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Related Concept Videos

Maxam-Gilbert Sequencing01:05

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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.
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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
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Bisulfite Sequence Analyses Using CyVerse Discovery Environment: From Mapping to DMRs.

Jawon Song1, Greg Zynda1, Samuel Beck2

  • 1Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas.

Current Protocols in Plant Biology
|November 15, 2019
PubMed
Summary

DNA methylation influences gene suppression, but mechanisms remain unclear. New user-friendly pipelines, ZED-align and BisuKit, aid plant DNA methylation analysis, especially in CpG, CHG, and CHH contexts.

Keywords:
DNA methylationbisulfite alignmentdifferentially methylated regionsepigenetic modificationslow-coverage sequencing data analysiswhole genome bisulfite sequencing

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DNA Methylation: Bisulphite Modification and Analysis
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Area of Science:

  • Epigenetics and Genomics
  • Plant Molecular Biology

Background:

  • DNA methylation is a key epigenetic mechanism regulating gene expression and biological processes.
  • While CpG methylation is well-studied in mammals, plant methylation involves CpG, CHG, and CHH contexts, with less developed analytical tools.
  • Understanding plant DNA methylation is crucial for deciphering gene regulation and development.

Purpose of the Study:

  • To address the need for efficient and user-friendly pipelines for analyzing plant DNA methylation.
  • To provide tools for deciphering methylation patterns in CpG, CHG, and CHH contexts in plants.

Main Methods:

  • Development and deployment of ZED-align and BisuKit on the CyVerse infrastructure.
  • User-friendly applications designed for bisulfite sequencing data analysis.
  • Minimal user intervention required for running multiple command-line based bioinformatics packages.

Main Results:

  • Introduction of ZED-align and BisuKit as accessible tools for plant DNA methylation analysis.
  • Facilitation of the study of diverse plant methylation contexts (CpG, CHG, CHH).
  • Empowerment of researchers to analyze bisulfite sequencing data with ease.

Conclusions:

  • ZED-align and BisuKit provide essential, user-friendly pipelines for plant DNA methylation research.
  • These tools simplify the analysis of complex methylation patterns, advancing the field of plant epigenetics.
  • The developed pipelines enhance the ability to investigate gene suppression and other biological roles of DNA methylation in plants.