title: A high-throughput ChIP-Seq for large-scale chromatin studies.
abstract: We present a modified approach of chromatin immuno-precipitation followed by sequencing (ChIP-Seq), which relies on the direct ligation of molecular barcodes to chromatin fragments, thereby permitting experimental scale-up. With Bar-ChIP now enabling the concurrent profiling of multiple DNA-protein interactions, we report the simultaneous generation of 90 ChIP-Seq datasets without any robotic instrumentation. We demonstrate that application of Bar-ChIP to a panel of Saccharomyces cerevisiae chromatin-associated mutants provides a rapid and accurate genome-wide overview of their chromatin status. Additionally, we validate the utility of this technology to derive novel biological insights by identifying a role for the Rpd3S complex in maintaining H3K14 hypo-acetylation in gene bodies. We also report an association between the presence of intragenic H3K4 tri-methylation and the emergence of cryptic transcription in a Set2 mutant. Finally, we uncover a crosstalk between H3K14 acetylation and H3K4 methylation in this mutant. These results show that Bar-ChIP enables biological discovery through rapid chromatin profiling at single-nucleosome resolution for various conditions and protein modifications at once.
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
authors.forename: Christophe D
authors.initials: CD
authors.lastname: Chabbert
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
authors.forename: Sophie H
authors.initials: SH
authors.lastname: Adjalley
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Klaus
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
authors.forename: Emilie S
authors.initials: ES
authors.lastname: Fritsch
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
authors.forename: Ishaan
authors.initials: I
authors.lastname: Gupta
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany pelechan@embl.de larsms@embl.de.
authors.forename: Vicent
authors.initials: V
authors.lastname: Pelechano
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany Stanford Genome Technology Center, Palo Alto, CA, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA pelechan@embl.de larsms@embl.de.
authors.forename: Lars M
authors.initials: LM
authors.lastname: Steinmetz
mesh_terms: D000107:Acetylation; D002843:Chromatin / Q000737:chemistry / Q000235:genetics*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004271:DNA, Fungal / Q000235:genetics; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D056726:Genetic Association Studies; D005819:Genetic Markers; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006657:Histones / Q000235:genetics / Q000378:metabolism; D008745:Methylation; D009707:Nucleosomes; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D002843:Chromatin; D004271:DNA, Fungal; D005819:Genetic Markers; D006657:Histones; D009707:Nucleosomes
keywords: ChIP‐Seq; chromatin; high‐throughput; histone marks; histone methyltransferase