MersV1, PubMed, Curation, bibRecord, 001824

Sequence specificity incompletely defines the genome-wide occupancy of Myc.

Identifieur interne : 001824 ( PubMed/Curation ); précédent : 001823; suivant : 001825

Sequence specificity incompletely defines the genome-wide occupancy of Myc.

Auteurs : Jiannan Guo [États-Unis] ; Tiandao Li ; Joshua Schipper ; Kyle A. Nilson ; Francis K. Fordjour ; Jeffrey J. Cooper ; Raluca Gordân ; David H. Price

Source :

Genome biology [ 1474-760X ] ; 2014.

RBID : pubmed:25287278

Descripteurs français

English descriptors

KwdEn :
- Basic Helix-Loop-Helix Leucine Zipper Transcription Factors (chemistry), Basic Helix-Loop-Helix Leucine Zipper Transcription Factors (metabolism), Basic Helix-Loop-Helix Leucine Zipper Transcription Factors (physiology), Chromatin Immunoprecipitation, E-Box Elements, Electrophoretic Mobility Shift Assay, Genome, Human, Humans, Promoter Regions, Genetic, Proto-Oncogene Proteins c-myc (chemistry), Proto-Oncogene Proteins c-myc (metabolism), Proto-Oncogene Proteins c-myc (physiology), RNA Polymerase II (metabolism), RNA Polymerase II (physiology), Sequence Analysis, DNA, Transcription, Genetic (physiology).
MESH :
- chemical , chemistry : Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Proto-Oncogene Proteins c-myc.
- chemical , metabolism : Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Proto-Oncogene Proteins c-myc, RNA Polymerase II.
- chemical , physiology : Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Proto-Oncogene Proteins c-myc, RNA Polymerase II.
- physiology : Transcription, Genetic.
- Chromatin Immunoprecipitation, E-Box Elements, Electrophoretic Mobility Shift Assay, Genome, Human, Humans, Promoter Regions, Genetic, Sequence Analysis, DNA.

Abstract

The Myc-Max heterodimer is a transcription factor that regulates expression of a large number of genes. Genome occupancy of Myc-Max is thought to be driven by Enhancer box (E-box) DNA elements, CACGTG or variants, to which the heterodimer binds in vitro.

