A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design
Identifieur interne : 002070 ( Main/Exploration ); précédent : 002069; suivant : 002071A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design
Auteurs : Robin P. Smith [États-Unis] ; Samantha J. Riesenfeld [États-Unis] ; Alisha K. Holloway [États-Unis] ; Qiang Li [États-Unis, République populaire de Chine] ; Karl K. Murphy [États-Unis] ; Natalie M. Feliciano [États-Unis] ; Lorenzo Orecchia [États-Unis] ; Nir Oksenberg [États-Unis] ; Katherine S. Pollard [États-Unis] ; Nadav Ahituv [États-Unis]Source :
- Genome Biology [ 1465-6906 ] ; 2013.
Descripteurs français
- KwdFr :
- Animaux, Biologie synthétique (), Danio zébré (embryologie), Danio zébré (génétique), Dissection, Données de séquences moléculaires, Embryon non mammalien (métabolisme), Gene Ontology, Motifs nucléotidiques (génétique), Oligonucléotides (génétique), Régulation de l'expression des gènes au cours du développement, Spécificité d'organe (génétique), Séquence nucléotidique, Séquences d'acides nucléiques régulatrices (génétique), Éléments activateurs (génétique).
- MESH :
- embryologie : Danio zébré.
- génétique : Danio zébré, Motifs nucléotidiques, Oligonucléotides, Spécificité d'organe, Séquences d'acides nucléiques régulatrices.
- métabolisme : Embryon non mammalien.
- Animaux, Biologie synthétique, Dissection, Données de séquences moléculaires, Gene Ontology, Régulation de l'expression des gènes au cours du développement, Séquence nucléotidique, Éléments activateurs (génétique).
English descriptors
- KwdEn :
- Animals, Base Sequence, Dissection, Embryo, Nonmammalian (metabolism), Enhancer Elements, Genetic, Gene Expression Regulation, Developmental, Gene Ontology, Molecular Sequence Data, Nucleotide Motifs (genetics), Oligonucleotides (genetics), Organ Specificity (genetics), Regulatory Sequences, Nucleic Acid (genetics), Synthetic Biology (methods), Zebrafish (embryology), Zebrafish (genetics).
- MESH :
- chemical , genetics : Oligonucleotides.
- embryology : Zebrafish.
- genetics : Nucleotide Motifs, Organ Specificity, Regulatory Sequences, Nucleic Acid, Zebrafish.
- metabolism : Embryo, Nonmammalian.
- methods : Synthetic Biology.
- Animals, Base Sequence, Dissection, Enhancer Elements, Genetic, Gene Expression Regulation, Developmental, Gene Ontology, Molecular Sequence Data.
Abstract
Large-scale annotation efforts have improved our ability to coarsely predict regulatory elements throughout vertebrate genomes. However, it is unclear how complex spatiotemporal patterns of gene expression driven by these elements emerge from the activity of short, transcription factor binding sequences.
We describe a comprehensive promoter extension assay in which the regulatory potential of all 6 base-pair (bp) sequences was tested in the context of a minimal promoter. To enable this large-scale screen, we developed algorithms that use a reverse-complement aware decomposition of the de Bruijn graph to design a library of DNA oligomers incorporating every 6-bp sequence exactly once. Our library multiplexes all 4,096 unique 6-mers into 184 double-stranded 15-bp oligomers, which is sufficiently compact for
This work introduces a unique
Url:
DOI: 10.1186/gb-2013-14-7-r72
PubMed: 23867016
PubMed Central: 4054837
Affiliations:
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Le document en format XML
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Smith</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Riesenfeld, Samantha J" sort="Riesenfeld, Samantha J" uniqKey="Riesenfeld S" first="Samantha J" last="Riesenfeld">Samantha J. Riesenfeld</name><affiliation wicri:level="2"><nlm:aff id="I3">Gladstone Institutes, University of California San Francisco, 1650 Owens St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Gladstone Institutes, University of California San Francisco, 1650 Owens St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Holloway, Alisha K" sort="Holloway, Alisha K" uniqKey="Holloway A" first="Alisha K" last="Holloway">Alisha K. Holloway</name><affiliation wicri:level="2"><nlm:aff id="I3">Gladstone Institutes, University of California San Francisco, 1650 Owens St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Gladstone Institutes, University of California San Francisco, 1650 Owens St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Li, Qiang" sort="Li, Qiang" uniqKey="Li Q" first="Qiang" last="Li">Qiang Li</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="I6">Current address: Institute for Pediatrics, Translational Research Center for Development and Disease, Children's Hospital of Fudan University, Shanghai, 201102, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Current