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...

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Bibliographic Details
Published in:Molecular systems biology 2015-01, Vol.11 (1), p.777-n/a
Main Authors: Chabbert, Christophe D, Adjalley, Sophie H, Klaus, Bernd, Fritsch, Emilie S, Gupta, Ishaan, Pelechano, Vicent, Steinmetz, Lars M
Format: Article
Language:English
Subjects:
Acetylation
Bar codes
Binding sites
ChIP‐Seq
Chromatin
Chromatin - chemistry
Chromatin - genetics
Chromatin Immunoprecipitation - methods
Crosstalk
Databases, Genetic
Deoxyribonucleic acid
DNA
DNA fingerprinting
DNA methylation
DNA, Fungal - genetics
Experiments
Gene Expression Profiling
Genes
Genetic Association Studies
Genetic Markers
Genomes
Genomics
High-Throughput Nucleotide Sequencing - methods
high‐throughput
histone marks
histone methyltransferase
Histones - genetics
Histones - metabolism
Instrumentation
Laboratories
Methylation
Mutants
Nucleosomes
Protein interaction
Proteins
Reproducibility of Results
Saccharomyces cerevisiae
Saccharomyces cerevisiae - genetics
Sequence Alignment
Sequence Analysis, DNA
Studies
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Summary: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 set2∆. 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.
ISSN:1744-4292
1744-4292
DOI:10.15252/msb.20145776