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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

Generating Multiple Base-Resolution DNA Methylomes Using Reduced Representation Bisulfite Sequencing.

Aniruddha Chatterjee^1,2, Euan J Rodger³, Peter A Stockwell⁴

¹Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand. aniruddha.chatterjee@otago.ac.nz.

Methods in Molecular Biology (Clifton, N.J.)

|December 8, 2016

Summary

This summary is machine-generated.

This study presents a protocol for multiplexing reduced representation bisulfite sequencing (RRBS) libraries, enabling efficient, large-scale genome-wide DNA methylation analysis. This method generates base-resolution methylomes for multiple samples in a single sequencing run.

Keywords:

CpG island DMAP DNA methylation Epigenetics Multiplexed Reduced representation bisulfite sequencing Second-generation sequencing

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Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Area of Science:

Genomics
Epigenetics
Molecular Biology

Background:

Reduced representation bisulfite sequencing (RRBS) is a key technique for genome-wide DNA methylation profiling.
Advancements in sequencing technology and cost reduction enable large-scale methylation studies.
Existing methods may not be optimized for simultaneous analysis of multiple samples.

Purpose of the Study:

To describe a protocol for multiplexing RRBS libraries for efficient sequencing.
To enable the generation of base-resolution methylomes from multiple samples in a single reaction.
To provide guidelines for data analysis of multiplexed RRBS libraries.

Main Methods:

Coupling size selection, bisulfite conversion, and second-generation sequencing.
Enriching for CpG-dense genomic regions.
Sequencing multiple RRBS libraries in a single reaction.

Main Results:

A protocol for generating base-resolution methylomes from multiplexed RRBS libraries.
Guidelines for base-calling and data analysis of multiplexed libraries.
Demonstration of feasibility for large-scale DNA methylation analysis.

Conclusions:

Multiplexed RRBS is an effective strategy for large-scale, genome-wide DNA methylation studies.
This approach facilitates cost-effective and efficient methylome profiling.
The described protocol and guidelines support broader application of RRBS.