address: Institute for Pediatrics, Translational Research Center for Development and Disease, Children's Hospital of Fudan University, Shanghai, 201102</wicri:regionArea><wicri:noRegion>201102</wicri:noRegion></affiliation></author><author><name sortKey="Murphy, Karl K" sort="Murphy, Karl K" uniqKey="Murphy K" first="Karl K" last="Murphy">Karl K. Murphy</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Feliciano, Natalie M" sort="Feliciano, Natalie M" uniqKey="Feliciano N" first="Natalie M" last="Feliciano">Natalie M. Feliciano</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Orecchia, Lorenzo" sort="Orecchia, Lorenzo" uniqKey="Orecchia L" first="Lorenzo" last="Orecchia">Lorenzo Orecchia</name><affiliation wicri:level="2"><nlm:aff id="I4">Division of Biostatistics, University of California San Francisco, 1650 Owens St, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Biostatistics, University of California San Francisco, 1650 Owens St, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Oksenberg, Nir" sort="Oksenberg, Nir" uniqKey="Oksenberg N" first="Nir" last="Oksenberg">Nir Oksenberg</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Pollard, Katherine S" sort="Pollard, Katherine S" uniqKey="Pollard K" first="Katherine S" last="Pollard">Katherine S. Pollard</name><affiliation wicri:level="2"><nlm:aff id="I2">Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Gladstone Institutes, University of California San Francisco, 1650 Owens St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Gladstone Institutes, University of California San Francisco, 1650 Owens St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I5">Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Ahituv, Nadav" sort="Ahituv, Nadav" uniqKey="Ahituv N" first="Nadav" last="Ahituv">Nadav Ahituv</name><affiliation wicri:level="2"><nlm:aff id="I1">Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author></analytic><series><title level="j">Genome Biology</title><idno type="ISSN">1465-6906</idno><idno type="eISSN">1465-6914</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Dissection</term><term>Embryo, Nonmammalian (metabolism)</term><term>Enhancer Elements, Genetic</term><term>Gene Expression Regulation, Developmental</term><term>Gene Ontology</term><term>Molecular Sequence Data</term><term>Nucleotide Motifs (genetics)</term><term>Oligonucleotides (genetics)</term><term>Organ Specificity (genetics)</term><term>Regulatory Sequences, Nucleic Acid (genetics)</term><term>Synthetic Biology (methods)</term><term>Zebrafish (embryology)</term><term>Zebrafish (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Biologie synthétique ()</term><term>Danio zébré (embryologie)</term><term>Danio zébré (génétique)</term><term>Dissection</term><term>Données de séquences moléculaires</term><term>Embryon non mammalien (métabolisme)</term><term>Gene Ontology</term><term>Motifs nucléotidiques (génétique)</term><term>Oligonucléotides (génétique)</term><term>Régulation de l'expression des gènes au cours du développement</term><term>Spécificité d'organe (génétique)</term><term>Séquence nucléotidique</term><term>Séquences d'acides nucléiques régulatrices (génétique)</term><term>Éléments activateurs (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Oligonucleotides</term></keywords><keywords scheme="MESH" qualifier="embryologie" xml:lang="fr"><term>Danio zébré</term></keywords><keywords scheme="MESH" qualifier="embryology" xml:lang="en"><term>Zebrafish</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Nucleotide Motifs</term><term>Organ Specificity</term><term>Regulatory Sequences, Nucleic Acid</term><term>Zebrafish</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Danio zébré</term><term>Motifs nucléotidiques</term><term>Oligonucléotides</term><term>Spécificité d'organe</term><term>Séquences d'acides nucléiques régulatrices</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Embryo, Nonmammalian</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Synthetic Biology</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Embryon non mammalien</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Dissection</term><term>Enhancer Elements, Genetic</term><term>Gene Expression Regulation, Developmental</term><term>Gene Ontology</term><term>Molecular Sequence Data</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Biologie synthétique</term><term>Dissection</term><term>Données de séquences moléculaires</term><term>Gene Ontology</term><term>Régulation de l'expression des gènes au cours du développement</term><term>Séquence nucléotidique</term><term>Éléments activateurs (génétique)</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Large-scale annotation efforts have improved our ability to coarsely predict regulatory elements throughout vertebrate genomes. However, it is unclear how complex spatiotemporal patterns of gene expression driven by these elements emerge from the activity of short, transcription factor binding sequences.