Dynamic changes in RNA m 6 A and 5 hmC influence gene expression programs during macrophage differentiation and polarisation

• Published in: Cellular and molecular life sciences : CMLS Vol. 81; no. 1; p. 229
• Main Authors: Pinello, Natalia, Song, Renhua, Lee, Quintin, Calonne, Emilie, Duan, Kun-Long, Wong, Emilie, Tieng, Jessica, Mehravar, Majid, Rong, Bowen, Lan, Fei, Roediger, Ben, Ma, Cheng-Jie, Yuan, Bi-Feng, Rasko, John E J, Larance, Mark, Ye, Dan, Fuks, François, Wong, Justin J-L
• Format: Journal Article
• Language: English
• Published: Switzerland 23-05-2024
• Subjects: Adenosine - metabolism; Cell Differentiation - genetics; Cell Polarity - genetics; Gene Expression Regulation; Humans; Macrophages - cytology; Macrophages - immunology; Macrophages - metabolism; Monocytes - cytology; Monocytes - metabolism; RNA - genetics; RNA - metabolism; RNA Processing, Post-Transcriptional; RNA, Messenger - genetics; RNA, Messenger - metabolism; Transcriptome; Epitranscriptomics; 5 hmC; M6A; Macrophages; RNA modifications
• ISSN: 1420-9071

RNA modifications are essential for the establishment of cellular identity. Although increasing evidence indicates that RNA modifications regulate the innate immune response, their role in monocyte-to-macrophage differentiation and polarisation is unclear. While m
A has been widely studied, other RNA modifications, including 5 hmC, remain poorly characterised. We profiled m
A and 5 hmC epitranscriptomes, transcriptomes, translatomes and proteomes of monocytes and macrophages at rest and pro- and anti-inflammatory states. Transcriptome-wide mapping of m
A and 5 hmC reveals enrichment of m
A and/or 5 hmC on specific categories of transcripts essential for macrophage differentiation. Our analyses indicate that m
A and 5 hmC modifications are present in transcripts with critical functions in pro- and anti-inflammatory macrophages. Notably, we also discover the co-occurrence of m
A and 5 hmC on alternatively-spliced isoforms and/or opposing ends of the untranslated regions (UTR) of mRNAs with key roles in macrophage biology. In specific examples, RNA 5 hmC controls the decay of transcripts independently of m
A. This study provides (i) a comprehensive dataset to interrogate the role of RNA modifications in a plastic system (ii) a resource for exploring different layers of gene expression regulation in the context of human monocyte-to-macrophage differentiation and polarisation, (iii) new insights into RNA modifications as central regulators of effector cells in innate immunity.