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 journalArticle

37 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)979-989
Number of pages11
JournalEpigenetics
Volume8
Issue number9
DOIs
Publication statusPublished - 2013 Sep
Externally publishedYes

Fingerprint

Brain Mapping
Zebrafish
CpG Islands
Genome
DNA Methylation
Base Pairing
hydrogen sulfite
Brain
Computer Simulation
Methylation
Genes
Libraries
Nucleotides
Animal Models
Liver
DNA

Keywords

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

ASJC Scopus subject areas

  • Molecular Biology
  • Cancer Research

Cite this

Chatterjee, A., Ozaki, Y., Stockwell, P. A., Horsfield, J. A., Morison, I. M., & Nakagawa, S. (2013). Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing. Epigenetics, 8(9), 979-989. https://doi.org/10.4161/epi.25797

Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing. / Chatterjee, Aniruddha; Ozaki, Yuichi; Stockwell, Peter A.; Horsfield, Julia A.; Morison, Ian M.; Nakagawa, Shinichi.

In: Epigenetics, Vol. 8, No. 9, 09.2013, p. 979-989.

Research output: Contribution to journalArticle

Chatterjee, A, Ozaki, Y, Stockwell, PA, Horsfield, JA, Morison, IM & Nakagawa, S 2013, 'Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing', Epigenetics, vol. 8, no. 9, pp. 979-989. https://doi.org/10.4161/epi.25797
Chatterjee A, Ozaki Y, Stockwell PA, Horsfield JA, Morison IM, Nakagawa S. Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing. Epigenetics. 2013 Sep;8(9):979-989. https://doi.org/10.4161/epi.25797
Chatterjee, Aniruddha ; Ozaki, Yuichi ; Stockwell, Peter A. ; Horsfield, Julia A. ; Morison, Ian M. ; Nakagawa, Shinichi. / Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing. In: Epigenetics. 2013 ; Vol. 8, No. 9. pp. 979-989.
@article{209b8b6290f545498854998a81bc2e6f,
title = "Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing",
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 = "Brain, CpG site, CpG, DNA methylation, MspI, RRBS, Zebrafish",
author = "Aniruddha Chatterjee and Yuichi Ozaki and Stockwell, {Peter A.} and Horsfield, {Julia A.} and Morison, {Ian M.} and Shinichi Nakagawa",
year = "2013",
month = "9",
doi = "10.4161/epi.25797",
language = "English",
volume = "8",
pages = "979--989",
journal = "Epigenetics",
issn = "1559-2294",
publisher = "Landes Bioscience",
number = "9",

}

TY - JOUR

T1 - Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing

AU - Chatterjee, Aniruddha

AU - Ozaki, Yuichi

AU - Stockwell, Peter A.

AU - Horsfield, Julia A.

AU - Morison, Ian M.

AU - Nakagawa, Shinichi

PY - 2013/9

Y1 - 2013/9

N2 - 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.

AB - 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.

KW - Brain

KW - CpG site

KW - CpG

KW - DNA methylation

KW - MspI

KW - RRBS

KW - Zebrafish

UR - http://www.scopus.com/inward/record.url?scp=84883524651&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84883524651&partnerID=8YFLogxK

U2 - 10.4161/epi.25797

DO - 10.4161/epi.25797

M3 - Article

C2 - 23975027

AN - SCOPUS:84883524651

VL - 8

SP - 979

EP - 989

JO - Epigenetics

JF - Epigenetics

SN - 1559-2294

IS - 9

ER -