Methylation of microRNA genes and its effect on secondary xylem development of stem in poplar

MicroRNAs (miRNAs) and DNA methylation are both vital regulators of gene expression. DNA methylation can affect the transcription of miRNAs, just like coding genes, through methylating the CpG islands in the gene regions of miRNAs. Although previous studies have shown that DNA methylation and miRNAs can each be involved in the process of wood formation, the relationship between the two has been relatively little studied in plant wood formation. Studies have shown that the second internode (IN2) (from top to bottom) of 3‐month‐old poplar trees can represent the primary stage of poplar stem development and IN8 can represent the secondary stage. There were also significant differences in DNA methylation patterns and miRNA expression patterns obtained from PS and SS. In this study, we first interactively analyzed methylation and miRNA sequencing data to identify 43 differentially expressed miRNAs regulated by differential methylation from the primary stage and secondary stage, which were found to be involved in multiple biological processes related to wood formation by enrichment analysis. In addition, six miRNA/target gene modules were finally identified as potentially involved in secondary xylem development of poplar stems through degradome sequencing and functional analysis. In conclusion, this study provides important reference information on the mechanism of interaction between different regulatory pathways of wood formation. Core Ideas Identification of miRNAs is regulated by methylation during poplar stem development. The function of miRNAs regulated by methylation was explored. Functional pathways of miRNAs regulated by methylation in secondary xylem are summarized. Plain Language Summary Methylation and small RNA sequencing data of poplar stems were jointly analyzed and used to elucidate miRNAs regulated by methylation during the whole stem development of poplar. Secondary xylem degradome sequencing data of poplar stems were used to obtain the targets of methylated miRNAs genes. We identified the methylation–miRNA–target gene pathway that is functionally important in poplar secondary xylem by gene function enrichment.