A toolbox and procedural notes for characterizing novel zinc finger nucleases for genome editing in plant cells.
Identifieur interne : 000663 ( Main/Exploration ); précédent : 000662; suivant : 000664A toolbox and procedural notes for characterizing novel zinc finger nucleases for genome editing in plant cells.
Auteurs : Andriy Tovkach [États-Unis] ; Vardit Zeevi ; Tzvi TzfiraSource :
- The Plant journal : for cell and molecular biology [ 1365-313X ] ; 2009.
Descripteurs français
- KwdFr :
- ADN bactérien (métabolisme), ADN des plantes (métabolisme), Arabidopsis (génétique), Cassures double-brin de l'ADN (MeSH), Doigts de zinc (MeSH), Endonucleases (génétique), Endonucleases (métabolisme), Génome végétal (MeSH), Ingénierie des protéines (méthodes), Mutagenèse dirigée (MeSH), Réparation de l'ADN (MeSH), Transformation génétique (MeSH), Vecteurs génétiques (MeSH), Végétaux génétiquement modifiés (génétique).
- MESH :
- génétique : Arabidopsis, Endonucleases, Végétaux génétiquement modifiés.
- métabolisme : ADN bactérien, ADN des plantes, Endonucleases.
- méthodes : Ingénierie des protéines.
- Cassures double-brin de l'ADN, Doigts de zinc, Génome végétal, Mutagenèse dirigée, Réparation de l'ADN, Transformation génétique, Vecteurs génétiques.
English descriptors
- KwdEn :
- Arabidopsis (genetics), DNA Breaks, Double-Stranded (MeSH), DNA Repair (MeSH), DNA, Bacterial (metabolism), DNA, Plant (metabolism), Endonucleases (genetics), Endonucleases (metabolism), Genetic Vectors (MeSH), Genome, Plant (MeSH), Mutagenesis, Site-Directed (MeSH), Plants, Genetically Modified (genetics), Protein Engineering (methods), Transformation, Genetic (MeSH), Zinc Fingers (MeSH).
- MESH :
- chemical , genetics : Endonucleases.
- chemical , metabolism : DNA, Bacterial, DNA, Plant, Endonucleases.
- genetics : Arabidopsis, Plants, Genetically Modified.
- methods : Protein Engineering.
- DNA Breaks, Double-Stranded, DNA Repair, Genetic Vectors, Genome, Plant, Mutagenesis, Site-Directed, Transformation, Genetic, Zinc Fingers.
Abstract
The induction of double-strand breaks (DSBs) in plant genomes can lead to increased homologous recombination or site-specific mutagenesis at the repair site. This phenomenon has the potential for use in gene targeting applications in plant cells upon the induction of site-specific genomic DSBs using zinc finger nucleases (ZFNs). Zinc finger nucleases are artificial restriction enzymes, custom-designed to cleave a specific DNA sequence. The tools and methods for ZFN assembly and validation could potentially boost their application for plant gene targeting. Here we report on the design of biochemical and in planta methods for the analysis of newly designed ZFNs. Cloning begins with de novo assembly of the DNA-binding regions of new ZFNs from overlapping oligonucleotides containing modified helices responsible for DNA-triplet recognition, and the fusion of the DNA-binding domain with a FokI endonuclease domain in a dedicated plant expression cassette. Following the transfer of fully assembled ZFNs into Escherichia coli expression vectors, bacterial lysates were found to be most suitable for in vitro digestion analysis of palindromic target sequences. A set of three in planta activity assays was also developed to confirm the nucleic acid digestion activity of ZFNs in plant cells. The assays are based on the reconstruction of GUS expression following transient or stable delivery of a mutated uidA and ZFN-expressing cassettes into target plants cells. Our tools and assays offer cloning flexibility and simple assembly of tested ZFNs and their corresponding target sites into Agrobacterium tumefaciens binary plasmids, allowing efficient implementation of ZFN-validation assays in planta.
DOI: 10.1111/j.1365-313X.2008.03718.x
PubMed: 18980651
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109</wicri:regionArea><placeName><region type="state">Michigan</region></placeName></affiliation></author><author><name sortKey="Zeevi, Vardit" sort="Zeevi, Vardit" uniqKey="Zeevi V" first="Vardit" last="Zeevi">Vardit Zeevi</name></author><author><name sortKey="Tzfira, Tzvi" sort="Tzfira, Tzvi" uniqKey="Tzfira T" first="Tzvi" last="Tzfira">Tzvi Tzfira</name></author></analytic><series><title level="j">The Plant journal : for cell and molecular biology</title><idno type="eISSN">1365-313X</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>DNA Breaks, Double-Stranded (MeSH)</term><term>DNA Repair (MeSH)</term><term>DNA, Bacterial (metabolism)</term><term>DNA, Plant (metabolism)</term><term>Endonucleases (genetics)</term><term>Endonucleases (metabolism)</term><term>Genetic Vectors (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Mutagenesis, Site-Directed (MeSH)</term><term>Plants, Genetically Modified (genetics)</term><term>Protein Engineering (methods)</term><term>Transformation, Genetic (MeSH)</term><term>Zinc Fingers (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN bactérien (métabolisme)</term><term>ADN des plantes (métabolisme)</term><term>Arabidopsis (génétique)</term><term>Cassures double-brin de l'ADN (MeSH)</term><term>Doigts de zinc (MeSH)</term><term>Endonucleases (génétique)</term><term>Endonucleases (métabolisme)</term><term>Génome végétal (MeSH)</term><term>Ingénierie des protéines (méthodes)</term><term>Mutagenèse dirigée (MeSH)</term><term>Réparation de l'ADN (MeSH)</term><term>Transformation génétique (MeSH)</term><term>Vecteurs génétiques (MeSH)</term><term>Végétaux génétiquement modifiés (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Endonucleases</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA, Bacterial</term><term>DNA, Plant</term><term>Endonucleases</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Plants, Genetically Modified</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Endonucleases</term><term>Végétaux génétiquement modifiés</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Protein Engineering</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN bactérien</term><term>ADN des plantes</term><term>Endonucleases</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Ingénierie des