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Single cell epigenetic visualization assay.

Sam Kint^1,2, Wim Van Criekinge¹, Linos Vandekerckhove²

¹Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium.

Nucleic Acids Research

|January 29, 2021

Summary

This summary is machine-generated.

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A new microscopy assay, the epigenetic visualization assay (EVA), quantifies epigenetic marks in single cells. This method links epigenetic modifications to gene transcription, advancing our understanding of cellular epigenetic regulation.

Area of Science:

Molecular Biology
Epigenetics
Cell Biology

Background:

Characterizing single-cell epigenetic status is challenging due to limited sequencing coverage.
Current methods struggle to correlate epigenetic marks with transcription states at individual gene alleles within the same cell.

Purpose of the Study:

To develop a microscopy-based assay for detecting and quantifying epigenetic marks in single cells.
To link epigenetic modifications to the transcriptional activity of specific gene alleles.

Main Methods:

Developed the epigenetic visualization assay (EVA), a targeted microscopy-based method.
EVA utilizes an in situ biochemical reaction involving antibody-conjugated alkaline phosphatase and a fluorophore-labeled DNA oligo.
Combined EVA with RNA-FISH to correlate epigenetic marks with gene transcription.

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Main Results:

Successfully measured 5-methylcytosine (5mC) and H3K9Ac levels at target genes and the HIV-1 provirus.
Demonstrated higher 5mC levels at silenced XIST gene alleles compared to transcribed alleles.
Validated EVA's ability to relate epigenetic marks to individual gene allele transcription status.

Conclusions:

EVA provides a quantitative method for analyzing epigenetic marks at the gene level in single cells.
The assay successfully links epigenetic modifications to gene transcription status.
EVA offers a valuable tool for studying gene regulation and epigenetic heterogeneity.