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Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies

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Comparative epigenome analysis using Infinium DNA methylation BeadChips.

Wubin Ding¹, Diljeet Kaur¹, Steve Horvath^2,3

¹Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA, 19104, USA.

Briefings in Bioinformatics

|January 8, 2023

Summary

This summary is machine-generated.

New informatics tools enable DNA methylation analysis across diverse mammalian species, including mice. This advances epigenetics research by providing accurate, species-specific data for model organisms and domesticated animals.

Keywords:

DNA methylation comparative epigenetics mouse epigenetics

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A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

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Published on: August 13, 2020

Area of Science:

Epigenetics
Bioinformatics
Comparative Genomics

Background:

Infinium DNA methylation BeadChips are available for non-human mammals, but supporting informatics lags.
Epigenetics studies in model organisms require specialized analytical tools.

Purpose of the Study:

To develop informatics infrastructure for DNA methylation analysis across multiple mammalian species.
To enable accurate epigenome research in domesticated animals and inbred laboratory mice.

Main Methods:

Developed a data-driven analysis pipeline (SeSAMe version 1.16.0+) for species inference, genome-specific preprocessing, and regression modeling.
Applied methods to 310 species and 37 inbred mouse strains.
Performed comparative analysis to study epigenome evolution across genomic territories and tissue types.

Main Results:

Genome-specific preprocessing demonstrated improved accuracy over generic pipelines, preventing artifacts.
Identified a catalog of inbred mouse strain-specific DNA methylation differences.
Discovered links between methylation differences and strain-specific immune, metabolic, and neurological phenotypes.

Conclusions:

Streamlined DNA methylation array analysis for non-model organisms.
Extended epigenome research capabilities to a broader range of species.
Provided insights into epigenome evolution and strain-specific variations in mammals.