DNA methylation dynamics play crucial roles in shaping the distinct transcriptomic profiles for different root-type initiation in rice
Monocots possess a fibrous root system comprising an embryonic root (ER), crown roots (CR), and lateral roots (LR), which share striking similarities in adult anatomical structures and functions across the three root types. Nonetheless, their distinct cellular origins highlight the diversity of the initiation mechanism. Through our study, we conducted a comprehensive transcriptome and DNA methylome assay of these root types during their initiation. Our findings indicated significant divergence in transcriptome regulation trajectories with apparent transcriptional activation in post-embryonic root initials (CR and LR) contrasted by suppression in embryonic root (ER) generation. Additionally, CHH methylation was found dynamically and differentially regulated across the initiation stages of the various root types, and significantly associated with the short transposon element within the promoter regions of functional genes, which played crucial roles in determining the genes' spatiotemporal transcription. Moreover, our work revealed that the activation of DNG702 and repression of DRM2 played important roles in the erasure of CHH methylation and activation of functional genes during the processes, such as a novel identified key regulatory bZip65, thus directly impacting the initiation of post-embryonic roots in rice. In conclusion, our extensive analysis delineates the landscapes of spatiotemporal transcriptomes and DNA methylomes during the initiation of the three root types in rice, shedding light on the pivotal role of CHH methylation in the spatiotemporal regulation of various key genes, ensuring the successful initiation of distinct root types in rice. Overall design: RNA-seq and BS-seq data of four stages of rice crown, lateral, embryonic root initials derived from laser microdissection, two biological replicates were represented for each sample.