title: Quantitative ChIP-Seq normalization reveals global modulation of the epigenome.
abstract: Epigenomic profiling by chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq) is a prevailing methodology used to investigate chromatin-based regulation in biological systems such as human disease, but the lack of an empirical methodology to enable normalization among experiments has limited the precision and usefulness of this technique. Here, we describe a method called ChIP with reference exogenous genome (ChIP-Rx) that allows one to perform genome-wide quantitative comparisons of histone modification status across cell populations using defined quantities of a reference epigenome. ChIP-Rx enables the discovery and quantification of dynamic epigenomic profiles across mammalian cells that would otherwise remain hidden using traditional normalization methods. We demonstrate the utility of this method for measuring epigenomic changes following chemical perturbations and show how reference normalization of ChIP-seq experiments enables the discovery of disease-relevant changes in histone modification occupancy.
authors.affiliation: Syros Pharmaceuticals, 480 Arsenal Street, Watertown, MA 02472, USA. Electronic address: dorlando@syros.com.
authors.forename: David A
authors.initials: DA
authors.lastname: Orlando
authors.affiliation: Syros Pharmaceuticals, 480 Arsenal Street, Watertown, MA 02472, USA.
authors.forename: Mei Wei
authors.initials: MW
authors.lastname: Chen
authors.affiliation: Syros Pharmaceuticals, 480 Arsenal Street, Watertown, MA 02472, USA.
authors.forename: Victoria E
authors.initials: VE
authors.lastname: Brown
authors.affiliation: Syros Pharmaceuticals, 480 Arsenal Street, Watertown, MA 02472, USA.
authors.forename: Snehakumari
authors.initials: S
authors.lastname: Solanki
authors.affiliation: Syros Pharmaceuticals, 480 Arsenal Street, Watertown, MA 02472, USA.
authors.forename: Yoon J
authors.initials: YJ
authors.lastname: Choi
authors.affiliation: Syros Pharmaceuticals, 480 Arsenal Street, Watertown, MA 02472, USA.
authors.forename: Eric R
authors.initials: ER
authors.lastname: Olson
authors.affiliation: Syros Pharmaceuticals, 480 Arsenal Street, Watertown, MA 02472, USA.
authors.forename: Christian C
authors.initials: CC
authors.lastname: Fritz
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: James E
authors.initials: JE
authors.lastname: Bradner
authors.affiliation: Syros Pharmaceuticals, 480 Arsenal Street, Watertown, MA 02472, USA. Electronic address: mguenther@syros.com.
authors.forename: Matthew G
authors.initials: MG
authors.lastname: Guenther
mesh_terms: D000818:Animals; D001562:Benzimidazoles / Q000494:pharmacology; D047369:Chromatin Immunoprecipitation / Q000379:methods* / Q000592:standards*; D004331:Drosophila melanogaster / Q000187:drug effects / Q000235:genetics; D044127:Epigenesis, Genetic / Q000187:drug effects; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000592:standards*; D006657:Histones / Q000378:metabolism; D006801:Humans; D019169:Jurkat Cells; D008239:Lysine / Q000378:metabolism; D008745:Methylation / Q000187:drug effects; D012015:Reference Standards
chemical_list: D001562:Benzimidazoles; C583893:EPZ-5676; D006657:Histones; D008239:Lysine