protéines</term></keywords><keywords scheme="MESH" xml:lang="en"><term>DNA Breaks, Double-Stranded</term><term>DNA Repair</term><term>Genetic Vectors</term><term>Genome, Plant</term><term>Mutagenesis, Site-Directed</term><term>Transformation, Genetic</term><term>Zinc Fingers</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cassures double-brin de l'ADN</term><term>Doigts de zinc</term><term>Génome végétal</term><term>Mutagenèse dirigée</term><term>Réparation de l'ADN</term><term>Transformation génétique</term><term>Vecteurs génétiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The induction of double-strand breaks (DSBs) in plant genomes can lead to increased homologous recombination or site-specific mutagenesis at the repair site. This phenomenon has the potential for use in gene targeting applications in plant cells upon the induction of site-specific genomic DSBs using zinc finger nucleases (ZFNs). Zinc finger nucleases are artificial restriction enzymes, custom-designed to cleave a specific DNA sequence. The tools and methods for ZFN assembly and validation could potentially boost their application for plant gene targeting. Here we report on the design of biochemical and in planta methods for the analysis of newly designed ZFNs. Cloning begins with de novo assembly of the DNA-binding regions of new ZFNs from overlapping oligonucleotides containing modified helices responsible for DNA-triplet recognition, and the fusion of the DNA-binding domain with a FokI endonuclease domain in a dedicated plant expression cassette. Following the transfer of fully assembled ZFNs into Escherichia coli expression vectors, bacterial lysates were found to be most suitable for in vitro digestion analysis of palindromic target sequences. A set of three in planta activity assays was also developed to confirm the nucleic acid digestion activity of ZFNs in plant cells. The assays are based on the reconstruction of GUS expression following transient or stable delivery of a mutated uidA and ZFN-expressing cassettes into target plants cells. Our tools and assays offer cloning flexibility and simple assembly of tested ZFNs and their corresponding target sites into Agrobacterium tumefaciens binary plasmids, allowing efficient implementation of ZFN-validation assays in planta.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18980651</PMID><DateCompleted><Year>2009</Year><Month>02</Month><Day>27</Day></DateCompleted><DateRevised><Year>2009</Year><Month>02</Month><Day>17</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-313X</ISSN><JournalIssue CitedMedium="Internet"><Volume>57</Volume><Issue>4</Issue><PubDate><Year>2009</Year><Month>Feb</Month></PubDate></JournalIssue><Title>The Plant journal : for cell and molecular biology</Title><ISOAbbreviation>Plant J</ISOAbbreviation></Journal><ArticleTitle>A toolbox and procedural notes for characterizing novel zinc finger nucleases for genome editing in plant cells.</ArticleTitle><Pagination><MedlinePgn>747-57</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/j.1365-313X.2008.03718.x</ELocationID><Abstract><AbstractText>The induction of double-strand breaks (DSBs) in plant genomes can lead to increased homologous recombination or site-specific mutagenesis at the repair site. This phenomenon has the potential for use in gene targeting applications in plant cells upon the induction of site-specific genomic DSBs using zinc finger nucleases (ZFNs). Zinc finger nucleases are artificial restriction enzymes, custom-designed to cleave a specific DNA sequence. The tools and methods for ZFN assembly and validation could potentially boost their application for plant gene targeting. Here we report on the design of biochemical and in planta methods for the analysis of newly designed ZFNs. Cloning begins with de novo assembly of the DNA-binding regions of new ZFNs from overlapping oligonucleotides containing modified helices responsible for DNA-triplet recognition, and the fusion of the DNA-binding domain with a FokI endonuclease domain in a dedicated plant expression cassette. Following the transfer of fully assembled ZFNs into Escherichia coli expression vectors, bacterial lysates were found to be most suitable for in vitro digestion analysis of palindromic target sequences. A set of three in planta activity assays was also developed to confirm the nucleic acid digestion activity of ZFNs in plant cells. The assays are based on the reconstruction of GUS expression following transient or stable delivery of a mutated uidA and ZFN-expressing cassettes into target plants cells. Our tools and assays offer cloning flexibility and simple assembly of tested ZFNs and their corresponding target sites into Agrobacterium tumefaciens binary plasmids, allowing efficient implementation of ZFN-validation assays in planta.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tovkach</LastName><ForeName>Andriy</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zeevi</LastName><ForeName>Vardit</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Tzfira</LastName><ForeName>Tzvi</ForeName><Initials>T</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. 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PubStatus="medline"><Year>2009</Year><Month>2</Month><Day>28</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2008</Year><Month>11</Month><Day>5</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">18980651</ArticleId><ArticleId IdType="pii">TPJ3718</ArticleId><ArticleId IdType="doi">10.1111/j.1365-313X.2008.03718.x</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Michigan</li></region></list><tree><noCountry><name sortKey="Tzfira, Tzvi" sort="Tzfira, Tzvi" uniqKey="Tzfira T" first="Tzvi" last="Tzfira">Tzvi Tzfira</name><name sortKey="Zeevi, Vardit" sort="Zeevi, Vardit" uniqKey="Zeevi V" first="Vardit" last="Zeevi">Vardit Zeevi</name></noCountry><country name="États-Unis"><region name="Michigan"><name sortKey="Tovkach, Andriy" sort="Tovkach, Andriy" uniqKey="Tovkach A" first="Andriy" last="Tovkach">Andriy Tovkach</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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