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

Chabbert CD, Adjalley SH, Klaus B, Fritsch ES, Gupta I, Pelechano V, Steinmetz LM

Mol Syst Biol 11 (1) 777 [2015-01-12; online 2015-01-12]

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.

SciLifeLab Fellow

Vicent Pelechano

PubMed 25583149

DOI 10.15252/msb.20145776

Crossref 10.15252/msb.20145776

pmc: PMC4332152

Publications 9.5.0