In: BMC Genomics, 20 (2019), Nr. 54. S. 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.
Dokumententyp: | Artikel |
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Titel der Zeitschrift: | BMC Genomics |
Band: | 20 |
Nummer: | 54 |
Verlag: | BioMed Central ; Springer |
Ort der Veröffentlichung: | London ; Berlin, Heidelberg |
Erstellungsdatum: | 22 Feb. 2019 12:30 |
Erscheinungsjahr: | 2019 |
ISSN: | 1471-2164 |
Seitenbereich: | S. 1-10 |
Institute/Einrichtungen: | Zentrale und Sonstige Einrichtungen > Bioquant |
DDC-Sachgruppe: | 570 Biowissenschaften, Biologie
610 Medizin |
Freie Schlagwörter: | Chromatin immunoprecipitation, ChIP-seq, Spike-in, Normalization, Chromosomal proteins, Post-translational modification, Meiosis, S. cerevisiae |