Identifying N6-Methyladenosine Sites in HepG2 Cell Lines Using Oxford Nanopore Technology
RNA modifications, particularly N6-methyladenosine (m6A), are pivotal regulators of RNA functionality and cellular processes. We analyzed m6A modifications by employing Oxford Nanopore technology and the m6Anet algorithm, focusing on the HepG2 cell line. We identified 3968 potential m6A modification...
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Published in | International journal of molecular sciences Vol. 24; no. 22; p. 16477 |
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Main Authors | , , , , , , |
Format | Journal Article |
Language | English |
Published |
Basel
MDPI AG
01.11.2023
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Subjects | |
Online Access | Get full text |
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Summary: | RNA modifications, particularly N6-methyladenosine (m6A), are pivotal regulators of RNA functionality and cellular processes. We analyzed m6A modifications by employing Oxford Nanopore technology and the m6Anet algorithm, focusing on the HepG2 cell line. We identified 3968 potential m6A modification sites in 2851 transcripts, corresponding to 1396 genes. A gene functional analysis revealed the active involvement of m6A-modified genes in ubiquitination, transcription regulation, and protein folding processes, aligning with the known role of m6A modifications in histone ubiquitination in cancer. To ensure data robustness, we assessed reproducibility across technical replicates. This study underscores the importance of evaluating algorithmic reproducibility, especially in supervised learning. Furthermore, we examined correlations between transcriptomic, translatomic, and proteomic levels. A strong transcriptomic–translatomic correlation was observed. In conclusion, our study deepens our understanding of m6A modifications’ multifaceted impacts on cellular processes and underscores the importance of addressing reproducibility concerns in analytical approaches. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
ISSN: | 1422-0067 1661-6596 1422-0067 |
DOI: | 10.3390/ijms242216477 |