Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma
ObjectiveTo comprehensively analyze the global N6-methyladenosine (m6A) modification pattern in ameloblastoma.Methodsm6A peaks in ameloblastoma and normal oral tissues were detected by MeRIP-seq. Differentially methylated m6A sites within messenger RNAs (mRNAs), long no-coding RNA (lncRNAs) and circ...
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doaj-5b2b550fbe31410b877cede9c9c8c3a92020-11-25T02:46:28ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2020-10-011010.3389/fonc.2020.556497556497Landscape of N6-Methyladenosine Modification Patterns in Human AmeloblastomaXing Niu0Xing Niu1Jingping Xu2Jinwen Liu3Lijie Chen4Lijie Chen5Xue Qiao6Ming Zhong7Ming Zhong8Department of Stomatology, Xiang’an Hospital of Xiamen University, Xiamen, ChinaDepartment of Oral Histopathology, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, ChinaDepartment of Stomatology, Xiang’an Hospital of Xiamen University, Xiamen, ChinaDepartment of Oral Histopathology, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, ChinaDepartment of Stomatology, Xiang’an Hospital of Xiamen University, Xiamen, ChinaDepartment of Oral Histopathology, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, ChinaDepartment of Central Laboratory, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, ChinaDepartment of Stomatology, Xiang’an Hospital of Xiamen University, Xiamen, ChinaDepartment of Oral Histopathology, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, ChinaObjectiveTo comprehensively analyze the global N6-methyladenosine (m6A) modification pattern in ameloblastoma.Methodsm6A peaks in ameloblastoma and normal oral tissues were detected by MeRIP-seq. Differentially methylated m6A 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 m6A sites.ResultsIn total, 3,673 differentially methylated m6A 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 m6A sites within lncRNAs were identified, of which 29.4% (1,465/4,975) were upmethylated sites in ameloblastoma. We also found 364 differentially methylated m6A sites within circRNAs, of which 22.5% (82/364) were upmethylated sites in ameloblastoma. Differentially methylated m6A was most often harbored in the CDS (54.10%), followed by 5’UTR (21.71%). Functional enrichment analysis revealed that m6A modification could be involved in the development of ameloblastoma by organism developmental processes. A total of 158 RBPs within differentially methylated m6A sites were identified, which were significantly involved in mRNA metabolic process, mRNA processing, RNA processing, RNA splicing and RNA transport.ConclusionOur findings for the first time provide m6A landscape of human ameloblastoma, which expand the understanding of m6A modifications and uncover regulation of lncRNAs and circRNAs through m6A modification in ameloblastoma.https://www.frontiersin.org/article/10.3389/fonc.2020.556497/fullm6A modificationameloblastomamessenger RNAlong noncoding RNAcircular RNA |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Xing Niu Xing Niu Jingping Xu Jinwen Liu Lijie Chen Lijie Chen Xue Qiao Ming Zhong Ming Zhong |
spellingShingle |
Xing Niu Xing Niu Jingping Xu Jinwen Liu Lijie Chen Lijie Chen Xue Qiao Ming Zhong Ming Zhong Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma Frontiers in Oncology m6A modification ameloblastoma messenger RNA long noncoding RNA circular RNA |
author_facet |
Xing Niu Xing Niu Jingping Xu Jinwen Liu Lijie Chen Lijie Chen Xue Qiao Ming Zhong Ming Zhong |
author_sort |
Xing Niu |
title |
Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma |
title_short |
Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma |
title_full |
Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma |
title_fullStr |
Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma |
title_full_unstemmed |
Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma |
title_sort |
landscape of n6-methyladenosine modification patterns in human ameloblastoma |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Oncology |
issn |
2234-943X |
publishDate |
2020-10-01 |
description |
ObjectiveTo comprehensively analyze the global N6-methyladenosine (m6A) modification pattern in ameloblastoma.Methodsm6A peaks in ameloblastoma and normal oral tissues were detected by MeRIP-seq. Differentially methylated m6A 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 m6A sites.ResultsIn total, 3,673 differentially methylated m6A 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 m6A sites within lncRNAs were identified, of which 29.4% (1,465/4,975) were upmethylated sites in ameloblastoma. We also found 364 differentially methylated m6A sites within circRNAs, of which 22.5% (82/364) were upmethylated sites in ameloblastoma. Differentially methylated m6A was most often harbored in the CDS (54.10%), followed by 5’UTR (21.71%). Functional enrichment analysis revealed that m6A modification could be involved in the development of ameloblastoma by organism developmental processes. A total of 158 RBPs within differentially methylated m6A sites were identified, which were significantly involved in mRNA metabolic process, mRNA processing, RNA processing, RNA splicing and RNA transport.ConclusionOur findings for the first time provide m6A landscape of human ameloblastoma, which expand the understanding of m6A modifications and uncover regulation of lncRNAs and circRNAs through m6A modification in ameloblastoma. |
topic |
m6A modification ameloblastoma messenger RNA long noncoding RNA circular RNA |
url |
https://www.frontiersin.org/article/10.3389/fonc.2020.556497/full |
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