rRNA 5-methylcytosine in Arabidopsis thaliana

Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites in ribosomal RNAs of all three sub-cellular transcriptomes in Arabidopsis thaliana. m5C sites in rRNAs were also anlyzed in Arabidopsis T-DNA knockouts for the RNA methyltransferases TRM4A, TRM4B, TRDMT1, NSUN5, NOP2A, NOP2B and NOP2C. Overall design: RNA Bisulfite sequencing was used to identify candidate m5C sites in rRNAs of Arabidopsis thaliana. Illumina sequencing was performed on a MiSeq platform. Two experiments were performed; experiment 1 and experiment 2. In experiment 1, one to three biological replicates were performed for the genotypes wild type, nop2a-2, nop2b-1, nop2b-2, nop2c-1, nop2c-2, nsun5-1 and nsun5-2. In experiment 2, one biological replicate was performed for each of the genotypes wild type, trm4a, trm4b-1, trdmt1 and trdmt1 trm4b.