Base-resolution DNA methylation landscape of zebrafish brain and liver.
Zebrafish (Danio rerio) is a vertebrate model organism that is widely used for studying a plethora of biological questions, including developmental processes, effects of external cues on phenotype, and human disease modeling. DNA methylation is an important epigenetic mechanism that contributes to gene regulation, and is prevalent in all vertebrates. Reduced representation bisulfite sequencing (RRBS) is a cost-effective technique to generate genome-wide DNA methylation maps and has been used in mammalian genomes (e.g., human, mouse and rat) but not in zebrafish. High-resolution DNA methylation data in zebrafish are limited: increased availability of such data will enable us to model and better understand the roles, causes and consequences of changes in DNA methylation. Here we present five high-resolution DNA methylation maps for wild-type zebrafish brain (two pooled male and two pooled female methylomes) and liver. These data were generated using the RRBS technique (includes 1.43 million CpG sites of zebrafish genome) on the Illumina HiSeq platform. Alignment to the reference genome was performed using the Zv9 genome assembly. To our knowledge, these datasets are the only RRBS datasets and base-resolution DNA methylation data available at this time for zebrafish brain and liver. These datasets could serve as a resource for future studies to document the functional role of DNA methylation in zebrafish. In addition, these datasets could be used as controls while performing analysis on treated samples.
Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand ; Gravida: National Centre for Growth and Development, 85 Park Road, Grafton, Auckland 1142, New Zealand.
Aniruddha
A
Chatterjee
Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand ; Otago Genomics and Bioinformatics Facility, Centre for Innovation, 87 St David Street, Dunedin 9016, New Zealand.
Peter A
PA
Stockwell
Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand ; Gravida: National Centre for Growth and Development, 85 Park Road, Grafton, Auckland 1142, New Zealand.
Julia A
JA
Horsfield
Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand ; Gravida: National Centre for Growth and Development, 85 Park Road, Grafton, Auckland 1142, New Zealand.
Ian M
IM
Morison
Gravida: National Centre for Growth and Development, 85 Park Road, Grafton, Auckland 1142, New Zealand ; Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9054, New Zealand.
Shinichi
S
Nakagawa
Brain; DNA methylation; Genome sequencing; Liver; RRBS; Zebrafish