PT  - JOURNAL ARTICLE
AU  - Luis A. Vale-Silva
AU  - Tovah E. Markowitz
AU  - Andreas Hochwagen
TI  - SNP-ChIP: A versatile and tag-free method to quantify changes in protein binding across the genome
AID  - 10.1101/390005
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 390005
4099  - http://biorxiv.org/content/early/2018/08/10/390005.short
4100  - http://biorxiv.org/content/early/2018/08/10/390005.full
AB  - 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. 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. 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.