Comprehensive analysis of mRNA 5-methylcytosine modification in Eimeria tenella oocysts

5-methylcytosine (m5C) is a type of RNA modifications reported to regulate diverse biological processes. However, the distribution and biological functions of m5C in E. tenella mRNAs remain largely unknown. Herein, we report transcriptome-wide profiling of mRNA m5C in E. tenella by applying m5C RNA immunoprecipitation followed by a deep-sequencing approach (m5C-RIP-seq). Our data showed that m5C peaks were distributed across the whole mRNA body. There were 2813 hypermethylated and 1850 hypomethylated m5C peaks in sporulated oocysts compared with unsporulated oocysts. Further joint analysis showed a positive correlation between m5C modification and gene expression levels. The mRNA sequencing and m5C-RIP-seq data were consistent with the results of the quantitative reverse transcription PCR (RT-qPCR) and m5C-RIP-qPCR, respectively. Gene ontology (GO) and pathway enrichment analysis predicated diverse biological functions and pathways, including microtubule motor activity, helicase activity, cGMP-PKG signaling pathway, aminoacyl-tRNA biosynthesis, glycolysis/gluconeogenesis and spliceosome. Meanwhile, stage-specific gene expression signatures of m5C-related enzymes were observed. Altogether, our findings revealed the transcriptional significance of m5C modification in E. tenella oocysts, providing clues for in-depth research. Overall design: MeRIP-seq and RNA-seq of sporulated and unsporulated oocysts of E. tenella.