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DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Updated: Oct 4, 2025

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

A mammalian methylation array for profiling methylation levels at conserved sequences.

Adriana Arneson^1,2, Amin Haghani³, Michael J Thompson⁴

¹Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA.

Nature Communications

|February 11, 2022

Summary

This summary is machine-generated.

Researchers developed a mammalian methylation array for cross-species epigenetic studies. This array measures conserved CpGs across mammals, enabling biomarker discovery and comparative epigenomics.

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Area of Science:

Epigenetics
Comparative Genomics
Mammalian Biology

Background:

Infinium methylation arrays are limited to specific species, hindering cross-species epigenetic research.
Species-specific arrays present probe differences that confound comparative analyses.

Purpose of the Study:

To develop a universal mammalian methylation array for cross-species epigenetic comparisons.
To enable epigenetic biomarker discovery and facilitate translation of biological insights across mammalian species.

Main Methods:

Designed a custom array targeting up to 36,000 conserved CpGs per species.
Developed probes tolerant to cross-species mutations for broad applicability.
Annotated the array across over 200 mammalian species, including CpG island and chromatin state analysis.

Main Results:

Demonstrated high-fidelity calibration experiments in humans, rats, and mice.
The array is applicable to all mammalian species, including unsequenced ones.
Provides deep coverage of conserved cytosines for biomarker development.

Conclusions:

The mammalian methylation array overcomes limitations of existing technologies for cross-species epigenetics.
Facilitates robust comparative epigenomic studies and epigenetic biomarker development in mammals.
Enhances the translatability of biological insights from model organisms to other mammalian species.