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Related Concept Videos

DNA Isolation01:24

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
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Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
Restriction Enzymes01:11

Restriction Enzymes

Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called restriction sites. Such palindromic DNA sequences or inverted repeats are commonly found in regions of functional significance, such as the origin of replication, gene operator sites, and regions containing transcription termination signals.
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...

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Related Experiment Video

Updated: Jun 15, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

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Novel enzyme-based reduced representation method for DNA methylation profiling with low inputs.

Qianli Liu1,2, Kathryn A Helmin1, Zachary D Dortzbach1

  • 1Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, United States.

Nucleic Acids Research
|June 30, 2025
PubMed
Summary
This summary is machine-generated.

Reduced representation enzymatic methylation sequencing (RREM-seq) enables accurate DNA methylation profiling from low-input samples. This method overcomes limitations of traditional bisulfite sequencing, offering superior coverage and reliable results even with minimal DNA.

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DNA Methylation: Bisulphite Modification and Analysis
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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
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DNA Methylation: Bisulphite Modification and Analysis
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DNA Methylation: Bisulphite Modification and Analysis

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Area of Science:

  • Epigenetics
  • Genomics
  • Molecular Biology

Background:

  • Bisulfite-based DNA methylation sequencing methods can degrade DNA, particularly in low-input samples, compromising data quality.
  • Enzymatic Methylation Sequencing (EM-seq) offers a less biased alternative with improved genome coverage.
  • Reduced representation approaches increase efficiency and cost-effectiveness by enriching CpG-rich regions.

Purpose of the Study:

  • To adapt enzymatic methylation sequencing technology for reduced representation approaches (RREM-seq).
  • To enable DNA methylation profiling from low-input samples.
  • To compare RREM-seq performance against reduced representation bisulfite sequencing (RRBS).

Main Methods:

  • Developed and implemented a reduced representation EM-seq (RREM-seq) protocol.
  • Compared RREM-seq with RRBS using varying amounts of mouse and human DNA.
  • Analyzed DNA methylation profiles in mouse T cell populations and human clinical samples.

Main Results:

  • RRBS failed with <2 ng DNA, while RREM-seq successfully generated libraries from 1-25 ng DNA.
  • Low-input RREM-seq libraries showed >10-fold greater regulatory genomic element coverage than RRBS.
  • RREM-seq detected methylation differences between T cell populations in severe SARS-CoV-2 pneumonia patients.

Conclusions:

  • RREM-seq is a robust method for DNA methylation profiling of low-input samples.
  • The technique provides single-nucleotide resolution and enhanced genomic coverage.
  • RREM-seq is suitable for clinical samples and advancing epigenetic research.