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Updated: Jan 28, 2026
10:57
Mapping Absolute DNA Density in Cell Nuclei using Single-molecule Localization Microscopy
Published on: November 11, 2025
795
Long-read single-molecule maps of the functional methylome
Hila Sharim1, Assaf Grunwald1, Tslil Gabrieli1
1School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel.
Genome Research
|March 9, 2019
Summary
We developed a new workflow for optical detection of DNA methylation, creating genome-wide maps. This method analyzes methylation patterns and structural variations, aiding in diseases like facioscapulohumeral muscular dystrophy (FSHD).
Area of Science:
- Genomics
- Epigenetics
- Molecular Biology
Background:
- Accurate genome-wide methylation analysis is crucial for understanding gene regulation and diseases.
- Existing methods like whole-genome bisulfite sequencing (WGBS) have limitations in analyzing long DNA molecules and structural variations.
Purpose of the Study:
- To develop a novel workflow for optical detection of fluorescent methylation profiles along long DNA molecules.
- To create a hybrid genetic/epigenetic genome-wide map using Bionano Genomics technology.
- To apply this method for studying complex genetic disorders such as facioscapulohumeral muscular dystrophy (FSHD).
Main Methods:
- Development of a methylation analysis workflow utilizing optical detection of fluorescent methylation profiles.
- Integration with Bionano Genomics genome mapping technology for long single-molecule reads (hundreds of kilobase pairs).
- Application to analyze haplotype, copy number, and methylation status at the Chromosome 4q locus associated with FSHD.
Main Results:
- Achieved kilobase pair-scale genomic methylation patterns comparable to WGBS along genes and regulatory elements.
- Enabled methylation variation calling and analysis of large structural aberrations not accessible to second-generation sequencing.
- Successfully applied the method to study the complex locus in FSHD, simultaneously assessing genetic and epigenetic information.
Conclusions:
- The developed workflow provides a powerful tool for genome-wide methylation analysis and structural variation detection.
- This hybrid approach offers a comprehensive view of genetic and epigenetic landscapes at kilobase pair resolution.
- The method is particularly valuable for studying diseases with complex repetitive loci, such as FSHD.
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