Genome-Wide Mapping of in Vivo Protein-DNA Interactions

Johnson, David S.; Mortazavi, Ali; Myers, Richard M.; Wold, Barbara

doi:10.1126/science.1141319

Cited by 2,927Genomics and Chromatin DynamicsChromatin Remodeling and CancerEpigenetics and DNA Methylation

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

Johnson, David S., Mortazavi, Ali, Myers, Richard M., Wold, Barbara·2007·Science

DOI 10.1126/science.1141319

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Abstract

In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. To map these protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ultrahigh-throughput DNA sequencing. This sequence census method was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST, for repressor element–1 silencing transcription factor) to 1946 locations in the human genome. The data display sharp resolution of binding position [±50 base pairs (bp)], which facilitated our finding motifs and allowed us to identify noncanonical NRSF-binding motifs. These ChIPSeq data also have high sensitivity and specificity [ROC (receiver operator characteristic) area ≥ 0.96] and statistical confidence ( P <10 –4 ), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development.

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This locus is within 100 kb of REST, a master negative regulator of neurogenesis.
“this locus is within 100kb of REST, a master negative regulator of neurogenesis163.”
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Authors: Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B.
Affiliations: California Institute of Technology (US)
Corresponding author: Johnson, David S.
Mortazavi, Ali
Myers, Richard M.
Wold, Barbara
ORCID: Johnson, David S.
Mortazavi, Ali
Myers, Richard M.
Wold, Barbara
Venue: Science
Publisher: American Association for the Advancement of Science (AAAS)
Published: 2007-06-08
Volume: 316
Issue: 5830
Pages: 1497-1502
ISSN: 0036-8075 (ISSN-L)
1095-9203
DOI: 10.1126/science.1141319
OpenAlex: W2129795133
Cited by: 2,927
References: 23
Citations by year: 2026: 97 · 2025: 131 · 2024: 124 · 2023: 142 · 2022: 134 · 2021: 144 · 2020: 144 · 2019: 133 · 2018: 141 · 2017: 110 · 2016: 132 · 2015: 178 · 2014: 172 · 2013: 169 · 2012: 192
FWCI: 72.51
Type: journal article
Language: en
Open access: closed
Locations: Science (publishedVersion)
PubMed (publishedVersion)
CaltechAUTHORS (California Institute of Technology) (submittedVersion)
Funders: National Human Genome Research Institute (U01HG003162)
National Institute of General Medical Sciences (T32GM007616)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords: protein-DNA interactions, transcription factor binding sites, rest, NRSF, ChIP-seq, gene regulatory networks, pancreatic islet development, transcriptional repression
MeSH terms: RE1-Silencing Transcription Factor, Algorithms, Binding Sites, DNA, DNA-Binding Proteins, Humans, Synaptic Transmission, Neurons, Promoter Regions, Genetic, Protein Binding, Repressor Proteins, Sensitivity and Specificity, T-Lymphocytes, Transcription Factors, Transcription, Genetic, Genome, Human, Zinc Fingers, Sequence Analysis, DNA, Amino Acid Motifs, MicroRNAs, Chromatin Immunoprecipitation, Insulin-Secreting Cells, Gene Regulatory Networks

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Genome-Wide Mapping of in Vivo Protein-DNA Interactions

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