Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma

Xing Niu; Jingping Xu; Jinwen Liu; Lijie Chen; Xue Qiao; Ming Zhong

doi:10.3389/fonc.2020.556497

Landscape of N⁶-Methyladenosine Modification Patterns in Human Ameloblastoma

Front Oncol. 2020 Oct 14:10:556497. doi: 10.3389/fonc.2020.556497. eCollection 2020.

Authors

Xing Niu^{1

2}, Jingping Xu¹, Jinwen Liu², Lijie Chen^{1

2}, Xue Qiao³, Ming Zhong^{1

2}

Affiliations

¹ Department of Stomatology, Xiang'an Hospital of Xiamen University, Xiamen, China.
² Department of Oral Histopathology, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China.
³ Department of Central Laboratory, School and Hospital of Stomatology, China Medical University, Liaoning Province Key Laboratory of Oral Disease, Shenyang, China.

Abstract

Objective: To comprehensively analyze the global N⁶-methyladenosine (m⁶A) modification pattern in ameloblastoma.

Methods: m⁶A 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.

Results: In 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.

Conclusion: Our 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.

Keywords: ameloblastoma; circular RNA; long noncoding RNA; m6A modification; messenger RNA.