DOI: 10.1186/s13059-014-0482-3
PubMed: 25287278

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Le document en format XML

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<term>Basic Helix-Loop-Helix Leucine Zipper Transcription Factors (physiology)</term>
<term>Chromatin Immunoprecipitation</term>
<term>E-Box Elements</term>
<term>Electrophoretic Mobility Shift Assay</term>
<term>Genome, Human</term>
<term>Humans</term>
<term>Promoter Regions, Genetic</term>
<term>Proto-Oncogene Proteins c-myc (chemistry)</term>
<term>Proto-Oncogene Proteins c-myc (metabolism)</term>
<term>Proto-Oncogene Proteins c-myc (physiology)</term>
<term>RNA Polymerase II (metabolism)</term>
<term>RNA Polymerase II (physiology)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Facteurs de transcription à motifs basiques hélice-boucle-hélice et à glissière à leucines ()</term>
<term>Facteurs de transcription à motifs basiques hélice-boucle-hélice et à glissière à leucines (métabolisme)</term>
<term>Facteurs de transcription à motifs basiques hélice-boucle-hélice et à glissière à leucines (physiologie)</term>
<term>Génome humain</term>
<term>Humains</term>
<term>Immunoprécipitation de la chromatine</term>
<term>Protéines proto-oncogènes c-myc ()</term>
<term>Protéines proto-oncogènes c-myc (métabolisme)</term>
<term>Protéines proto-oncogènes c-myc (physiologie)</term>
<term>RNA polymerase II (métabolisme)</term>
<term>RNA polymerase II (physiologie)</term>
<term>Régions promotrices (génétique)</term>
<term>Test de retard de migration électrophorétique</term>
<term>Transcription génétique (physiologie)</term>
<term>Éléments E-box</term>
</keywords>
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<term>Proto-Oncogene Proteins c-myc</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Basic Helix-Loop-Helix Leucine Zipper Transcription Factors</term>
<term>Proto-Oncogene Proteins c-myc</term>
<term>RNA Polymerase II</term>
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<keywords scheme="MESH" type="chemical" qualifier="physiology" xml:lang="en"><term>Basic Helix-Loop-Helix Leucine Zipper Transcription Factors</term>
<term>Proto-Oncogene Proteins c-myc</term>
<term>RNA Polymerase II</term>
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<term>Protéines proto-oncogènes c-myc</term>
<term>RNA polymerase II</term>
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<term>RNA polymerase II</term>
<term>Transcription génétique</term>
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</keywords>
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<term>E-Box Elements</term>
<term>Electrophoretic Mobility Shift Assay</term>
<term>Genome, Human</term>
<term>Humans</term>
<term>Promoter Regions, Genetic</term>
<term>Sequence Analysis, DNA</term>
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<term>Facteurs de transcription à motifs basiques hélice-boucle-hélice et à glissière à leucines</term>
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<term>Humains</term>
<term>Immunoprécipitation de la chromatine</term>
<term>Protéines proto-oncogènes c-myc</term>
<term>Régions promotrices (génétique)</term>
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<front><div type="abstract" xml:lang="en">The Myc-Max heterodimer is a transcription factor that regulates expression of a large number of genes. Genome occupancy of Myc-Max is thought to be driven by Enhancer box (E-box) DNA elements, CACGTG or variants, to which the heterodimer binds in vitro.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25287278</PMID>
<DateCompleted><Year>2015</Year>
<Month>10</Month>
<Day>26</Day>
</DateCompleted>
<DateRevised><Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
</DateRevised>
<Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1474-760X</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>15</Volume>
<Issue>10</Issue>
<PubDate><Year>2014</Year>
</PubDate>
</JournalIssue>
<Title>Genome biology</Title>
<ISOAbbreviation>Genome Biol.</ISOAbbreviation>
</Journal>
<ArticleTitle>Sequence specificity incompletely defines the  genome-wide occupancy of Myc.</ArticleTitle>
<Pagination><MedlinePgn>482</MedlinePgn>
</Pagination>
<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The Myc-Max heterodimer is a transcription factor that regulates expression of a large number of genes. Genome occupancy of Myc-Max is thought to be driven by Enhancer box (E-box) DNA elements, CACGTG or variants, to which the heterodimer binds in vitro.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">By analyzing ChIP-Seq datasets, we demonstrate that the positions occupied by Myc-Max across the human genome correlate with the RNA polymerase II, Pol II, transcription machinery significantly better than with E-boxes. Metagene analyses show that in promoter regions, Myc is uniformly positioned about 100 bp upstream of essentially all promoter proximal paused polymerases with Max about 15 bp upstream of Myc. We re-evaluate the DNA binding properties of full length Myc-Max proteins. Electrophoretic mobility shift assay results demonstrate Myc-Max heterodimers display significant sequence preference, but have high affinity for any DNA. Quantification of the relative affinities of Myc-Max for all possible 8-mers using universal protein-binding microarray assays shows that sequences surrounding core 6-mers significantly affect binding. Compared to the in vitro sequence preferences,Myc-Max genomic occupancy measured by ChIP-Seq is largely, although not completely, independent of sequence specificity.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">We quantified the affinity of Myc-Max to all possible 8-mers and compared this with the sites of Myc binding across the human genome. Our results indicate that the genomic occupancy of Myc cannot be explained by its intrinsic DNA specificity and suggest that the transcription machinery and associated promoter accessibility play a predominant role in Myc recruitment.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Guo</LastName>
<ForeName>Jiannan</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Li</LastName>
<ForeName>Tiandao</ForeName>
<Initials>T</Initials>
</Author>
<Author ValidYN="Y"><LastName>Schipper</LastName>
<ForeName>Joshua</ForeName>
<Initials>J</Initials>
</Author>
<Author ValidYN="Y"><LastName>Nilson</LastName>
<ForeName>Kyle A</ForeName>
<Initials>KA</Initials>
</Author>
<Author ValidYN="Y"><LastName>Fordjour</LastName>
<ForeName>Francis K</ForeName>
<Initials>FK</Initials>
</Author>
<Author ValidYN="Y"><LastName>Cooper</LastName>
<ForeName>Jeffrey J</ForeName>
<Initials>JJ</Initials>
</Author>
<Author ValidYN="Y"><LastName>Gordân</LastName>
<ForeName>Raluca</ForeName>
<Initials>R</Initials>
</Author>
<Author ValidYN="Y"><LastName>Price</LastName>
<ForeName>David H</ForeName>
<Initials>DH</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<GrantList CompleteYN="Y"><Grant><GrantID>R01 GM035500</GrantID>
<Acronym>GM</Acronym>
<Agency>NIGMS NIH HHS</Agency>
<Country>United States</Country>
</Grant>
<Grant><GrantID>GM35500</GrantID>
<Acronym>GM</Acronym>
<Agency>NIGMS NIH HHS</Agency>
<Country>United States</Country>
</Grant>
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<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Genome Biol</MedlineTA>
<NlmUniqueID>100960660</NlmUniqueID>
<ISSNLinking>1474-7596</ISSNLinking>
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<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D051778">Basic Helix-Loop-Helix Leucine Zipper Transcription Factors</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="C499330">MAX protein, human</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D016271">Proto-Oncogene Proteins c-myc</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>EC 2.7.7.-</RegistryNumber>
<NameOfSubstance UI="D012319">RNA Polymerase II</NameOfSubstance>
</Chemical>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D051778" MajorTopicYN="N">Basic Helix-Loop-Helix Leucine Zipper Transcription Factors</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
<QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D047369" MajorTopicYN="N">Chromatin Immunoprecipitation</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D024721" MajorTopicYN="Y">E-Box Elements</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D024202" MajorTopicYN="N">Electrophoretic Mobility Shift Assay</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D015894" MajorTopicYN="Y">Genome, Human</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D011401" MajorTopicYN="N">Promoter Regions, Genetic</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016271" MajorTopicYN="N">Proto-Oncogene Proteins c-myc</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
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<MeshHeading><DescriptorName UI="D012319" MajorTopicYN="N">RNA Polymerase II</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
<QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D014158" MajorTopicYN="N">Transcription, Genetic</DescriptorName>
<QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName>
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Sequence specificity incompletely defines the genome-wide occupancy of Myc.

Sequence specificity incompletely defines the genome-wide occupancy of Myc.

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