Sex differences in DNA methylation and expression in zebrafish brain: a test of an extended 'male sex drive' hypothesis.
The sex drive hypothesis predicts that stronger selection on male traits has resulted in masculinization of the genome. Here we test whether such masculinizing effects can be detected at the level of the transcriptome and methylome in the adult zebrafish brain. Although methylation is globally similar, we identified 914 specific differentially methylated CpGs (DMCs) between males and females (435 were hypermethylated and 479 were hypomethylated in males compared to females). These DMCs were prevalent in gene body, intergenic regions and CpG island shores. We also discovered 15 distinct CpG clusters with striking sex-specific DNA methylation differences. In contrast, at transcriptome level, more female-biased genes than male-biased genes were expressed, giving little support for the male sex drive hypothesis. Our study provides genome-wide methylome and transcriptome assessment and sheds light on sex-specific epigenetic patterns and in zebrafish for the first time.
Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand. Electronic address: aniruddha.chatterjee@otago.ac.nz.
Aniruddha
A
Chatterjee
Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9054, New Zealand; Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, 2052 Sydney, NSW, Australia. Electronic address: m.nakagawa-lagisz@unsw.edu.au.
Malgorzata
M
Lagisz
Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand. Electronic address: euan.rodger@otago.ac.nz.
Euan J
EJ
Rodger
LKC School of Medicine, Nanyang Technological University and Human Genetics Division, Genome Institute of Singapore, Singapore. Electronic address: liz10@gis.a-star.edu.sg.
Li
L
Zhen
Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand. Electronic address: peter.stockwell@otago.ac.nz.
Peter A
PA
Stockwell
Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand. Electronic address: elizabeth.duncan@otago.ac.nz.
Elizabeth J
EJ
Duncan
Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand. Electronic address: julia.horsfield@otago.ac.nz.
Julia A
JA
Horsfield
LKC School of Medicine, Nanyang Technological University and Human Genetics Division, Genome Institute of Singapore, Singapore. Electronic address: gnanakkan@gis.a-star.edu.sg.
Justin
J
Jeyakani
LKC School of Medicine, Nanyang Technological University and Human Genetics Division, Genome Institute of Singapore, Singapore. Electronic address: mathavans@ntu.edu.sg.
Sinnakaruppan
S
Mathavan
Department of Biology, Keio University, 4-1-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8521, Japan. Electronic address: yuichi.ozaki@otago.ac.nz.
Yuichi
Y
Ozaki
Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9054, New Zealand; Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, 2052 Sydney, NSW, Australia; Diabetes and Metabolism Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia. Electronic address: s.nakagawa@unsw.edu.au.
Shinichi
S
Nakagawa
D000818:Animals; D001921:Brain / Q000378:metabolism*; D002875:Chromosomes / Q000235:genetics; D016000:Cluster Analysis; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D016678:Genome / Q000235:genetics; D008297:Male; D008954:Models, Biological; D012727:Sex Characteristics; D014158:Transcription, Genetic; D015027:Zebrafish / Q000235:genetics*
D021901:DNA, Intergenic
Brain; CpG island; CpG site; DNA methylation; Male sex drive; Masculinization; RNA-Seq; RRBS; Sexual dimorphism; Zebrafish