ArticleNucleic acids research2018
Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Genome-wide chromatin profiling reveals a nonlimiting role for RXR in macrophage-like cells stimulated with multiple nuclear receptor agonists.The Journal of biological chemistry · 2026Article
- ChIP happens: from biochemical origins to the modern omics toolbox for understanding steroid hormone receptors.The Biochemical journal · 2026Review
- Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing.Cell reports methods · 2025Article
- SpikeFlow: automated and flexible analysis of ChIP-Seq data with spike-in control.NAR genomics and bioinformatics · 2024Article
- The Wild West of spike-in normalization.Nature biotechnology · 2024Article
- ZMIZ1 enhances ERα-dependent expression of E2F2 in breast cancer.Journal of molecular endocrinology · 2024Article
- Cell-specific and shared regulatory elements control a multigene locus active in mammary and salivary glands.Nature communications · 2023Article
- Streamlined quantitative analysis of histone modification abundance at nucleosome-scale resolution with siQ-ChIP version 2.0.Scientific reports · 2023Article
- Titration-based normalization of antibody amount improves consistency of ChIP-seq experiments.BMC genomics · 2023Article
- CBP Is Required for Establishing Adaptive Gene Programs in the Adult Mouse Brain.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2022Article
- SpikChIP: a novel computational methodology to compare multiple ChIP-seq using spike-in chromatin.NAR genomics and bioinformatics · 2021Article
- A new approach for quantifying epigenetic landscapes.The Journal of biological chemistry · 2020Article
- ARF-AID: A Rapidly Inducible Protein Degradation System That Preserves Basal Endogenous Protein Levels.Current protocols in molecular biology · 2020Article
- qDRIP: a method to quantitatively assess RNA-DNA hybrid formation genome-wide.Nucleic acids research · 2020Article
- Article
- Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications.Nature protocols · 2019Article
- VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer.Genome biology · 2019Article
- Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription.Cell reports · 2019Article
- Article
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Authors and funding
4 authors.
Funding
Abstract
A key challenge in quantitative ChIP combined with high-throughput sequencing (ChIP-seq) is the normalization of data in the presence of genome-wide changes in occupancy. Analysis-based normalization methods were developed for transcriptomic data and these are dependent on the underlying assumption that total transcription does not change between conditions. For genome-wide changes in transcription factor (TF) binding, these assumptions do not hold true. The challenges in normalization are confounded by experimental variability during sample preparation, processing and recovery. We present a novel normalization strategy utilizing an internal standard of unchanged peaks for reference. Our method can be readily applied to monitor genome-wide changes by ChIP-seq that are otherwise lost or misrepresented through analytical normalization. We compare our approach to normalization by total read depth and two alternative methods that utilize external experimental controls to study TF binding. We successfully resolve the key challenges in quantitative ChIP-seq analysis and demonstrate its application by monitoring the loss of Estrogen Receptor-alpha (ER) binding upon fulvestrant treatment, ER binding in response to estrodiol, ER mediated change in H4K12 acetylation and profiling ER binding in patient-derived xenographs. This is supported by an adaptable pipeline to normalize and quantify differential TF binding genome-wide and generate metrics for differential binding at individual sites.
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