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Mol Syst Biol. 2015 Jan 12;11(1):777. doi: 10.15252/msb.20145776.

A high-throughput ChIP-Seq for large-scale chromatin studies.

Author information

1
European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
2
European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany pelechan@embl.de larsms@embl.de.
3
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.

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.

KEYWORDS:

ChIP‐Seq; chromatin; high‐throughput; histone marks; histone methyltransferase

PMID:
25583149
PMCID:
PMC4332152
[Indexed for MEDLINE]
Free PMC Article

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