Optical Mapping Discerns Genome Wide DNA Methylation Profiles

Overview

Journal BMC Mol Biol

Publisher Biomed Central

Specialty Molecular Biology

Date 2008 Aug 1

PMID 18667073

Citations 22

Authors

Gene E Ananiev

Steve Goldstein

Rod Runnheim

Dan K Forrest

Shiguo Zhou

Konstantinos Potamousis

Chris P Churas

Veit Bergendahl

James A Thomson

David C Schwartz

Affiliations

Soon will be listed here.

Abstract

Background: Methylation of CpG dinucleotides is a fundamental mechanism of epigenetic regulation in eukaryotic genomes. Development of methods for rapid genome wide methylation profiling will greatly facilitate both hypothesis and discovery driven research in the field of epigenetics. In this regard, a single molecule approach to methylation profiling offers several unique advantages that include elimination of chemical DNA modification steps and PCR amplification.

Results: A single molecule approach is presented for the discernment of methylation profiles, based on optical mapping. We report results from a series of pilot studies demonstrating the capabilities of optical mapping as a platform for methylation profiling of whole genomes. Optical mapping was used to discern the methylation profile from both an engineered and wild type Escherichia coli. Furthermore, the methylation status of selected loci within the genome of human embryonic stem cells was profiled using optical mapping.

Conclusion: The optical mapping platform effectively detects DNA methylation patterns. Due to single molecule detection, optical mapping offers significant advantages over other technologies. This advantage stems from obviation of DNA modification steps, such as bisulfite treatment, and the ability of the platform to assay repeat dense regions within mammalian genomes inaccessible to techniques using array-hybridization technologies.

Citing Articles

DNA Manipulation and Single-Molecule Imaging.

Takahashi S, Oshige M, Katsura S Molecules. 2021; 26(4).

PMID: 33671359 PMC: 7922115. DOI: 10.3390/molecules26041050.

Advances in optical mapping for genomic research.

Yuan Y, Chung C, Chan T Comput Struct Biotechnol J. 2020; 18:2051-2062.

PMID: 32802277 PMC: 7419273. DOI: 10.1016/j.csbj.2020.07.018.

Long walk to genomics: History and current approaches to genome sequencing and assembly.

Giani A, Gallo G, Gianfranceschi L, Formenti G Comput Struct Biotechnol J. 2020; 18:9-19.

PMID: 31890139 PMC: 6926122. DOI: 10.1016/j.csbj.2019.11.002.

Microscale Objects via Restructuring of Large, Double-Stranded DNA Molecules.

Krerowicz S, Hernandez-Ortiz J, Schwartz D ACS Appl Mater Interfaces. 2018; 10(48):41215-41223.

PMID: 30403478 PMC: 6453721. DOI: 10.1021/acsami.8b18157.

Determining if DNA Stained with a Cyanine Dye Can Be Digested with Restriction Enzymes.

Maschmann A, Masters C, Davison M, Lallman J, Thompson D, Kounovsky-Shafer K J Vis Exp. 2018; (132).

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