TY  - JOUR
UR  - https://archiv.ub.uni-heidelberg.de/volltextserver/25916/
N2  - 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 ?-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.
CY  - London ; Berlin, Heidelberg
A1  - Vale-Silva, Luis A.
A1  - Markowitz, Tovah E.
A1  - Hochwagen, Andreas
SN  - 1471-2164
IS  - 54
KW  - Chromatin immunoprecipitation
KW  -  ChIP-seq
KW  -  Spike-in
KW  -  Normalization
KW  -  Chromosomal proteins
KW  -  Post-translational modification
KW  -  Meiosis
KW  -  S. cerevisiae
Y1  - 2019///
PB  - BioMed Central ; Springer
EP  - 10
VL  - 20
ID  - heidok25916
AV  - public
JF  - BMC Genomics
SP  - 1
TI  - SNP-ChIP: a versatile and tag-free method to quantify changes in protein binding across the genome
ER  -