ArticleBMC genomics2010
ChIP on Chip: surprising results are often artifacts.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
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- NKX2-5 congenital heart disease mutations show diverse loss and gain of epigenomic, biochemical and chromatin search functions underpinning pathogenicity.bioRxiv : the preprint server for biology · 2025Article
- UV induces codirectional replication-transcription conflicts and an alternative DnaA-dependent replication origin in the rnhAB mutants of Escherichiacoli.Nucleic acids research · 2025Article
- Transcriptome data are insufficient to control false discoveries in regulatory network inference.Cell systems · 2024Article
- Bradyrhizobium japonicum HmuP is an RNA-binding protein that positively controls hmuR operon expression by suppression of a negative regulatory RNA element in the 5' untranslated region.Molecular microbiology · 2024Article
- Single-nucleotide resolution detection of Topo IV cleavage activity in theFrontiers in microbiology · 2023Article
- Gawky modulates MTF-1-mediated transcription activation and metal discrimination.Nucleic acids research · 2021Article
- Whole-Genome Analysis Reveals That the Nucleoid Protein IHF Predominantly Binds to the Replication OriginFrontiers in microbiology · 2021Article
- SAMMY-seq reveals early alteration of heterochromatin and deregulation of bivalent genes in Hutchinson-Gilford Progeria Syndrome.Nature communications · 2020Article
- RNA polymerase II (RNAP II)-associated factors are recruited to tRNA loci, revealing that RNAP II- and RNAP III-mediated transcriptions overlap in yeast.The Journal of biological chemistry · 2019Article
- ChIPulate: A comprehensive ChIP-seq simulation pipeline.PLoS computational biology · 2019Article
- A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0.BMC biology · 2018Article
- The regulon of the RNA chaperone CspA and its auto-regulation in Staphylococcus aureus.Nucleic acids research · 2018Article
- Phenotypes ofJournal of bacteriology · 2017Article
- Asymmetric positioning of Cas1-2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system.Nucleic acids research · 2017Article
- Prediction and validation of protein-protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach.Open biology · 2016Article
- Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic.Genome research · 2016Article
- FabR regulates Salmonella biofilm formation via its direct target FabB.BMC genomics · 2016Article
- Systems Level Analyses Reveal Multiple Regulatory Activities of CodY Controlling Metabolism, Motility and Virulence in Listeria monocytogenes.PLoS genetics · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe method of chromatin immunoprecipitation combined with microarrays (ChIP-Chip) is a powerful tool for genome-wide analysis of protein binding. However, a high background signal is a common phenomenon.
resultsReinvestigation of the chromatin immunoprecipitation procedure led us to discover four causes of high background: i) non-unique sequences, ii) incomplete reversion of crosslinks, iii) retention of protein in spin-columns and iv) insufficient RNase treatment. The chromatin immunoprecipitation method was modified and applied to analyze genome-wide binding of SeqA and sigma(32) in Escherichia coli.
conclusionsFalse positive findings originating from these shortcomings of the method could explain surprising and contradictory findings in published ChIP-Chip studies. We present a modified chromatin immunoprecipitation method greatly reducing the background signal.
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