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

Vale-Silva, Luis A. ; Markowitz, Tovah E. ; Hochwagen, Andreas

In: BMC Genomics, 20 (2019), Nr. 54. pp. 1-10. ISSN 1471-2164

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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 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.

Item Type: Article
Journal or Publication Title: BMC Genomics
Volume: 20
Number: 54
Publisher: BioMed Central ; Springer
Place of Publication: London ; Berlin, Heidelberg
Date Deposited: 22 Feb 2019 12:30
Date: 2019
ISSN: 1471-2164
Page Range: pp. 1-10
Faculties / Institutes: Service facilities > Bioquant
Subjects: 570 Life sciences
610 Medical sciences Medicine
Uncontrolled Keywords: Chromatin immunoprecipitation, ChIP-seq, Spike-in, Normalization, Chromosomal proteins, Post-translational modification, Meiosis, S. cerevisiae
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