ArticleBMC genomics2019
SNP-ChIP: a versatile and tag-free method to quantify changes in protein binding across the genome.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Separable downmodulation of meiotic axis protein deposition and DNA break induction at chromosome ends.eLife · 2026Article
- Appropriate normalization is critical to improve reproducibility of tissue ChIP-seq.Serican journal of medicine · 2025Article
- Distinct chromatin regulators downmodulate meiotic axis formation and DNA break induction at chromosome ends.bioRxiv : the preprint server for biology · 2025Article
- The Wild West of spike-in normalization.Nature biotechnology · 2024Article
- Swi/Snf chromatin remodeling regulates transcriptional interference and gene repression.Molecular cell · 2024Article
- Review
- Meiotic DNA break resection and recombination rely on chromatin remodeler Fun30.bioRxiv : the preprint server for biology · 2024Article
- Chromatin binding by HORMAD proteins regulates meiotic recombination initiation.The EMBO journal · 2024Article
- Context-dependent function of the transcriptional regulator Rap1 in gene silencing and activation inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Context dependent function of the transcriptional regulator Rap1 in gene silencing and activation inbioRxiv : the preprint server for biology · 2023Article
- Swi/Snf Chromatin Remodeling Regulates Transcriptional Interference and Gene Repression.bioRxiv : the preprint server for biology · 2023Article
- Two pathways drive meiotic chromosome axis assembly in Saccharomyces cerevisiae.Nucleic acids research · 2022Article
- How do small chromosomes know they are small? Maximizing meiotic break formation on the shortest yeast chromosomes.Current genetics · 2021Review
- qDRIP: a method to quantitatively assess RNA-DNA hybrid formation genome-wide.Nucleic acids research · 2020Article
- Topoisomerases Modulate the Timing of Meiotic DNA Breakage and Chromosome Morphogenesis inGenetics · 2020Article
- Persistent DNA-break potential near telomeres increases initiation of meiotic recombination on short chromosomes.Nature communications · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundChromatin-immunoprecipitation followed by sequencing (ChIP-seq) is the method of choice for mapping genome-wide binding of chromatin-associated factors. However, broadly applicable methods for between-sample comparisons are lacking.
resultsHere, we introduce SNP-ChIP, a method that leverages small-scale intra-species polymorphisms, mainly SNPs, for quantitative spike-in normalization of ChIP-seq results. Sourcing spike-in material from the same species ensures antibody cross-reactivity and physiological coherence, thereby eliminating two central limitations of traditional spike-in approaches. We show that SNP-ChIP is robust to changes in sequencing depth and spike-in proportions, and reliably identifies changes in overall protein levels, irrespective of changes in binding distribution. Application of SNP-ChIP to test cases from budding yeast meiosis allowed discovery of novel regulators of the chromosomal protein Red1 and quantitative analysis of the DNA-damage associated histone modification γ-H2AX.
conclusionSNP-ChIP is fully compatible with the intra-species diversity of humans and most model organisms and thus offers a general method for normalizing ChIP-seq results.
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