. alba</i> (at the time of study), and to identify epigenetic variations related to stress, probably caused by different and changing pedoclimatic conditions, to which the poplar stands have been exposed.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">33036388</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>30</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1422-0067</ISSN><JournalIssue CitedMedium="Internet"><Volume>21</Volume><Issue>19</Issue><PubDate><Year>2020</Year><Month>Oct</Month><Day>07</Day></PubDate></JournalIssue><Title>International journal of molecular sciences</Title><ISOAbbreviation>Int J Mol Sci</ISOAbbreviation></Journal><ArticleTitle>Epigenetic Analysis through MSAP-NGS Coupled Technology: The Case Study of White Poplar Monoclonal Populations/Stands.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">E7393</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/ijms21197393</ELocationID><Abstract><AbstractText>Over the last several decades, several lines of evidence have shown that epigenetic modifications modulate phenotype and mediate an organism's response to environmental stimuli. Plant DNA is normally highly methylated, although notable differences exist between species. Many biomolecular techniques based on PCR have been developed to analyse DNA methylation status, however a qualitative leap was made with the advent of next-generation sequencing (NGS). In the case of large, repetitive, or not-yet-sequenced genomes characterised by a high level of DNA methylation, the NGS analysis of bisulphite pre-treated DNA is expensive and time consuming, and moreover, in some cases data analysis is a major challenge. Methylation-sensitive amplification polymorphism (MSAP) analysis is a highly effective method to study DNA methylation. The method is based on the comparison of double DNA digestion profiles (<i>Eco</i>RI-<i>Hpa</i>II and <i>Eco</i>RI-<i>Msp</i>I) to reveal methylation pattern variations. These are often attributable to pedoclimatic and stress conditions which affect all organisms during their lifetime. In our study, five white poplar (<i>Populus alba</i> L.) specimens were collected from different monoclonal stands in the Maltese archipelago, and their DNA was processed by means of an innovative approach where MSAP analysis was followed by NGS. This allowed us to identify genes that were differentially methylated among the different specimens and link them to specific biochemical pathways. Many differentially methylated genes were found to encode transfer RNAs (tRNAs) related to photosynthesis or light reaction pathways. Our results clearly demonstrate that this combinatorial method is suitable for epigenetic studies of unsequenced genomes like <i>P. alba</i> (at the time of study), and to identify epigenetic variations related to stress, probably caused by different and changing pedoclimatic conditions, to which the poplar stands have been exposed.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Guarino</LastName><ForeName>Francesco</ForeName><Initials>F</Initials><Identifier Source="ORCID">0000-0001-8536-4257</Identifier><AffiliationInfo><Affiliation>Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Heinze</LastName><ForeName>Berthold</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Forest Genetics, Austrian Federal Research Centre for Forests, 1131 Vienna, Austria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Castiglione</LastName><ForeName>Stefano</ForeName><Initials>S</Initials><Identifier Source="ORCID">0000-0002-0632-4677</Identifier><AffiliationInfo><Affiliation>Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cicatelli</LastName><ForeName>Angela</ForeName><Initials>A</Initials><Identifier Source="ORCID">0000-0001-6996-3495</Identifier><AffiliationInfo><Affiliation>Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>284181</GrantID><Agency>Seventh Framework Programme</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>10</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Int J Mol Sci</MedlineTA><NlmUniqueID>101092791</NlmUniqueID><ISSNLinking>1422-0067</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">MSAP</Keyword><Keyword MajorTopicYN="N">NGS</Keyword><Keyword MajorTopicYN="N">epigenetic</Keyword><Keyword MajorTopicYN="N">methylation</Keyword><Keyword 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IdType="pubmed">12952881</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Autriche</li><li>Italie</li></country><region><li>Vienne (Autriche)</li></region><settlement><li>Vienne (Autriche)</li></settlement></list><tree><country name="Italie"><noRegion><name sortKey="Guarino, Francesco" sort="Guarino, Francesco" uniqKey="Guarino F" first="Francesco" last="Guarino">Francesco Guarino</name></noRegion><name sortKey="Castiglione, Stefano" sort="Castiglione, Stefano" uniqKey="Castiglione S" first="Stefano" last="Castiglione">Stefano Castiglione</name><name sortKey="Cicatelli, Angela" sort="Cicatelli, Angela" uniqKey="Cicatelli A" first="Angela" last="Cicatelli">Angela Cicatelli</name></country><country name="Autriche"><region name="Vienne (Autriche)"><name sortKey="Heinze, Berthold" sort="Heinze, Berthold" uniqKey="Heinze B" first="Berthold" last="Heinze">Berthold Heinze</name></region></country></tree></affiliations></record>Pour 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