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Changes in DNA methylation during epigenetic-associated sex reversal under low temperature in Takifugu rubripes

DNA methylation has frequently been implicated in sex determination and differentiation in teleost species. In order to detect the DNA methylation patterns established during sexual differentiation in tiger pufferfish T. rubripes, we performed comprehensive whole genome methylation sequencing and an...

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Autores principales: Zhou, He, Zhuang, Zi-Xin, Sun, Yu-Qing, Chen, Qi, Zheng, Xin-Yi, Liang, Yu-Ting, Mahboob, Shahid, Wang, Qian, Zhang, Rui, Al-Ghanim, Khalid A., Shao, Chang-Wei, Li, Ya-Juan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711519/
https://www.ncbi.nlm.nih.gov/pubmed/31454376
http://dx.doi.org/10.1371/journal.pone.0221641
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author Zhou, He
Zhuang, Zi-Xin
Sun, Yu-Qing
Chen, Qi
Zheng, Xin-Yi
Liang, Yu-Ting
Mahboob, Shahid
Wang, Qian
Zhang, Rui
Al-Ghanim, Khalid A.
Shao, Chang-Wei
Li, Ya-Juan
author_facet Zhou, He
Zhuang, Zi-Xin
Sun, Yu-Qing
Chen, Qi
Zheng, Xin-Yi
Liang, Yu-Ting
Mahboob, Shahid
Wang, Qian
Zhang, Rui
Al-Ghanim, Khalid A.
Shao, Chang-Wei
Li, Ya-Juan
author_sort Zhou, He
collection PubMed
description DNA methylation has frequently been implicated in sex determination and differentiation in teleost species. In order to detect the DNA methylation patterns established during sexual differentiation in tiger pufferfish T. rubripes, we performed comprehensive whole genome methylation sequencing and analyses of the gonads of male, female, and pseudo male. We obtained a total of 33.12, 32.44, and 31.60 Gb clean data for male, female, and pseudo male, with a sequencing depth of 66.44×, 60.47× and 54.86×, respectively. The methylation level of cytosine (C) residues in the genomic DNA from gonads was 11.016%, 10.428%, and 11.083% in male, female, and pseudo male, respectively. More than 65% of C methylation was at CpG sites, and less than 1% was at CHG and CHH sites. In each regulatory element, there were low methylation levels on both sides of the transcription start site, and higher methylation levels in exons, introns, and downstream of genes. The highest mCpG was on chromosome 8 and the lowest mCpG was on chromosome 5. Comparisons of whole-genome DNA methylation between pairs of samples revealed that there were 3,173 differentially methylated regions (DMRs) between female and male, and 3,037 DMRs between male and pseudo male, corresponding to 0.232% and 0.223% of the length of the genome, respectively. There were only 1,635 DMRs between female and pseudo male, representing 0.127% of the length of the genome. A number of differentially methylated genes (DMGs) related to sex determination and differentiation were selected, such as amhr2 and pfcyp19a. After Bisulfite Sequencing PCR (BSP) verification, amhr2 was exhibited low methylation level in normal males and pseudo male, and high methylation level in normal females but pfcyp19a showed low methylation level in normal females and high methylation level in normal males and pseudo males. These results provide information about the molecular epigenetic mechanisms of DNA methylation during low-temperature induced masculinization of tiger pufferfish, and increase our understanding of the mechanisms of sex determination and differentiation in this important aquaculture fish species.
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spelling pubmed-67115192019-09-10 Changes in DNA methylation during epigenetic-associated sex reversal under low temperature in Takifugu rubripes Zhou, He Zhuang, Zi-Xin Sun, Yu-Qing Chen, Qi Zheng, Xin-Yi Liang, Yu-Ting Mahboob, Shahid Wang, Qian Zhang, Rui Al-Ghanim, Khalid A. Shao, Chang-Wei Li, Ya-Juan PLoS One Research Article DNA methylation has frequently been implicated in sex determination and differentiation in teleost species. In order to detect the DNA methylation patterns established during sexual differentiation in tiger pufferfish T. rubripes, we performed comprehensive whole genome methylation sequencing and analyses of the gonads of male, female, and pseudo male. We obtained a total of 33.12, 32.44, and 31.60 Gb clean data for male, female, and pseudo male, with a sequencing depth of 66.44×, 60.47× and 54.86×, respectively. The methylation level of cytosine (C) residues in the genomic DNA from gonads was 11.016%, 10.428%, and 11.083% in male, female, and pseudo male, respectively. More than 65% of C methylation was at CpG sites, and less than 1% was at CHG and CHH sites. In each regulatory element, there were low methylation levels on both sides of the transcription start site, and higher methylation levels in exons, introns, and downstream of genes. The highest mCpG was on chromosome 8 and the lowest mCpG was on chromosome 5. Comparisons of whole-genome DNA methylation between pairs of samples revealed that there were 3,173 differentially methylated regions (DMRs) between female and male, and 3,037 DMRs between male and pseudo male, corresponding to 0.232% and 0.223% of the length of the genome, respectively. There were only 1,635 DMRs between female and pseudo male, representing 0.127% of the length of the genome. A number of differentially methylated genes (DMGs) related to sex determination and differentiation were selected, such as amhr2 and pfcyp19a. After Bisulfite Sequencing PCR (BSP) verification, amhr2 was exhibited low methylation level in normal males and pseudo male, and high methylation level in normal females but pfcyp19a showed low methylation level in normal females and high methylation level in normal males and pseudo males. These results provide information about the molecular epigenetic mechanisms of DNA methylation during low-temperature induced masculinization of tiger pufferfish, and increase our understanding of the mechanisms of sex determination and differentiation in this important aquaculture fish species. Public Library of Science 2019-08-27 /pmc/articles/PMC6711519/ /pubmed/31454376 http://dx.doi.org/10.1371/journal.pone.0221641 Text en © 2019 Zhou et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Zhou, He
Zhuang, Zi-Xin
Sun, Yu-Qing
Chen, Qi
Zheng, Xin-Yi
Liang, Yu-Ting
Mahboob, Shahid
Wang, Qian
Zhang, Rui
Al-Ghanim, Khalid A.
Shao, Chang-Wei
Li, Ya-Juan
Changes in DNA methylation during epigenetic-associated sex reversal under low temperature in Takifugu rubripes
title Changes in DNA methylation during epigenetic-associated sex reversal under low temperature in Takifugu rubripes
title_full Changes in DNA methylation during epigenetic-associated sex reversal under low temperature in Takifugu rubripes
title_fullStr Changes in DNA methylation during epigenetic-associated sex reversal under low temperature in Takifugu rubripes
title_full_unstemmed Changes in DNA methylation during epigenetic-associated sex reversal under low temperature in Takifugu rubripes
title_short Changes in DNA methylation during epigenetic-associated sex reversal under low temperature in Takifugu rubripes
title_sort changes in dna methylation during epigenetic-associated sex reversal under low temperature in takifugu rubripes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711519/
https://www.ncbi.nlm.nih.gov/pubmed/31454376
http://dx.doi.org/10.1371/journal.pone.0221641
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