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

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. Synopsis A new approach provides a rapid and accurate genome-wide overview of the chromatin status of multiple yeast chromatin-associated mutants at once. The simultaneous profiling of epigenetic marks in the mutants is achieved by multiplex immuno-precipitation of barcoded chromatin samples. Bar-ChIP is based on the immuno-precipitation of barcoded chromatin and permits sample multiplexing, thereby increasing the throughput of ChIP-Seq experiments. Application of the method to yeast chromatin-associated mutants enabled the concurrent generation of 90 ChIP-Seq datasets without the need for robotic instrumentation. The rapid chromatin profiling of the mutants at single-nucleosome resolution uncovered an association between intragenic H3K4 tri-methylation and cryptic transcription in set2Π. A new approach provides a rapid and accurate genome-wide overview of the chromatin status of multiple yeast chromatin-associated mutants at once. The simultaneous profiling of epigenetic marks in the mutants is achieved by multiplex immuno-precipitation of barcoded chromatin samples. © 2015 The Authors. Published under the terms of the CC BY 4.0 license.