Regulatory interactions of non-coding RNAs during maternal-to-zygotic transition in Arabidopsisthaliana

The maternal-to-zygotic transition (MZT) signifies the shift from maternal genome control to zygotic genome control during zygote development. However, the regulatory role of non-coding RNAs (ncRNA), such as micro RNA (miRNA) and long non-coding RNAs (lncRNAs), in plants during MZT remains inadequately studied. Furthermore, the competitive endogenous RNA network (ceRNA), which involves interactions among messenger RNA (mRNA), miRNA, and lncRNA across developmental stages, has not been thoroughly investigated. To address this gap, we conducted an analysis of previously generated RNA-Seq data from egg and zygotes at 14 and 24 h after pollination, and 1 cell embryos of the Columbia ecotype in Arabidopsis thaliana. Through this analysis, we identified over 1900 differentially expressed mRNAs, 80 known lncRNAs, and 300 novel lncRNAs. Additionally, we identified lncRNAs specific to the MZT transition phases and observed differential expression of experimentally validated lncRNAs throughout MZT. Furthermore, we predicted hub-miRNAs across the three distinct stages of zygote development. Overall, our study provides valuable insights into the interactions among mRNA, miRNA, and lncRNA, as well as the differential rewiring patterns of the ceRNA networks during MZT.