SNP-ChIP: a versatile and tag-free method to quantify changes in protein binding across the genome

BMC Genomics. 2019 Jan 17;20(1):54. doi: 10.1186/s12864-018-5368-4.


Background: Chromatin-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.

Results: Here, 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.

Conclusion: SNP-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.

Keywords: ChIP-seq; Chromatin immunoprecipitation; Chromosomal proteins; Meiosis; Normalization; Post-translational modification; S. cerevisiae; Spike-in.

MeSH terms

  • Cell Cycle Proteins / metabolism
  • Chromatin Immunoprecipitation / methods*
  • Chromosomal Proteins, Non-Histone / metabolism
  • Genome, Fungal*
  • Mutation / genetics
  • Polymorphism, Single Nucleotide / genetics*
  • Protein Binding
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Sequence Analysis, DNA


  • Cell Cycle Proteins
  • Chromosomal Proteins, Non-Histone
  • Saccharomyces cerevisiae Proteins
  • cohesins