Transcriptome-wide N ⁶-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification

Abstract

N ⁶-methyladenosine (m ⁶A) is the most prevalent internal modification present in mRNAs of all higher eukaryotes. With the development of MeRIP-seq technique, in-depth identification of mRNAs with m ⁶A modification becomes feasible. Here we present a transcriptome-wide m ⁶A modification profiling effort for rice transcriptomes of differentiated callus and leaf, which yields 8,138 and 14,253 m ⁶A-modified genes, respectively. The m ⁶A peak (m ⁶A-modified nucleotide position on mRNAs) distribution exhibits preference toward both translation termination and initiation sites. The m ⁶A peak enrichment is negatively correlated with gene expression and weakly positively correlated with certain gene features, such as exon length and number. By comparing m ⁶A-modified genes between the 2 samples, we define 1,792 and 6,508 tissue-specific m ⁶A-modified genes (TSMGs) in callus and leaf, respectively. Among which, 626 and 5,509 TSMGs are actively expressed in both tissues but are selectively m ⁶A- modified (SMGs) only in one of the 2 tissues. Further analyses reveal characteristics of SMGs: (1) Most SMGs are differentially expressed between callus and leaf. (2) Two conserved RNA-binding motifs, predicted to be recognized by PUM and RNP4F, are significantly over-represented in SMGs. (3) GO enrichment analysis shows that SMGs in callus mainly participate in transcription regulator/factor activity whereas SMGs in leaf are mainly involved in plastid and thylakoid. Our results suggest the presence of tissue-specific competitors involved in SMGs. These findings provide a resource for plant RNA epitranscriptomic studies and further enlarge our knowledge on the function of RNA m ⁶A modification.