Comparative epigenomic profiling of the DNA methylome in mouse and Zebrafish uncovers high interspecies divergence

Chi Zhang, Yujin Hoshida, Kirsten C. Sadler

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

The DNA methylation landscape is dynamically patterned during development and distinct methylation patterns distinguish healthy from diseased cells. However, whether tissue-specific methylation patterns are conserved across species is not known. We used comparative methylome analysisof base-resolution DNA methylation profiles from the liver and brain ofmouse and zebrafish generated by reduced representation bisulfite sequencing to identify the conserved and divergent aspects of the methylome in these commonly used vertebrate model organisms. On average, 24% of CpGs are methylated in mouse livers and the pattern of methylation was highly concordant among four male mice from two different strains. The same level of methylation (24.2%) was identified in mouse brain. In striking contrast, zebrafish had 63 and 70% of CpG methylation in the liver and brain, respectively. This is attributed, in part, to the higher percentage of the zebrafish genome occupied by transposable elements (52% vs. 45%in mice). Thus, the species identity was more significant in determining methylome patterning than was the similarity in organ function. Conserved features of the methylome across tissues and species was the exclusion of methylation from promoters and from CpG islands near transcriptionstart sites, and the clustering of methylated CpGs in gene bodies and intragenic regions. These data suggest that DNA methylation reflects species-specific genome structure, and supports the notion that DNA methylation in non-promoter regions may contribute to genome evolution.

Original languageEnglish (US)
Article number110
JournalFrontiers in Genetics
Volume7
Issue numberJUN
DOIs
StatePublished - Jun 17 2016
Externally publishedYes

Fingerprint

DNA Fingerprinting
Zebrafish
Epigenomics
Methylation
DNA Methylation
Genome
Liver
Brain
Body Regions
CpG Islands
DNA Transposable Elements
Cluster Analysis
Vertebrates
Genes

Keywords

  • Brain
  • Comparative epigenomics
  • DNA methylation
  • Liver
  • Mouse
  • Zebrafish

ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Genetics(clinical)

Cite this

Comparative epigenomic profiling of the DNA methylome in mouse and Zebrafish uncovers high interspecies divergence. / Zhang, Chi; Hoshida, Yujin; Sadler, Kirsten C.

In: Frontiers in Genetics, Vol. 7, No. JUN, 110, 17.06.2016.

Research output: Contribution to journalArticle

@article{421886af80dc43d3b7358c84d65de87b,
title = "Comparative epigenomic profiling of the DNA methylome in mouse and Zebrafish uncovers high interspecies divergence",
abstract = "The DNA methylation landscape is dynamically patterned during development and distinct methylation patterns distinguish healthy from diseased cells. However, whether tissue-specific methylation patterns are conserved across species is not known. We used comparative methylome analysisof base-resolution DNA methylation profiles from the liver and brain ofmouse and zebrafish generated by reduced representation bisulfite sequencing to identify the conserved and divergent aspects of the methylome in these commonly used vertebrate model organisms. On average, 24{\%} of CpGs are methylated in mouse livers and the pattern of methylation was highly concordant among four male mice from two different strains. The same level of methylation (24.2{\%}) was identified in mouse brain. In striking contrast, zebrafish had 63 and 70{\%} of CpG methylation in the liver and brain, respectively. This is attributed, in part, to the higher percentage of the zebrafish genome occupied by transposable elements (52{\%} vs. 45{\%}in mice). Thus, the species identity was more significant in determining methylome patterning than was the similarity in organ function. Conserved features of the methylome across tissues and species was the exclusion of methylation from promoters and from CpG islands near transcriptionstart sites, and the clustering of methylated CpGs in gene bodies and intragenic regions. These data suggest that DNA methylation reflects species-specific genome structure, and supports the notion that DNA methylation in non-promoter regions may contribute to genome evolution.",
keywords = "Brain, Comparative epigenomics, DNA methylation, Liver, Mouse, Zebrafish",
author = "Chi Zhang and Yujin Hoshida and Sadler, {Kirsten C.}",
year = "2016",
month = "6",
day = "17",
doi = "10.3389/fgene.2016.00110",
language = "English (US)",
volume = "7",
journal = "Frontiers in Genetics",
issn = "1664-8021",
publisher = "Frontiers Media S. A.",
number = "JUN",

}

TY - JOUR

T1 - Comparative epigenomic profiling of the DNA methylome in mouse and Zebrafish uncovers high interspecies divergence

AU - Zhang, Chi

AU - Hoshida, Yujin

AU - Sadler, Kirsten C.

PY - 2016/6/17

Y1 - 2016/6/17

N2 - The DNA methylation landscape is dynamically patterned during development and distinct methylation patterns distinguish healthy from diseased cells. However, whether tissue-specific methylation patterns are conserved across species is not known. We used comparative methylome analysisof base-resolution DNA methylation profiles from the liver and brain ofmouse and zebrafish generated by reduced representation bisulfite sequencing to identify the conserved and divergent aspects of the methylome in these commonly used vertebrate model organisms. On average, 24% of CpGs are methylated in mouse livers and the pattern of methylation was highly concordant among four male mice from two different strains. The same level of methylation (24.2%) was identified in mouse brain. In striking contrast, zebrafish had 63 and 70% of CpG methylation in the liver and brain, respectively. This is attributed, in part, to the higher percentage of the zebrafish genome occupied by transposable elements (52% vs. 45%in mice). Thus, the species identity was more significant in determining methylome patterning than was the similarity in organ function. Conserved features of the methylome across tissues and species was the exclusion of methylation from promoters and from CpG islands near transcriptionstart sites, and the clustering of methylated CpGs in gene bodies and intragenic regions. These data suggest that DNA methylation reflects species-specific genome structure, and supports the notion that DNA methylation in non-promoter regions may contribute to genome evolution.

AB - The DNA methylation landscape is dynamically patterned during development and distinct methylation patterns distinguish healthy from diseased cells. However, whether tissue-specific methylation patterns are conserved across species is not known. We used comparative methylome analysisof base-resolution DNA methylation profiles from the liver and brain ofmouse and zebrafish generated by reduced representation bisulfite sequencing to identify the conserved and divergent aspects of the methylome in these commonly used vertebrate model organisms. On average, 24% of CpGs are methylated in mouse livers and the pattern of methylation was highly concordant among four male mice from two different strains. The same level of methylation (24.2%) was identified in mouse brain. In striking contrast, zebrafish had 63 and 70% of CpG methylation in the liver and brain, respectively. This is attributed, in part, to the higher percentage of the zebrafish genome occupied by transposable elements (52% vs. 45%in mice). Thus, the species identity was more significant in determining methylome patterning than was the similarity in organ function. Conserved features of the methylome across tissues and species was the exclusion of methylation from promoters and from CpG islands near transcriptionstart sites, and the clustering of methylated CpGs in gene bodies and intragenic regions. These data suggest that DNA methylation reflects species-specific genome structure, and supports the notion that DNA methylation in non-promoter regions may contribute to genome evolution.

KW - Brain

KW - Comparative epigenomics

KW - DNA methylation

KW - Liver

KW - Mouse

KW - Zebrafish

UR - http://www.scopus.com/inward/record.url?scp=84977480159&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84977480159&partnerID=8YFLogxK

U2 - 10.3389/fgene.2016.00110

DO - 10.3389/fgene.2016.00110

M3 - Article

C2 - 27379160

AN - SCOPUS:84977480159

VL - 7

JO - Frontiers in Genetics

JF - Frontiers in Genetics

SN - 1664-8021

IS - JUN

M1 - 110

ER -