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Journal Article

Standardizing chromatin research: a simple and universal method for ChIP-seq

MPS-Authors

Arrigoni,  Laura
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Richter,  Andreas S.
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Betancourt,  Emily
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Bruder,  Kerstin
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Manke,  Thomas
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

Bönisch,  Ulrike
Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Citation

Arrigoni, L., Richter, A. S., Betancourt, E., Bruder, K., Diehl, S., Manke, T., et al. (2016). Standardizing chromatin research: a simple and universal method for ChIP-seq. Nucelic Acids Research, 44, e67. doi:10.1093/nar/gkv1495.


Cite as: http://hdl.handle.net/11858/00-001M-0000-002C-A8C1-B
Abstract
Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) is a key technique in chromatin research. Although heavily applied, existing ChIP-seq protocols are often highly fine-tuned workflows, optimized for specific experimental requirements. Especially the initial steps of ChIP-seq, particularly chromatin shearing, are deemed to be exceedingly cell-type-specific, thus impeding any protocol standardization efforts. Here we demonstrate that harmonization of ChIP-seq workflows across cell types and conditions is possible when obtaining chromatin from properly isolated nuclei. We established an ultrasound-based nuclei extraction method (NEXSON: Nuclei EXtraction by SONication) that is highly effective across various organisms, cell types and cell numbers. The described method has the potential to replace complex cell-type-specific, but largely ineffective, nuclei isolation protocols. By including NEXSON in ChIP-seq workflows, we completely eliminate the need for extensive optimization and sample-dependent adjustments. Apart from this significant simplification, our approach also provides the basis for a fully standardized ChIP-seq and yields highly reproducible transcription factor and histone modifications maps for a wide range of different cell types. Even small cell numbers (∼10,000 cells per ChIP) can be easily processed without application of modified chromatin or library preparation protocols.