Methylome data derived from maternal-zygotic DNA methyltransferase 3aa-/- zebrafish

Masaki Shirai; Kazuya Takayama; Haruko Takahashi; Yudai Hirose; Masashi Fujii; Akinori Awazu; Nobuyoshi Shimoda; Yutaka Kikuchi

doi:10.1016/j.dib.2022.108514

Methylome data derived from maternal-zygotic DNA methyltransferase 3aa^-/- zebrafish

Data Brief. 2022 Aug 5:44:108514. doi: 10.1016/j.dib.2022.108514. eCollection 2022 Oct.

Authors

Masaki Shirai¹, Kazuya Takayama¹, Haruko Takahashi^{1

2}, Yudai Hirose³, Masashi Fujii², Akinori Awazu², Nobuyoshi Shimoda⁴, Yutaka Kikuchi^{1

2}

Affiliations

¹ Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526 Japan.
² Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
³ Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526 Japan.
⁴ Laboratory of Molecular Analysis, Research and Development Management Center, National Center for Geriatrics and Gerontology, 7-430, Morioka, Obu, Aichi 474-8522, Japan.

Abstract

Genomic DNA methylation is an epigenetic marker mediated by DNA methyltransferases (Dnmts); in vertebrates, it comprises of a maintenance DNA methyltransferase, Dnmt1, and two de novo DNA methyltransferases (Dnmt3a and Dnmt3b). In zebrafish, there are two homologs of the mammalian Dnmt3a: Dnmt3aa and Dnmt3ab. A knockout (KO) mutant of zebrafish dnmt3aa was generated using the CRISPR/Cas9 genome-editing system as a new model for DNA methylation research. Since zebrafish dnmt3aa KO mutants were viable and fertile, a maternal-zygotic dnmt3aa deficient mutant (MZdnmt3aa) was generated. We performed whole-genome bisulfite sequencing (WGBS) to reveal the DNA methylation profile using this mutant and identified genomic regions with altered CpG methylation as differentially methylated regions (DMRs) in this mutant compared to those in the wild-type fish. We provided novel raw and processed datasets using the MZdnmt3aa KO mutant, and the raw data of WGBS are available through the Gene Expression Omnibus (GEO), accession number GSE178690.

Keywords: DNA methylation; Dnmt3aa; Whole genome bisulfate sequencing; Zebrafish.