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Transcriptome-wide N(6)-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern
BACKGROUND: N (6)-methyladenosine (m(6)A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and potential regulatory functions of reversible m(6)A methylation on mRNA have been revealed by mapping of m(6)A methylomes in several species. m(6)A modification in a...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5410061/ https://www.ncbi.nlm.nih.gov/pubmed/28454518 http://dx.doi.org/10.1186/s12864-017-3719-1 |
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author | Tao, Xuelian Chen, Jianning Jiang, Yanzhi Wei, Yingying Chen, Yan Xu, Huaming Zhu, Li Tang, Guoqing Li, Mingzhou Jiang, Anan Shuai, Surong Bai, Lin Liu, Haifeng Ma, Jideng Jin, Long Wen, Anxiang Wang, Qin Zhu, Guangxiang Xie, Meng Wu, Jiayun He, Tao Huang, Chunyu Gao, Xiang Li, Xuewei |
author_facet | Tao, Xuelian Chen, Jianning Jiang, Yanzhi Wei, Yingying Chen, Yan Xu, Huaming Zhu, Li Tang, Guoqing Li, Mingzhou Jiang, Anan Shuai, Surong Bai, Lin Liu, Haifeng Ma, Jideng Jin, Long Wen, Anxiang Wang, Qin Zhu, Guangxiang Xie, Meng Wu, Jiayun He, Tao Huang, Chunyu Gao, Xiang Li, Xuewei |
author_sort | Tao, Xuelian |
collection | PubMed |
description | BACKGROUND: N (6)-methyladenosine (m(6)A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and potential regulatory functions of reversible m(6)A methylation on mRNA have been revealed by mapping of m(6)A methylomes in several species. m(6)A modification in active gene regulation manifests itself as altered methylation profiles in a tissue-specific manner or in response to changing cellular or species living environment. However, up to date, there has no data on m(6)A porcine transcriptome-wide map and its potential biological roles in adipose deposition and muscle growth. METHODS: In this work, we used methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq) technique to acquire the first ever m(6)A porcine transcriptome-wide map. Transcriptomes of muscle and adipose tissues from three different pig breeds, the wild boar, Landrace, and Rongchang pig, were used to generate these maps. RESULTS: Our findings show that there were 5,872 and 2,826 m(6)A peaks respectively, in the porcine muscle and adipose tissue transcriptomes. Stop codons, 3′-untranslated regions, and coding regions were found to be mainly enriched for m(6)A peaks. Gene ontology analysis revealed that common m(6)A peaks in nuclear genes are associated with transcriptional factors, suggestive of a relationship between m(6)A mRNA methylation and nuclear genome transcription. Some genes showed tissue- and breed-differential methylation, and have novel biological functions. We also found a relationship between the m(6)A methylation extent and the transcript level, suggesting a regulatory role for m(6)A in gene expression. CONCLUSION: This comprehensive map provides a solid basis for the determination of potential functional roles for RNA m(6)A modification in adipose deposition and muscle growth. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3719-1) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5410061 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-54100612017-05-02 Transcriptome-wide N(6)-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern Tao, Xuelian Chen, Jianning Jiang, Yanzhi Wei, Yingying Chen, Yan Xu, Huaming Zhu, Li Tang, Guoqing Li, Mingzhou Jiang, Anan Shuai, Surong Bai, Lin Liu, Haifeng Ma, Jideng Jin, Long Wen, Anxiang Wang, Qin Zhu, Guangxiang Xie, Meng Wu, Jiayun He, Tao Huang, Chunyu Gao, Xiang Li, Xuewei BMC Genomics Research Article BACKGROUND: N (6)-methyladenosine (m(6)A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and potential regulatory functions of reversible m(6)A methylation on mRNA have been revealed by mapping of m(6)A methylomes in several species. m(6)A modification in active gene regulation manifests itself as altered methylation profiles in a tissue-specific manner or in response to changing cellular or species living environment. However, up to date, there has no data on m(6)A porcine transcriptome-wide map and its potential biological roles in adipose deposition and muscle growth. METHODS: In this work, we used methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq) technique to acquire the first ever m(6)A porcine transcriptome-wide map. Transcriptomes of muscle and adipose tissues from three different pig breeds, the wild boar, Landrace, and Rongchang pig, were used to generate these maps. RESULTS: Our findings show that there were 5,872 and 2,826 m(6)A peaks respectively, in the porcine muscle and adipose tissue transcriptomes. Stop codons, 3′-untranslated regions, and coding regions were found to be mainly enriched for m(6)A peaks. Gene ontology analysis revealed that common m(6)A peaks in nuclear genes are associated with transcriptional factors, suggestive of a relationship between m(6)A mRNA methylation and nuclear genome transcription. Some genes showed tissue- and breed-differential methylation, and have novel biological functions. We also found a relationship between the m(6)A methylation extent and the transcript level, suggesting a regulatory role for m(6)A in gene expression. CONCLUSION: This comprehensive map provides a solid basis for the determination of potential functional roles for RNA m(6)A modification in adipose deposition and muscle growth. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3719-1) contains supplementary material, which is available to authorized users. BioMed Central 2017-04-28 /pmc/articles/PMC5410061/ /pubmed/28454518 http://dx.doi.org/10.1186/s12864-017-3719-1 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Tao, Xuelian Chen, Jianning Jiang, Yanzhi Wei, Yingying Chen, Yan Xu, Huaming Zhu, Li Tang, Guoqing Li, Mingzhou Jiang, Anan Shuai, Surong Bai, Lin Liu, Haifeng Ma, Jideng Jin, Long Wen, Anxiang Wang, Qin Zhu, Guangxiang Xie, Meng Wu, Jiayun He, Tao Huang, Chunyu Gao, Xiang Li, Xuewei Transcriptome-wide N(6)-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern |
title | Transcriptome-wide N(6)-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern |
title_full | Transcriptome-wide N(6)-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern |
title_fullStr | Transcriptome-wide N(6)-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern |
title_full_unstemmed | Transcriptome-wide N(6)-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern |
title_short | Transcriptome-wide N(6)-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern |
title_sort | transcriptome-wide n(6)-methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5410061/ https://www.ncbi.nlm.nih.gov/pubmed/28454518 http://dx.doi.org/10.1186/s12864-017-3719-1 |
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