Pumilio-Homology Domain protein APUM9 regulates seed dormancy via decapping-dependent mRNA decay

APUM9 is a conserved PUF RNA-binding protein (RBP) and the expression of this protein is under complex epigenetic regulation. A transposable element (TE)-mediates this epigenetic regulation and thereby restricts its expression in Arabidopsis. Currently, little is known about the molecular function of the APUM protein family and the biological relevance of the TE-mediated epigenetic control of APUM9 in plant development and stress responses. By combining a range of transient assays, we show here that APUM9 binding to target transcripts can trigger their rapid decay via its conserved C-terminal RNA-binding domain. APUM9 directly interacts with DCP2, the catalytic subunits of the decapping complex suggesting that APUM9-mediated mRNA decay predominantly occurs via the decapping-dependent exonucleolytic pathway. APUM9 negatively regulates the expression of ABA signaling genes during seed imbibition, and thereby might contribute to the switch from dormant stage to seed germination. By contrast, strong TE-mediated repression of APUM9 is important for normal plant growth in the later developmental stages. Finally, APUM9 overexpression plants show slightly enhanced heat tolerance suggesting that TE-mediated epigenetic control of plant APUM9, might have a role not only in embryonic development, but also in plant adaptation to heat stress conditions. RNA sequencing on imbibed Arabidopsis seeds