期刊
BMC GENOMICS
卷 20, 期 -, 页码 -出版社
BMC
DOI: 10.1186/s12864-018-5368-4
关键词
Chromatin immunoprecipitation; ChIP-seq; Spike-in; Normalization; Chromosomal proteins; Post-translational modification; Meiosis; S; cerevisiae
资金
- NIH [R01 GM111715, R01 GM123035, FY16-208]
- March of Dimes Foundation
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 -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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