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

ABSTRACT:

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 i

SUBMITTER: Vale-Silva LA 

PROVIDER: S-EPMC6337847 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature