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An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
Published on: April 5, 2018
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ChIP-less analysis of chromatin states
Zhangli Su1, Melissa D Boersma2, Jin-Hee Lee1
1Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA ; Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA.
Epigenetics & Chromatin
|May 30, 2014
Summary
Researchers developed a novel antibody-free method using recombinant reader domains to identify specific combinations of histone post-translational modifications (PTMs) on nucleosomes, advancing epigenetic studies.
Area of Science:
- Epigenetics and Molecular Biology
- Chromatin Biology
- Proteomics
Background:
- Histone post-translational modifications (PTMs) are crucial epigenetic regulators.
- Combinatorial PTM patterns, not individual marks, define chromatin states.
- Direct molecular tools for interrogating nucleosomal PTM patterns are lacking.
Purpose of the Study:
- To develop an efficient, antibody-free method for interrogating combinatorial histone PTM patterns.
- To create a platform for capturing and analyzing unique chromatin states based on PTM combinations.
Main Methods:
- Utilized recombinant chromatin reader domains with specificity for PTM patterns.
- Developed a combinatorial histone peptide microarray for domain screening.
- Established a reader-based affinity enrichment platform (MARCC).
- Quantitatively profiled captured chromatin states using mass spectrometry.
Main Results:
- Demonstrated superior specificity of reader domains over antibodies for PTM patterns.
- Successfully applied MARCC to capture unique chromatin states.
- Identified a novel PTM combination (H3K4me0, H3K9me2/3, H3K79me0, H4K20me2/3) enriched in heterochromatin.
- Revealed interconnections between nucleosomal histone PTMs.
Conclusions:
- Recombinant reader domains are effective tools for enriching specific combinatorial PTM patterns.
- The reader affinity platform facilitates the study of co-existing nucleosomal PTM states.
- This workflow enhances understanding of chromatin states and reader domain functions in gene regulation.
