Single-nucleotide resolution mapping of m ⁶ A of zebrafish mRNAs in early embryonic development links m ⁶ A modifications to the maternal-to-zygotic transition

N ⁶ -methyladenosine (m ⁶ A) is the most abundant epigenetic modification on eukaryotic mRNA and has important roles in gene expression. While m ⁶ A distribution and localization have been defined in zebrafish using antibody-based methods, no research has been published on the distribution of m ⁶ A during zebrafish embryogenesis with single-base precision. Here, we present the transcriptome-wide m ⁶ A landscape at single-nucleotide resolution during zebrafish early embryonic development using m ⁶ A-selective allyl chemical labeling and sequencing (m ⁶ A-SAC-seq). We identify over 36,000 high-confidence unique m ⁶ A sites that are primarily located in the DRACH consensus motif in long internal exons, 3’UTRs, and near stop codons. Our results show a >4-fold decrease in m ⁶ A levels from 256-cell to 50% epiboly, clearly linking this methylation to zebrafish maternal-to-zygotic transition. We highlight that differential methylation between developmental stages was observed in transcripts associated with mRNA metabolism, translational processing, and organ development.