Cited by 169Genomics and Chromatin DynamicsChromatin Remodeling and CancerEpigenetics and DNA Methylation

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Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments

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Jain, Dhawal, Baldi, Sandro, Zabel, Angelika, Straub, Tobias, Becker, Peter B.·2015·Nucleic Acids Research

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Abstract

Chromatin immunoprecipitation (ChIP) is widely used to identify chromosomal binding sites. Chromatin proteins are cross-linked to their target sequences in living cells. The purified chromatin is sheared and the relevant protein is enriched by immunoprecipitation with specific antibodies. The co-purifying genomic DNA is then determined by massive parallel sequencing (ChIP-seq).We applied ChIP-seq to map the chromosomal binding sites for two ISWI-containing nucleosome remodeling factors, ACF and RSF, in Drosophila embryos. Employing several polyclonal and monoclonal antibodies directed against their signature subunits, ACF1 and RSF-1, robust profiles were obtained indicating that both remodelers co-occupied a large set of active promoters.Further validation included controls using chromatin of mutant embryos that do not express ACF1 or RSF-1. Surprisingly, the ChIP-seq profiles were unchanged, suggesting that they were not due to specific immunoprecipitation. Conservative analysis lists about 3000 chromosomal loci, mostly active promoters that are prone to non-specific enrichment in ChIP and appear as 'Phantom Peaks'. These peaks are not obtained with pre-immune serum and are not prominent in input chromatin.Mining the modENCODE ChIP-seq profiles identifies potential Phantom Peaks in many profiles of epigenetic regulators. These profiles and other ChIP-seq data featuring prominent Phantom Peaks must be validated with chromatin from cells in which the protein of interest has been depleted.

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Additional file 10 of Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets
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Additional file 15 of Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets
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Additional file 1 of Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets
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Additional file 3 of Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets
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Additional file 7 of Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets
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Self-citation

Authors: Jain, D., Baldi, S., Zabel, A., Straub, T., & Becker, P. B.
Affiliations: Center for Integrated Protein Science Munich (DE)
Corresponding author: Becker, Peter B.
ORCID: Jain, Dhawal
Baldi, Sandro
Straub, Tobias
Becker, Peter B.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2015-06-27
Volume: 43
Issue: 14
Pages: 6959-6968
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkv637
PMC: PMC4538825
OpenAlex: W1610193264
Cited by: 156
References: 65
Citations by year: 2026: 6 · 2025: 12 · 2024: 13 · 2023: 10 · 2022: 8 · 2021: 16 · 2020: 13 · 2019: 20 · 2018: 19 · 2017: 15 · 2016: 22 · 2015: 2
FWCI: 8.40
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (vor, 681 d)
Locations: Nucleic Acids Research (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Open access LMU (Ludwid Maxmilian's Universitat Munchen) (submittedVersion)
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: ACF, Drosophila embryo, chromatin immunoprecipitation, modENCODE
MeSH terms: RNA Splicing Factors, Animals, Binding Sites, Drosophila, Promoter Regions, Genetic, Repressor Proteins, Transcription Factors, Artifacts, RNA-Binding Proteins, Sequence Analysis, DNA, Drosophila Proteins, Databases, Genetic, Chromatin Immunoprecipitation, Chromosomes, Insect, High-Throughput Nucleotide Sequencing

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Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments

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