m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome

• Published in: Nature biotechnology Vol. 40; no. 8; pp. 1210 - 1219
• Main Authors: Hu, Lulu, Liu, Shun, Peng, Yong, Ge, Ruiqi, Su, Rui, Senevirathne, Chamara, Harada, Bryan T., Dai, Qing, Wei, Jiangbo, Zhang, Lisheng, Hao, Ziyang, Luo, Liangzhi, Wang, Huanyu, Wang, Yuru, Luo, Minkui, Chen, Mengjie, Chen, Jianjun, He, Chuan
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.08.2022; Nature Publishing Group
• Subjects: 631/45/500; 631/61/514/1949; Agriculture; Antibodies; Bioinformatics; Biological activity; Biology; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Calibration; Cancer; Cell differentiation; Cell lines; Cells (biology); Differentiation (biology); Enzymes; Epigenetics; Gene expression; Hematopoietic stem cells; HIV; Human immunodeficiency virus; Labeling; Laboratories; Life Sciences; Mammals; Methylation; Mutation; N6-methyladenosine; Nucleotides; Progenitor cells; Quantitative analysis; RNA modification; rRNA; Stoichiometry; Transcription factors; Transcriptomes
• ISSN: 1087-0156; 1546-1696; 1546-1696
• DOI: 10.1038/s41587-022-01243-z

Functional studies of the RNA N 6 -methyladenosine (m 6 A) modification have been limited by an inability to map individual m 6 A-modified sites in whole transcriptomes. To enable such studies, here, we introduce m 6 A-selective allyl chemical labeling and sequencing (m 6 A-SAC-seq), a method for quantitative, whole-transcriptome mapping of m 6 A at single-nucleotide resolution. The method requires only ~30 ng of poly(A) or rRNA-depleted RNA. We mapped m 6 A modification stoichiometries in RNA from cell lines and during in vitro monocytopoiesis from human hematopoietic stem and progenitor cells (HSPCs). We identified numerous cell-state-specific m 6 A sites whose methylation status was highly dynamic during cell differentiation. We observed changes of m 6 A stoichiometry as well as expression levels of transcripts encoding or regulated by key transcriptional factors (TFs) critical for HSPC differentiation. m 6 A-SAC-seq is a quantitative method to dissect the dynamics and functional roles of m 6 A sites in diverse biological processes using limited input RNA. m 6 A-SAC-seq uses chemical labeling to quantify m 6 A at single-base resolution in the mammalian transcriptome.