Mutational interference mapping experiment (MIME) for studying RNA structure and function.
Identifieur interne : 002B10 ( Main/Exploration ); précédent : 002B09; suivant : 002B11Mutational interference mapping experiment (MIME) for studying RNA structure and function.
Auteurs : Redmond P. Smyth [France] ; Laurence Despons [France] ; Gong Huili [République populaire de Chine] ; Serena Bernacchi [France] ; Marcel Hijnen [Australie] ; Johnson Mak [Australie] ; Fabrice Jossinet [France] ; Li Weixi [République populaire de Chine] ; Jean-Christophe Paillart [France] ; Max Von Kleist [Allemagne] ; Roland Marquet [France]Source :
- Nature methods [ 1548-7105 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Protein Precursors, RNA, Viral.
- genetics : Mutation, Protein Precursors, RNA, Viral.
- methods : Mutagenesis, Site-Directed, Sequence Analysis, RNA.
- Base Sequence, Molecular Sequence Data, Structure-Activity Relationship.
Abstract
RNA regulates many biological processes; however, identifying functional RNA sequences and structures is complex and time-consuming. We introduce a method, mutational interference mapping experiment (MIME), to identify, at single-nucleotide resolution, the primary sequence and secondary structures of an RNA molecule that are crucial for its function. MIME is based on random mutagenesis of the RNA target followed by functional selection and next-generation sequencing. Our analytical approach allows the recovery of quantitative binding parameters and permits the identification of base-pairing partners directly from the sequencing data. We used this method to map the binding site of the human immunodeficiency virus-1 (HIV-1) Pr55(Gag) protein on the viral genomic RNA in vitro, and showed that, by analyzing permitted base-pairing patterns, we could model RNA structure motifs that are crucial for protein binding.
DOI: 10.1038/nmeth.3490
PubMed: 26237229
Affiliations:
- Allemagne, Australie, France, République populaire de Chine
- Alsace (région administrative), Berlin, Grand Est, Guangdong
- Berlin, Shenzhen, Strasbourg
- Université de Strasbourg
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France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg</wicri:regionArea><placeName><region type="region">Grand Est</region><region type="old region">Alsace (région administrative)</region><settlement type="city">Strasbourg</settlement><settlement type="city">Strasbourg</settlement></placeName><orgName type="university">Université de Strasbourg</orgName></affiliation></author><author><name sortKey="Von Kleist, Max" sort="Von Kleist, Max" uniqKey="Von Kleist M" first="Max" last="Von Kleist">Max Von Kleist</name><affiliation wicri:level="3"><nlm:affiliation>Department of Mathematics and Computer Science, Freie Universität, Berlin, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Mathematics and Computer Science, Freie Universität, Berlin</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Marquet, Roland" sort="Marquet, Roland" uniqKey="Marquet R" first="Roland" last="Marquet">Roland Marquet</name><affiliation wicri:level="4"><nlm:affiliation>Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg</wicri:regionArea><placeName><region type="region">Grand Est</region><region type="old region">Alsace (région administrative)</region><settlement type="city">Strasbourg</settlement><settlement type="city">Strasbourg</settlement></placeName><orgName type="university">Université de Strasbourg</orgName></affiliation></author></analytic><series><title level="j">Nature methods</title><idno type="eISSN">1548-7105</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Molecular Sequence Data</term><term>Mutagenesis, Site-Directed (methods)</term><term>Mutation (genetics)</term><term>Protein Precursors (chemistry)</term><term>Protein Precursors (genetics)</term><term>RNA, Viral (chemistry)</term><term>RNA, Viral (genetics)</term><term>Sequence Analysis, RNA (methods)</term><term>Structure-Activity Relationship</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral ()</term><term>ARN viral (génétique)</term><term>Analyse de séquence d'ARN ()</term><term>Données