Format

Send to

Choose Destination
Epigenetics. 2013 Sep;8(9):979-89. doi: 10.4161/epi.25797. Epub 2013 Jul 24.

Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing.

Author information

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

Abstract

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.

KEYWORDS:

CpG site; CpG10; DNA methylation; MspI; RRBS; brain; zebrafish

PMID:
23975027
PMCID:
PMC3883775
DOI:
10.4161/epi.25797
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Taylor & Francis Icon for PubMed Central
Loading ...
Support Center