DIP-chip: rapid and accurate determination of DNA-binding specificity.

We have developed a new method for determining the DNA-binding specificity of proteins. In DIP-chip (DNA immunoprecipitation with microarray detection), protein.DNA complexes are isolated from an in vitro mixture of purified protein and naked genomic DNA. Whole-genome DNA microarrays are used to identify the protein-bound DNA fragments, and the sequence of the identified fragments is used to derive binding-site descriptions. Using objective criteria for assessing the accuracy of DNA-binding motifs, and using yeast Leu3p as a model, we demonstrate that motifs determined by DIP-chip are as effective at predicting the location of bound proteins in vivo as are motifs determined by conventional low-throughput in vitro methods.

• Publication year

  2005

• Venue

  Genome Research

• Publication date

  2005-03-01

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1101/GR.3256505PMID 15710749PMCID PMC551568
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Leucine Biosynthesis in Fungi: Entering Metabolism through the Back Door

  2003cited by this paper
• Rank order metrics for quantifying the association of sequence features with gene regulation

  2003cited by this paper
• High-throughput SELEX–SAGE method for quantitative modeling of transcription-factor binding sites

  2002cited by this paper
• An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments

  2002influential reference
• Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities.

  2002influential reference
• Exploring the DNA-binding specificities of zinc fingers with DNA microarrays

  2001cited by this paper
• Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA association

  2001influential reference
• Genome-wide location and function of DNA binding proteins.

  2000cited by this paper
• BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes

  2000cited by this paper
• Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles.

  2000cited by this paper
• Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR‐mediated gene disruption and other applications

  1998cited by this paper
• Specificity, free energy and information content in protein-DNA interactions.

  1998influential reference
• Controlling the false discovery rate: a practical and powerful approach to multiple testing

  1995cited by this paper
• Alternative splicing of human cyclin E.

  1994cited by this paper
• Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.

  1990influential reference
• Sequence logos: a new way to display consensus sequences.

  1990cited by this paper
• Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein

  1989cited by this paper
• A Leisurely Look at the Bootstrap, the Jackknife, and

  1983cited by this paper
• The meaning and use of the area under a receiver operating characteristic (ROC) curve.

  1982cited by this paper
• Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis.

  1981cited by this paper

• Footprint-seq: a simple method to quantitatively map in vitro protein-DNA interactions on a genome-wide scale at high spatial resolution

  2026cites this paper
• PPRTGI: A Personalized PageRank Graph Neural Network for TF-Target Gene Interaction Detection

  2024cites this paper
• Engineered transcription factor-binding diversed functional nucleic acid-based synthetic biosensor.

  2024cites this paper
• Harnessing genetic engineering to drive economic bioproduct production in algae

  2024cites this paper
• Genome-wide mapping of the binding sites of myocyte enhancer factor 2A in chicken primary myoblasts

  2024cites this paper
• Finding Needles in the Haystack: Strategies for Uncovering Noncoding Regulatory Variants.

  2023cites this paper
• Comparing Multiple Sclerosis Age of Onset in American American and European Cohorts via Polygenic Risk Scores

  2023cites this paper
• eScholarship@UMassChan eScholarship@UMassChan

  2022cites this paper
• Computational extraction and visualization of regulatory signals in the yeast transcriptional network from genome-wide data

  2022cites this paper
• Refactoring transcription factors for metabolic engineering.

  2022cites this paper
• A systematic genome-wide account of binding sites for the model transcription factor Gcn4

  2021cites this paper
• Tools to map target genes of bacterial two‐component system response regulators

  2020cites this paper
• Targeting of proteins to chromatin in Drosophila melanogaster

  2020cites this paper
• Advancement in Sustainable Agriculture: Computational and Bioinformatics Tools

  2019cites this paper
• Protein-DNA Interactions

  2019cites this paper
• The DNA damage response activates HPV16 late gene expression at the level of RNA processing

  2018influential citation
• Genetic and epigenetic control of life cycle transitions in the brown alga Ectocarpus sp.

  2018cites this paper
• Factor cooperation for chromosome discrimination in Drosophila

  2018cites this paper
• MADS specificity : Unravelling the dual function of the MADS domain protein FRUITFULL

  2017cites this paper
• Inherent limitations of probabilistic models for protein-DNA binding specificity

  2017cites this paper
• Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors

  2016cites this paper
• Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape.

  2016cites this paper
• Fast simulation of stochastic biochemical reaction networks on cytomorphic chips

  2016cites this paper
• Using protein-binding microarrays to study transcription factor specificity: homologs, isoforms and complexes.

  2015cites this paper
• Understanding DNA-binding specificity by bacteria hybrid selection.

  2015cites this paper
• A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes.

  2015cites this paper
• Next-Generation Sequencing of Genomic DNA Fragments Bound to a Transcription Factor in Vitro Reveals Its Regulatory Potential

  2014influential citation
• BIOINFORMATICS-A FUTURE TOOL IN RESEARCH

  2014cites this paper
• DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems.

  2014cites this paper
• DNA sequence motif: a jack of all trades for ChIP-Seq data.

  2013cites this paper
• Interindividual Variability in Stress Susceptibility: A Role for Epigenetic Mechanisms in PTSD

  2013cites this paper
• In silico investigation of glossina morsitans promoters

  2013cites this paper
• Mechanisms by which transcription factors gain access to target sequence elements in chromatin.