de séquences moléculaires</term><term>Mutagenèse dirigée ()</term><term>Mutation (génétique)</term><term>Précurseurs de protéines ()</term><term>Précurseurs de protéines (génétique)</term><term>Relation structure-activité</term><term>Séquence nucléotidique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Protein Precursors</term><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Mutation</term><term>Protein Precursors</term><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN viral</term><term>Mutation</term><term>Précurseurs de protéines</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Mutagenesis, Site-Directed</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Molecular Sequence Data</term><term>Structure-Activity Relationship</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN viral</term><term>Analyse de séquence d'ARN</term><term>Données de séquences moléculaires</term><term>Mutagenèse dirigée</term><term>Précurseurs de protéines</term><term>Relation structure-activité</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">RNA regulates many biological processes; however, identifying functional RNA sequences and structures is complex and time-consuming. We introduce a method, mutational interference mapping experiment (MIME), to identify, at single-nucleotide resolution, the primary sequence and secondary structures of an RNA molecule that are crucial for its function. MIME is based on random mutagenesis of the RNA target followed by functional selection and next-generation sequencing. Our analytical approach allows the recovery of quantitative binding parameters and permits the identification of base-pairing partners directly from the sequencing data. We used this method to map the binding site of the human immunodeficiency virus-1 (HIV-1) Pr55(Gag) protein on the viral genomic RNA in vitro, and showed that, by analyzing permitted base-pairing patterns, we could model RNA structure motifs that are crucial for protein binding.</div></front></TEI><affiliations><list><country><li>Allemagne</li><li>Australie</li><li>France</li><li>République populaire de Chine</li></country><region><li>Alsace (région administrative)</li><li>Berlin</li><li>Grand Est</li><li>Guangdong</li></region><settlement><li>Berlin</li><li>Shenzhen</li><li>Strasbourg</li></settlement><orgName><li>Université de Strasbourg</li></orgName></list><tree><country name="France"><region name="Grand Est"><name sortKey="Smyth, Redmond P" sort="Smyth, Redmond P" uniqKey="Smyth R" first="Redmond P" last="Smyth">Redmond P. Smyth</name></region><name sortKey="Bernacchi, Serena" sort="Bernacchi, Serena" uniqKey="Bernacchi S" first="Serena" last="Bernacchi">Serena Bernacchi</name><name sortKey="Despons, Laurence" sort="Despons, Laurence" uniqKey="Despons L" first="Laurence" last="Despons">Laurence Despons</name><name sortKey="Jossinet, Fabrice" sort="Jossinet, Fabrice" uniqKey="Jossinet F" first="Fabrice" last="Jossinet">Fabrice Jossinet</name><name sortKey="Marquet, Roland" sort="Marquet, Roland" uniqKey="Marquet R" first="Roland" last="Marquet">Roland Marquet</name><name sortKey="Paillart, Jean Christophe" sort="Paillart, Jean Christophe" uniqKey="Paillart J" first="Jean-Christophe" last="Paillart">Jean-Christophe Paillart</name></country><country name="République populaire de Chine"><region name="Guangdong"><name sortKey="Huili, Gong" sort="Huili, Gong" uniqKey="Huili G" first="Gong" last="Huili">Gong Huili</name></region><name sortKey="Weixi, Li" sort="Weixi, Li" uniqKey="Weixi L" first="Li" last="Weixi">Li Weixi</name></country><country name="Australie"><noRegion><name sortKey="Hijnen, Marcel" sort="Hijnen, Marcel" uniqKey="Hijnen M" first="Marcel" last="Hijnen">Marcel Hijnen</name></noRegion><name sortKey="Mak, Johnson" sort="Mak, Johnson" uniqKey="Mak J" first="Johnson" last="Mak">Johnson Mak</name></country><country name="Allemagne"><region name="Berlin"><name sortKey="Von Kleist, Max" sort="Von Kleist, Max" uniqKey="Von Kleist M" first="Max" last="Von Kleist">Max Von Kleist</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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