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Landscape of N(6)-Methyladenosine Modification Patterns in Human Ameloblastoma
OBJECTIVE: To comprehensively analyze the global N(6)-methyladenosine (m(6)A) modification pattern in ameloblastoma. METHODS: m(6)A peaks in ameloblastoma and normal oral tissues were detected by MeRIP-seq. Differentially methylated m(6)A sites within messenger RNAs (mRNAs), long no-coding RNA (lncR...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7592903/ https://www.ncbi.nlm.nih.gov/pubmed/33178585 http://dx.doi.org/10.3389/fonc.2020.556497 |
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author | Niu, Xing Xu, Jingping Liu, Jinwen Chen, Lijie Qiao, Xue Zhong, Ming |
author_facet | Niu, Xing Xu, Jingping Liu, Jinwen Chen, Lijie Qiao, Xue Zhong, Ming |
author_sort | Niu, Xing |
collection | PubMed |
description | OBJECTIVE: To comprehensively analyze the global N(6)-methyladenosine (m(6)A) modification pattern in ameloblastoma. METHODS: m(6)A peaks in ameloblastoma and normal oral tissues were detected by MeRIP-seq. Differentially methylated m(6)A sites within messenger RNAs (mRNAs), long no-coding RNA (lncRNAs) and circular RNA (circRNAs) were identified, followed by functional enrichment analysis. By comprehensively analyzing MeRIP-seq and RNA-seq data, differentially expressed mRNAs, lncRNAs and circRNAs containing differentially methylated sites were identified. RNA binding proteins (RBPs) were then identified for differentially methylated m(6)A sites. RESULTS: In total, 3,673 differentially methylated m(6)A sites within coding genes were detected, of which 16.2% (704/3,673) were significantly upmethylated sites in ameloblastoma compared to normal oral tissues. Furthermore, 4,975 differentially methylated m(6)A sites within lncRNAs were identified, of which 29.4% (1,465/4,975) were upmethylated sites in ameloblastoma. We also found 364 differentially methylated m(6)A sites within circRNAs, of which 22.5% (82/364) were upmethylated sites in ameloblastoma. Differentially methylated m(6)A was most often harbored in the CDS (54.10%), followed by 5’UTR (21.71%). Functional enrichment analysis revealed that m(6)A modification could be involved in the development of ameloblastoma by organism developmental processes. A total of 158 RBPs within differentially methylated m(6)A sites were identified, which were significantly involved in mRNA metabolic process, mRNA processing, RNA processing, RNA splicing and RNA transport. CONCLUSION: Our findings for the first time provide m(6)A landscape of human ameloblastoma, which expand the understanding of m(6)A modifications and uncover regulation of lncRNAs and circRNAs through m(6)A modification in ameloblastoma. |
format | Online Article Text |
id | pubmed-7592903 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-75929032020-11-10 Landscape of N(6)-Methyladenosine Modification Patterns in Human Ameloblastoma Niu, Xing Xu, Jingping Liu, Jinwen Chen, Lijie Qiao, Xue Zhong, Ming Front Oncol Oncology OBJECTIVE: To comprehensively analyze the global N(6)-methyladenosine (m(6)A) modification pattern in ameloblastoma. METHODS: m(6)A peaks in ameloblastoma and normal oral tissues were detected by MeRIP-seq. Differentially methylated m(6)A sites within messenger RNAs (mRNAs), long no-coding RNA (lncRNAs) and circular RNA (circRNAs) were identified, followed by functional enrichment analysis. By comprehensively analyzing MeRIP-seq and RNA-seq data, differentially expressed mRNAs, lncRNAs and circRNAs containing differentially methylated sites were identified. RNA binding proteins (RBPs) were then identified for differentially methylated m(6)A sites. RESULTS: In total, 3,673 differentially methylated m(6)A sites within coding genes were detected, of which 16.2% (704/3,673) were significantly upmethylated sites in ameloblastoma compared to normal oral tissues. Furthermore, 4,975 differentially methylated m(6)A sites within lncRNAs were identified, of which 29.4% (1,465/4,975) were upmethylated sites in ameloblastoma. We also found 364 differentially methylated m(6)A sites within circRNAs, of which 22.5% (82/364) were upmethylated sites in ameloblastoma. Differentially methylated m(6)A was most often harbored in the CDS (54.10%), followed by 5’UTR (21.71%). Functional enrichment analysis revealed that m(6)A modification could be involved in the development of ameloblastoma by organism developmental processes. A total of 158 RBPs within differentially methylated m(6)A sites were identified, which were significantly involved in mRNA metabolic process, mRNA processing, RNA processing, RNA splicing and RNA transport. CONCLUSION: Our findings for the first time provide m(6)A landscape of human ameloblastoma, which expand the understanding of m(6)A modifications and uncover regulation of lncRNAs and circRNAs through m(6)A modification in ameloblastoma. Frontiers Media S.A. 2020-10-14 /pmc/articles/PMC7592903/ /pubmed/33178585 http://dx.doi.org/10.3389/fonc.2020.556497 Text en Copyright © 2020 Niu, Xu, Liu, Chen, Qiao and Zhong http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Oncology Niu, Xing Xu, Jingping Liu, Jinwen Chen, Lijie Qiao, Xue Zhong, Ming Landscape of N(6)-Methyladenosine Modification Patterns in Human Ameloblastoma |
title | Landscape of N(6)-Methyladenosine Modification Patterns in Human Ameloblastoma |
title_full | Landscape of N(6)-Methyladenosine Modification Patterns in Human Ameloblastoma |
title_fullStr | Landscape of N(6)-Methyladenosine Modification Patterns in Human Ameloblastoma |
title_full_unstemmed | Landscape of N(6)-Methyladenosine Modification Patterns in Human Ameloblastoma |
title_short | Landscape of N(6)-Methyladenosine Modification Patterns in Human Ameloblastoma |
title_sort | landscape of n(6)-methyladenosine modification patterns in human ameloblastoma |
topic | Oncology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7592903/ https://www.ncbi.nlm.nih.gov/pubmed/33178585 http://dx.doi.org/10.3389/fonc.2020.556497 |
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