eprintid: 25916
rev_number: 14
eprint_status: archive
userid: 1589
dir: disk0/00/02/59/16
datestamp: 2019-02-22 12:30:03
lastmod: 2024-03-10 23:31:57
status_changed: 2019-02-22 12:30:03
type: article
metadata_visibility: show
creators_name: Vale-Silva, Luis A.
creators_name: Markowitz, Tovah E.
creators_name: Hochwagen, Andreas
title: SNP-ChIP: a versatile and tag-free method to quantify changes in protein binding across the genome
subjects: 570
subjects: 610
divisions: 716000
keywords: Chromatin immunoprecipitation, ChIP-seq, Spike-in, Normalization, Chromosomal proteins, Post-translational modification, Meiosis, S. cerevisiae
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.
date: 2019
publisher: BioMed Central ; Springer
id_scheme: DOI
ppn_swb: 1656012456
own_urn: urn:nbn:de:bsz:16-heidok-259162
language: eng
bibsort: VALESILVALSNPCHIPAVE2019
full_text_status: public
publication: BMC Genomics
volume: 20
number: 54
place_of_pub: London ; Berlin, Heidelberg
pagerange: 1-10
issn: 1471-2164
citation:   Vale-Silva, Luis A. ; Markowitz, Tovah E. ; Hochwagen, Andreas  (2019) SNP-ChIP: a versatile and tag-free method to quantify changes in protein binding across the genome.  BMC Genomics, 20 (54).  pp. 1-10.  ISSN 1471-2164     
document_url: https://archiv.ub.uni-heidelberg.de/volltextserver/25916/1/12864_2018_Article_5368.pdf