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Related Experiment Video

Updated: May 8, 2026

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

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

Published on: February 24, 2015

Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing.

Aniruddha Chatterjee1, Yuichi Ozaki, Peter A Stockwell

  • 1Department of Pathology; Dunedin School of Medicine; University of Otago; Dunedin, New Zealand; Gravida: National Centre for Growth and Development; Auckland, New Zealand.

Epigenetics
|August 27, 2013
PubMed
Summary
This summary is machine-generated.

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Reduced representation bisulfite sequencing (RRBS) is now validated for zebrafish DNA methylation analysis. This study provides the first base-pair resolution methylomes for zebrafish, revealing higher global DNA methylation than in humans.

Area of Science:

  • Epigenetics and Genomics
  • Comparative Methylomics
  • Model Organism Research

Background:

  • Reduced representation bisulfite sequencing (RRBS) is a key technique for profiling DNA methylation in mammalian genomes.
  • The zebrafish, a vital model organism, lacks base-pair resolution methylome characterization using RRBS.
  • Understanding zebrafish DNA methylation is crucial for comparative genomics and developmental biology.

Purpose of the Study:

  • To evaluate the suitability of RRBS for generating high-resolution DNA methylomes in zebrafish.
  • To create the first base-pair resolution methylomes of adult zebrafish brain.
  • To compare global DNA methylation patterns between zebrafish and human genomes.

Main Methods:

  • Generated four single-nucleotide resolution DNA methylomes of adult zebrafish brain using RRBS.
Keywords:
CpG siteCpG10DNA methylationMspIRRBSbrainzebrafish

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Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain
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Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain

Published on: July 12, 2012

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Last Updated: May 8, 2026

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

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

Published on: February 24, 2015

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain
13:11

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain

Published on: July 12, 2012

  • Performed in silico simulations to analyze fragment distribution and CpG enrichment in zebrafish genomes.
  • Sequenced 98 million reads across four RRBS brain libraries, analyzing mapping frequencies and CpG distribution.

    • Main Results:

    • Zebrafish RRBS libraries exhibited higher frequencies of multiple mapping compared to human libraries.
    • The zebrafish methylome shows significantly higher global DNA methylation than the human methylome.
    • CpG dinucleotides were enriched in CpG island shores and found predominantly in gene bodies (45%) and promoters (7%).

    Conclusions:

    • RRBS is a suitable and effective technique for comprehensive DNA methylation analysis in zebrafish.
    • This study establishes a reproducible roadmap for generating base-pair level methylomes in zebrafish.
    • The findings highlight significant differences in global DNA methylation between zebrafish and humans.