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Related Concept Videos

Restriction Enzymes01:11

Restriction Enzymes

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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.
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Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
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Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
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Related Experiment Video

Updated: Feb 15, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing
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msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data.

Benjamin T Mayne1,2, Shalem Y Leemaqz3,4, Sam Buckberry5,6

  • 1Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia. benjamin.mayne@adelaide.edu.au.

Scientific Reports
|February 3, 2018
PubMed
Summary

msgbsR is a new R package for analyzing DNA methylation using methylation-sensitive restriction enzyme sequencing (MRE-seq). It provides computational tools to identify and quantify methylation differences in large genomes, addressing limitations of current software.

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Area of Science:

  • Genomics
  • Epigenetics
  • Bioinformatics

Background:

  • Genotyping-by-sequencing (GBS) and RAD-seq are cost-effective for analyzing large genomes.
  • Methylation-sensitive restriction enzyme sequencing (MRE-seq) studies DNA methylation in previously inaccessible genomic regions.
  • Existing software lacks comprehensive tools for MRE-seq data analysis.

Purpose of the Study:

  • To develop an R package, msgbsR, for analyzing MRE-seq experiments.
  • To provide computational tools for identifying and quantifying DNA methylation differences between samples.
  • To enable analysis of methylation in large populations and unannotated genomic regions.

Main Methods:

  • Developed msgbsR, an R package for MRE-seq data analysis.
  • Implemented functions to identify and quantify read counts at methylated sites from BAM files.
  • Included functionality to verify restriction enzyme cut sites and assess DNA methylation based on read coverage.

Main Results:

  • msgbsR offers tools for analyzing MRE-seq experiments, including read count quantification and cut site verification.
  • The package assesses DNA methylation using read coverage, analogous to RNA sequencing analysis.
  • msgbsR is suitable for analyzing differential methylation in large populations.

Conclusions:

  • msgbsR addresses the computational gap for MRE-seq data analysis.
  • The package facilitates the study of DNA methylation in diverse and large-scale genomic studies.
  • msgbsR is freely available as a Bioconductor package.