  2013cites this paper
• Integrative analysis of ChIP-chipdatasets in Saccharomyces cerevisiae

  2012cites this paper
• DNA Sequence Preferences of Transcriptional Activators Correlate More Strongly than Repressors with Nucleosomes

  2012cites this paper
• DNA–protein interactions: methods for detection and analysis

  2012cites this paper
• Regulatory motif discovery using PWMs and the architecture of eukaryotic core promoters

  2012cites this paper
• Genome-wide mapping of the binding sites of proteins that interact with DNA.

  2012cites this paper
• Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo

  2012cites this paper
• Yeast Sen1 Helicase Protects the Genome from Transcription-Associated Instability

  2011influential citation
• Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium

  2011cites this paper
• YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

  2011cites this paper
• Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins.

  2011cites this paper
• A Linear Model for Transcription Factor Binding Affinity Prediction in Protein Binding Microarrays

  2011cites this paper
• In vitro DNA-binding profile of transcription factors: methods and new insights.

  2011cites this paper
• Sequence-specificity and energy landscapes of DNA-binding molecules.

  2011cites this paper
• Methods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro.

  2011cites this paper
• Etablierung der Chromatin-Immunopräzipitation für in vivo Untersuchungen der Genregulation durch Transkriptionsfaktoren bei der Honigbiene Apis mellifera

  2011cites this paper
• Quantitative Modeling Effects of Nucleosome on Transcription Factor-DNA Interactions

  2010cites this paper
• Finding regulatory DNA motifs using alignment-free evolutionary conservation information

  2010cites this paper
• Determining the specificity of protein–DNA interactions

  2010cites this paper
• Bayesian Model Based Approaches In The Analysis Of Chromatin Structure And Motif Discovery

  2010cites this paper
• Co-occurrence of transcription factor binding sites (Gemeinsames Auftreten von Transkriptionsfaktor-Bindungsstellen)

  2010cites this paper
• Analysis of DNA-binding proteins in yeast Saccharomyces cerevisiae

  2010cites this paper
• Experimental strategies for studying transcription factor-DNA binding specificities.

  2010cites this paper
• Towards a genome-wide reconstruction of cis-regulatory networks in the human genome.

  2009cites this paper
• Reconstructing transcriptional regulatory networks through genomics data

  2009cites this paper
• Experimentally based contact energies decode interactions responsible for protein–DNA affinity and the role of molecular waters at the binding interface

  2009cites this paper
• Protein-dna binding: discovering motifs and distinguishing direct from indirect interactions

  2009influential citation
• Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system.

  2009cites this paper
• QTL Analysis in the Pig : From the Identification of Quantitative Trait Loci to the Understanding of Molecular Mechanisms

  2009cites this paper
• Decoding the protein-DNA recognition rules

  2009cites this paper
• Methods for detection of protein-protein and protein-DNA interactions using HaloTag.

  2008cites this paper
• Interpreting Chromatin Immunoprecipitation Experiments

  2008cites this paper
• Discovery and verification of functional single nucleotide polymorphisms in regulatory genomic regions: current and developing technologies.

  2008cites this paper
• Predicting the binding preference of transcription factors to individual DNA k-mers

  2008cites this paper
• Expanding the specificity of DNA targeting by harnessing cooperative assembly.

  2008cites this paper
• Towards a Complete Transcriptional Regulatory Code: Improved Motif Discovery Using Informative Priors

  2008cites this paper
• Web-based resources for clinical bioinformatics.

  2008cites this paper
• DNA Immunoprecipitation (DIP) for the Determination of DNA-Binding Specificity.

  2008cites this paper
• A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.

  2008cites this paper
• The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors.

  2008cites this paper
• Clinical Bioinformatics

  2008cites this paper
• Algorithm for prediction of tumour suppressor p53 affinity for binding sites in DNA

  2008cites this paper
• Microbial regulatory and metabolic networks.

  2007cites this paper
• Genone-wide analysis of epigenetics and alternative promoters in cancer cells.

  2007cites this paper
• TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors

  2007cites this paper
• A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast

  2007cites this paper
• Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry

  2007cites this paper
• Connecting protein structure with predictions of regulatory sites

  2007cites this paper
• Nucleosome Occupancy Information Improves de novo Motif Discovery

  2007cites this paper
• Discriminative motif discovery in DNA and protein sequences using the DEME algorithm

  2007cites this paper
• RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors

  2007cites this paper
• In vitro analysis of DNA–protein interactions by proximity ligation

  2007cites this paper
• Predictive modeling of genome-wide mRNA expression: from modules to molecules.

  2007cites this paper
• Genomic DNA as a general cohybridization standard for ratiometric microarrays.

  2006cites this paper
• Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.

  2006influential citation
• Bioinformatics and its applications in plant biology.

  2006cites this paper
• Informative priors based on transcription factor structural class improve de novo motif discovery

  2006cites this paper
• Characterization of Binding Sites of Eukaryotic Transcription Factors

  2006cites this paper
• Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping.

  2006influential citation
• selection reveals the importance of nucleosome occupancy in target site Whole-genome comparison of Leu 3 binding in vitro and in vivo Material

  2006cites this paper
• Practical Strategies for Discovering Regulatory DNA Sequence Motifs

  2006cites this paper
• ChIP-chip comes of age for genome-wide functional analysis.

  2006cites this paper
• Defining the sequence-recognition profile of DNA-binding molecules.

  2006cites this paper
• Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE

  2006influential citation
• Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity.

  2006cites this paper
• Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques.

  2006cites this paper
• computational and experimental techniques Locating mammalian transcription factor binding sites : A survey of data

  2006cites this paper
• Walhout protein – protein interaction mapping Unraveling transcription regulatory networks by protein – DNA and

  2006influential citation