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Methodology for Accurate Detection of Mitochondrial DNA Methylation
Published on: May 20, 2018
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DAMEfinder: a method to detect differential allele-specific methylation
Stephany Orjuela1,2, Dania Machlab3, Mirco Menigatti2
1Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
Epigenetics & Chromatin
|June 4, 2020
Summary
A new R package, DAMEfinder, screens for differential allele-specific methylation (ASM) by analyzing bisulfite sequencing data. It identifies regions with altered ASM, aiding in understanding DNA methylation
Area of Science:
- Epigenetics
- Genomics
- Computational Biology
Background:
- DNA methylation is a key epigenetic regulator of gene expression.
- Allele-specific methylation (ASM) is crucial for genomic imprinting and X chromosome inactivation.
- Sequence-dependent ASM is linked to genetic variations like SNPs.
Purpose of the Study:
- To develop a computational method for screening genomic regions with altered ASM.
- To identify differential ASM (DAMEs) between conditions using bisulfite sequencing data.
- To provide an R package, DAMEfinder, for analyzing ASM changes.
Main Methods:
- Developed a novel ASM scoring method using bisulfite sequencing data.
- Leveraged existing computational techniques within the DAMEfinder R package.
- Quantified ASM changes between conditions and clustered regions with consistent alterations.
Main Results:
- DAMEfinder accurately distinguishes imprinted/non-imprinted regions and sexes based on X inactivation.
- The method identified differential ASM signatures in colorectal cancer subtypes.
- Successfully re-identified known instances of loss of imprinting.
Conclusions:
- DAMEfinder detects differential ASM (DAMEs), offering a refined view beyond differential methylation.
- This tool aids in deciphering the complex roles of DNA methylation in development and disease.
- The package facilitates the discovery of novel ASM patterns relevant to various biological contexts.