</p></sec><sec><title>Results</title><p>We describe a comprehensive promoter extension assay in which the regulatory potential of all 6 base-pair (bp) sequences was tested in the context of a minimal promoter. To enable this large-scale screen, we developed algorithms that use a reverse-complement aware decomposition of the de Bruijn graph to design a library of DNA oligomers incorporating every 6-bp sequence exactly once. Our library multiplexes all 4,096 unique 6-mers into 184 double-stranded 15-bp oligomers, which is sufficiently compact for <italic>in vivo </italic>testing. We injected each multiplexed construct into zebrafish embryos and scored GFP expression in 15 tissues at two developmental time points. Twenty-seven constructs produced consistent expression patterns, with the majority doing so in only one tissue. Functional sequences are enriched near biologically relevant genes, match motifs for developmental transcription factors, and are required for enhancer activity. By concatenating tissue-specific functional sequences, we generated completely synthetic enhancers for the notochord, epidermis, spinal cord, forebrain and otic lateral line, and show that short regulatory sequences do not always function modularly.</p></sec><sec><title>Conclusions</title><p>This work introduces a unique <italic>in vivo </italic>catalog of short, functional regulatory sequences and demonstrates several important principles of regulatory element organization. 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name="États-Unis"><region name="Californie"><name sortKey="Smith, Robin P" sort="Smith, Robin P" uniqKey="Smith R" first="Robin P" last="Smith">Robin P. Smith</name></region><name sortKey="Ahituv, Nadav" sort="Ahituv, Nadav" uniqKey="Ahituv N" first="Nadav" last="Ahituv">Nadav Ahituv</name><name sortKey="Ahituv, Nadav" sort="Ahituv, Nadav" uniqKey="Ahituv N" first="Nadav" last="Ahituv">Nadav Ahituv</name><name sortKey="Feliciano, Natalie M" sort="Feliciano, Natalie M" uniqKey="Feliciano N" first="Natalie M" last="Feliciano">Natalie M. Feliciano</name><name sortKey="Feliciano, Natalie M" sort="Feliciano, Natalie M" uniqKey="Feliciano N" first="Natalie M" last="Feliciano">Natalie M. Feliciano</name><name sortKey="Holloway, Alisha K" sort="Holloway, Alisha K" uniqKey="Holloway A" first="Alisha K" last="Holloway">Alisha K. Holloway</name><name sortKey="Li, Qiang" sort="Li, Qiang" uniqKey="Li Q" first="Qiang" last="Li">Qiang Li</name><name sortKey="Li, Qiang" sort="Li, Qiang" uniqKey="Li Q" first="Qiang" last="Li">Qiang Li</name><name sortKey="Murphy, Karl K" sort="Murphy, Karl K" uniqKey="Murphy K" first="Karl K" last="Murphy">Karl K. Murphy</name><name sortKey="Murphy, Karl K" sort="Murphy, Karl K" uniqKey="Murphy K" first="Karl K" last="Murphy">Karl K. Murphy</name><name sortKey="Oksenberg, Nir" sort="Oksenberg, Nir" uniqKey="Oksenberg N" first="Nir" last="Oksenberg">Nir Oksenberg</name><name sortKey="Oksenberg, Nir" sort="Oksenberg, Nir" uniqKey="Oksenberg N" first="Nir" last="Oksenberg">Nir Oksenberg</name><name sortKey="Orecchia, Lorenzo" sort="Orecchia, Lorenzo" uniqKey="Orecchia L" first="Lorenzo" last="Orecchia">Lorenzo Orecchia</name><name sortKey="Pollard, Katherine S" sort="Pollard, Katherine S" uniqKey="Pollard K" first="Katherine S" last="Pollard">Katherine S. Pollard</name><name sortKey="Pollard, Katherine S" sort="Pollard, Katherine S" uniqKey="Pollard K" first="Katherine S" last="Pollard">Katherine S. Pollard</name><name sortKey="Pollard, Katherine S" sort="Pollard, Katherine S" uniqKey="Pollard K" first="Katherine S" last="Pollard">Katherine S. Pollard</name><name sortKey="Riesenfeld, Samantha J" sort="Riesenfeld, Samantha J" uniqKey="Riesenfeld S" first="Samantha J" last="Riesenfeld">Samantha J. Riesenfeld</name><name sortKey="Smith, Robin P" sort="Smith, Robin P" uniqKey="Smith R" first="Robin P" last="Smith">Robin P. Smith</name></country><country name="République populaire de Chine"><noRegion><name sortKey="Li, Qiang" sort="Li, Qiang" uniqKey="Li Q" first="Qiang" last="Li">Qiang Li</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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}}
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HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:23867016" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |