SNP-ChIP

A versatile and tag-free method to quantify changes in protein binding across the genome

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

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number54
JournalBMC Genomics
Volume20
Issue number1
DOIs
StatePublished - Jan 17 2019

Fingerprint

Protein Binding
Single Nucleotide Polymorphism
Genome
Chromatin Immunoprecipitation
Histone Code
Saccharomycetales
Chromosome Mapping
Meiosis
DNA Damage
Chromatin
Proteins
Antibodies

Keywords

  • ChIP-seq
  • Chromatin immunoprecipitation
  • Chromosomal proteins
  • Meiosis
  • Normalization
  • Post-translational modification
  • S. cerevisiae
  • Spike-in

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

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, Vol. 20, No. 1, 54, 17.01.2019.

Research output: Contribution to journalArticle

@article{30942a10c64a4de59f690629a4d53cc0,
title = "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 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.",
keywords = "ChIP-seq, Chromatin immunoprecipitation, Chromosomal proteins, Meiosis, Normalization, Post-translational modification, S. cerevisiae, Spike-in",
author = "Vale-Silva, {Luis A.} and Markowitz, {Tovah E.} and Andreas Hochwagen",
year = "2019",
month = "1",
day = "17",
doi = "10.1186/s12864-018-5368-4",
language = "English (US)",
volume = "20",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - SNP-ChIP

T2 - A versatile and tag-free method to quantify changes in protein binding across the genome

AU - Vale-Silva, Luis A.

AU - Markowitz, Tovah E.

AU - Hochwagen, Andreas

PY - 2019/1/17

Y1 - 2019/1/17

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 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.

AB - 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.

KW - ChIP-seq

KW - Chromatin immunoprecipitation

KW - Chromosomal proteins

KW - Meiosis

KW - Normalization

KW - Post-translational modification

KW - S. cerevisiae

KW - Spike-in

UR - http://www.scopus.com/inward/record.url?scp=85060073613&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85060073613&partnerID=8YFLogxK

U2 - 10.1186/s12864-018-5368-4

DO - 10.1186/s12864-018-5368-4

M3 - Article

VL - 20

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 54

ER -