Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing

Aniruddha Chatterjee, Yuichi Ozaki, Peter A. Stockwell, Julia A. Horsfield, Ian M. Morison, Shinichi Nakagawa

Research output: Contribution to journalArticlepeer-review

56 Citations (Scopus)


Reduced representation bisulfite sequencing (RRBS) has been used to profile DNA methylation patterns in mammalian genomes such as human, mouse and rat. The methylome of the zebrafish, an important animal model, has not yet been characterized at base-pair resolution using RRBS. Therefore, we evaluated the technique of RRBS in this model organism by generating four single-nucleotide resolution DNA methylomes of adult zebrafish brain. We performed several simulations to show the distribution of fragments and enrichment of CpGs in different in silico reduced representation genomes of zebrafish. Four RRBS brain libraries generated 98 million sequenced reads and had higher frequencies of multiple mapping than equivalent human RRBS libraries. The zebrafish methylome indicates there is higher global DNA methylation in the zebrafish genome compared with its equivalent human methylome. This observation was confirmed by RRBS of zebrafish liver. High coverage CpG dinucleotides are enriched in CpG island shores more than in the CpG island core. We found that 45% of the mapped CpGs reside in gene bodies, and 7% in gene promoters. This analysis provides a roadmap for generating reproducible base-pair level methylomes for zebrafish using RRBS and our results provide the first evidence that RRBS is a suitable technique for global methylation analysis in zebrafish.

Original languageEnglish
Pages (from-to)979-989
Number of pages11
Issue number9
Publication statusPublished - 2013 Sept
Externally publishedYes


  • Brain
  • CpG site
  • DNA methylation
  • MspI
  • RRBS
  • Zebrafish

ASJC Scopus subject areas

  • Molecular Biology
  • Cancer Research


Dive into the research topics of 'Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing'. Together they form a unique fingerprint.

Cite this