Related Experiment Video
Updated: Jun 22, 2026
08:38
Targeted DNA Methylation Analysis by Next-generation Sequencing
Published on: February 24, 2015
Advantages of next-generation sequencing versus the microarray in epigenetic research
Paul J Hurd1, Christopher J Nelson
1School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK. p.j.hurd@qmul.ac.uk
Briefings in Functional Genomics & Proteomics
|June 19, 2009
Summary
Next-generation sequencing (NGS) offers advantages over microarrays for genome analysis, enabling new biological questions. While NGS is becoming dominant, microarrays still have uses, and a future symbiotic relationship is likely.
Area of Science:
- Epigenetics and Genomics
Background:
- Epigenetics studies histone post-translational modifications (PTM) and DNA methylation genome-wide.
- Chromatin-immunoprecipitation (ChIP) combined with sequencing technologies visualizes epigenetic marks.
Purpose of the Study:
- To compare next-generation sequencing (NGS) with microarray analysis for genome-wide epigenetic studies.
- To discuss the evolving role of sequencing technologies in genomic research.
Main Methods:
- Utilized chromatin-immunoprecipitation (ChIP) combined with next-generation high-throughput sequencing.
- Analyzed genome-wide distribution of histone post-translational modifications (PTM) and DNA methylation.
Main Results:
- NGS provides advantages over microarrays for visualizing epigenetic marks genome-wide.
- Increasing affordability of NGS enables new biological research questions.
Conclusions:
- Next-generation sequencing (NGS) technologies are increasingly preferred over microarrays for genome analysis.
- Microarrays retain specific applications, and a future integration of both technologies is anticipated.
Related Concept Videos
03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
02:34DNA 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...
03:21RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
02:36Chromatin Immunoprecipitation- ChIP
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...