Single-nucleotide resolution mapping of m6A in zebrafish early embryonic development identifies developmental stage-associated modification dynamics during the maternal-to-zygotic transition

Abstract

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, consistent with the timing of the zebrafish maternal-to-zygotic transition. Analyses suggest that m 6 A-modified transcripts are predominantly associated with maternal classes at early developmental stages, with increased representation among zygotic-associated classes by later development. We highlight that differential methylation between developmental stages was observed in transcripts associated with mRNA metabolism, translational processing, and organ development.