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Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
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Genome-wide positioning of bivalent mononucleosomes
Subhojit Sen1,2, Kirsten F Block1, Alice Pasini3
1CRB1, Room 530, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA.
BMC Medical Genomics
|September 17, 2016
Summary
Bivalent nucleosomes, marked by H3K4me3 and H3K27me3, are focally enriched near transcription start sites. This finding advances understanding of poised chromatin in stem cells.
Area of Science:
- Epigenetics
- Chromatin Biology
- Stem Cell Biology
Background:
- Bivalent chromatin involves overlapping activating (H3K4me3) and repressing (H3K27me3) histone marks.
- Previous studies focused on broad zones of overlapping marks, not individual bivalent nucleosomes.
- The precise genomic positioning of bivalent nucleosomes remained largely uncharacterized.
Purpose of the Study:
- To develop a technique for mapping individual bivalent nucleosomes genome-wide.
- To investigate the precise genomic locations of nucleosomes bearing both H3K4me3 and H3K27me3 marks.
- To correlate bivalent nucleosome positioning with gene expression and regulatory elements.
Main Methods:
- Developed a sequential ChIP technique to isolate and identify individual bivalent nucleosomes.
- Employed next-generation sequencing for genome-wide mapping of bivalent nucleosomes.
- Analyzed nucleosome positioning relative to transcription start sites (TSS), CpG islands, and DNA methylation.
Main Results:
- Bivalent nucleosomes are focally enriched near the transcription start site (TSS), distinct from broad overlapping mark zones.
- These bivalent nucleosomes occupy H2A.Z-enriched, salt-labile positions.
- Enrichment is dependent on CpG island content and anti-correlated with DNA methylation, linked to low gene expression.
Conclusions:
- Bivalent nucleosomes are primarily located promoter-proximal to CpG island genes with poised/low expression.
- Regional overlap of H3K4me3 and H3K27me3 marks is upstream of the TSS, while bivalent nucleosomes are near the TSS.
- Focal enrichment of bivalent nucleosomes at the TSS impacts the poised chromatin state in stem cells.
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