Mapping the m1A, m5C, m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP-seq

The epigenetic modifications play important regulatory roles in tissue development, maintenance of physiological functions and pathological process. RNA methylations, including newly identified m1A, m5C, m6A and m7G, are important epigenetic modifications. However, how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study, we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A, m5C, m6A and m7G methylation of mRNA, we found that within the whole brain transcriptome, with the increase of the gene expression levels, the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia-treated zebrafish brains, the proportion of m1A is decreased, affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A, m5C, m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A, m5C, m6A and m7G in the regulation of miRNA and repeat elements in vertebrates, and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. For each normoxia control and hypoxia experimental group, 10 adult male zebrafish (3-4 month old) were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues (around 0.02 g per brain) were then stored for further analysis in liquid nitrogen. For each analysis (m1A, m5C, m6A, m7G and RNA-Seq), the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA-seq and MeRIP-Seq.