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Single-base-resolution methylome of giant panda’s brain, liver and pancreatic tissue

The giant panda (Ailuropoda melanoleuca) is one of the most endangered mammals, and its conservation has significant ecosystem and cultural service value. Cytosine DNA methylation (5mC) is a stable epigenetic modification to the genome and has multiple functions such as gene regulation. However, DNA...

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Autores principales: Ren, Jianying, Shen, Fujun, Zhang, Liang, Sun, Jie, Yang, Miao, Yang, Mingyu, Hou, Rong, Yue, Bisong, Zhang, Xiuyue
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800980/
https://www.ncbi.nlm.nih.gov/pubmed/31637123
http://dx.doi.org/10.7717/peerj.7847
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author Ren, Jianying
Shen, Fujun
Zhang, Liang
Sun, Jie
Yang, Miao
Yang, Mingyu
Hou, Rong
Yue, Bisong
Zhang, Xiuyue
author_facet Ren, Jianying
Shen, Fujun
Zhang, Liang
Sun, Jie
Yang, Miao
Yang, Mingyu
Hou, Rong
Yue, Bisong
Zhang, Xiuyue
author_sort Ren, Jianying
collection PubMed
description The giant panda (Ailuropoda melanoleuca) is one of the most endangered mammals, and its conservation has significant ecosystem and cultural service value. Cytosine DNA methylation (5mC) is a stable epigenetic modification to the genome and has multiple functions such as gene regulation. However, DNA methylome of giant panda and its function have not been reported as of yet. Bisulfite sequencing was performed on a 4-day-old male giant panda’s brain, liver and pancreatic tissues. We found that the whole genome methylation level was about 0.05% based on reads normalization and mitochondrial DNA was not methylated. Three tissues showed similar methylation tendency in the protein-coding genes of their genomes, but the brain genome had a higher count of methylated genes. We obtained 467 and 1,013 different methylation regions (DMR) genes in brain vs. pancreas and liver, while only 260 DMR genes were obtained in liver vs pancreas. Some lncRNA were also DMR genes, indicating that methylation may affect biological processes by regulating other epigenetic factors. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that low methylated promoter, high methylated promoter and DMR genes were enriched at some important and tissue-specific items and pathways, like neurogenesis, metabolism and immunity. DNA methylation may drive or maintain tissue specificity and organic functions and it could be a crucial regulating factor for the development of newborn cubs. Our study offers the first insight into giant panda’s DNA methylome, laying a foundation for further exploration of the giant panda’s epigenetics.
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spelling pubmed-68009802019-10-21 Single-base-resolution methylome of giant panda’s brain, liver and pancreatic tissue Ren, Jianying Shen, Fujun Zhang, Liang Sun, Jie Yang, Miao Yang, Mingyu Hou, Rong Yue, Bisong Zhang, Xiuyue PeerJ Bioinformatics The giant panda (Ailuropoda melanoleuca) is one of the most endangered mammals, and its conservation has significant ecosystem and cultural service value. Cytosine DNA methylation (5mC) is a stable epigenetic modification to the genome and has multiple functions such as gene regulation. However, DNA methylome of giant panda and its function have not been reported as of yet. Bisulfite sequencing was performed on a 4-day-old male giant panda’s brain, liver and pancreatic tissues. We found that the whole genome methylation level was about 0.05% based on reads normalization and mitochondrial DNA was not methylated. Three tissues showed similar methylation tendency in the protein-coding genes of their genomes, but the brain genome had a higher count of methylated genes. We obtained 467 and 1,013 different methylation regions (DMR) genes in brain vs. pancreas and liver, while only 260 DMR genes were obtained in liver vs pancreas. Some lncRNA were also DMR genes, indicating that methylation may affect biological processes by regulating other epigenetic factors. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that low methylated promoter, high methylated promoter and DMR genes were enriched at some important and tissue-specific items and pathways, like neurogenesis, metabolism and immunity. DNA methylation may drive or maintain tissue specificity and organic functions and it could be a crucial regulating factor for the development of newborn cubs. Our study offers the first insight into giant panda’s DNA methylome, laying a foundation for further exploration of the giant panda’s epigenetics. PeerJ Inc. 2019-10-17 /pmc/articles/PMC6800980/ /pubmed/31637123 http://dx.doi.org/10.7717/peerj.7847 Text en © 2019 Ren et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Ren, Jianying
Shen, Fujun
Zhang, Liang
Sun, Jie
Yang, Miao
Yang, Mingyu
Hou, Rong
Yue, Bisong
Zhang, Xiuyue
Single-base-resolution methylome of giant panda’s brain, liver and pancreatic tissue
title Single-base-resolution methylome of giant panda’s brain, liver and pancreatic tissue
title_full Single-base-resolution methylome of giant panda’s brain, liver and pancreatic tissue
title_fullStr Single-base-resolution methylome of giant panda’s brain, liver and pancreatic tissue
title_full_unstemmed Single-base-resolution methylome of giant panda’s brain, liver and pancreatic tissue
title_short Single-base-resolution methylome of giant panda’s brain, liver and pancreatic tissue
title_sort single-base-resolution methylome of giant panda’s brain, liver and pancreatic tissue
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800980/
https://www.ncbi.nlm.nih.gov/pubmed/31637123
http://dx.doi.org/10.7717/peerj.7847
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