Temporal changes in transcripts of miniature inverted‐repeat transposable elements during rice endosperm development

SUMMARY The repression of transcription from transposable elements (TEs) by DNA methylation is necessary to maintain genome integrity and prevent harmful mutations. However, under certain circumstances, TEs may escape from the host defense system and reactivate their transcription. In Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), DNA demethylases target the sequences derived from TEs in the central cell, the progenitor cell for the endosperm in the female gametophyte. Genome‐wide DNA demethylation is also observed in the endosperm after fertilization. In the present study, we used a custom microarray to survey the transcripts generated from TEs during rice endosperm development and at selected time points in the embryo as a control. The expression patterns of TE transcripts are dynamically up‐ and downregulated during endosperm development, especially those of miniature inverted‐repeat TEs (MITEs). Some TE transcripts were directionally controlled, whereas the other DNA transposons and retrotransposons were not. We also discovered the NUCLEAR FACTOR Y binding motif, CCAAT, in the region near the 5′ terminal inverted repeat of Youren, one of the transcribed MITEs in the endosperm. Our results uncover dynamic changes in TE activity during endosperm development in rice. Significance Statement Transposable Elements provide cis‐elements for neighboring genes under certain circumstances. We found that many Youren MITEs had the CCAAT motif, known as the NF‐Y binding site, which enhanced directional transcription from the internal sequence of Youren. In addition, the temporal expression of Youren was confined to the mid‐stage of rice endosperm development. Our analysis provides a valuable framework to investigate differential gene expression networks in the endosperm and the role of TEs during rice evolution.