DNA demethylase ROS1 negatively regulates the imprinting of DOGL4 and seed dormancy in Arabidopsis thaliana

Abstract

Genomic imprinting is a form of epigenetic regulation resulting in differential gene expression that reflects the parent of origin. In plants, imprinted gene expression predominantly occurs in the seed endosperm. Maternal-specific DNA demethylation by the DNA demethylase DME frequently underlies genomic imprinting in endosperm. Whether other more ubiquitously expressed DNA demethylases regulate imprinting is unknown. Here, we found that the DNA demethylase ROS1 regulates the imprinting of DOGL4. DOGL4 is expressed from the maternal allele in endosperm and displays preferential methylation and suppression of the paternal allele. We found that ROS1 negatively regulates imprinting by demethylating the paternal allele, preventing its hypermethylation and complete silencing. Furthermore, we found that DOGL4 negatively affects seed dormancy and response to the phytohormone abscisic acid and that ROS1 controls these processes by regulating DOGL4. Our results reveal roles for ROS1 in mitigating imprinted gene expression and regulating seed dormancy.

DELAY OF GERMINATION 1‐LIKE 4 acts as an inducer of seed reserve accumulation

“…These results suggest that DOGL4 exerts little positive effect on seed dormancy. Recently, it was shown that DOGL4 affects seed dormancy rather negatively (Zhu et al ., ). Taken together, DOGL4 does not seem to be involved in the induction and maintenance of seed dormancy.…”

“…No phenotypes were observed for the dogl1 , dogl2 and dogl3 single mutants (Bentsink et al ., ). The dogl4 mutants exhibit moderately enhanced seed dormancy (Zhu et al ., ), suggesting instead that DOGL4 is a negative regulator of seed dormancy, unlike DOG1 . The dog1 single knock‐out mutant seeds exhibit a non‐dormant phenotype (Bentsink et al ., ).…”

Seed germination and dormancy: The classic story, new puzzles, and evolution

“…DOGL3 seems to function in dormancy while DOGL5.2 does not (Nishimura et al ). DOGL4 has been shown to be an imprinted gene and a negative regulator of seed dormancy (Zhu et al ), although the dogl4 dormancy phenotypes seem to be moderate and the biological significance of imprinting for dormancy is not clear. DOGL4 has also been suggested to be a master regulator of seed reserve accumulation and resource allocation (González‐Morales et al ; Sall et al ), which is a predicted target of imprinting to address the parental conflict between male and female (Haig and Westoby ).…”

A methylated‐DNA‐binding complex required for plant development mediates transcriptional activation of promoter methylated genes

“…An anti‐silencing protein complex, IDM, was thought to target ROS1, resulting in DNA demethylation at specific genomic loci (Qian et al ; Lang et al ; Wang et al ; Duan et al ; Li et al ). The active DNA demethylation mechanism is involved in diverse biological processes including seed development and dormancy (Gehring et al ; Zhu et al ), fruit ripening (Liu et al ; Lang et al ), stomata formation (Yamamuro et al ), and nodule development (Satge et al ), suggesting biological significance of the active DNA demethylation mechanism. Although ROS1 is a major ubiquitously expressed 5‐mC DNA glycosylase involved in DNA demethylation, the loss‐of‐function mutant of ROS1 was not observed to show obvious developmental defects except for enhancement of seed dormancy and overproduction of stomatal lineage cells (Yamamuro et al ; Zhu et al ).…”

“…The active DNA demethylation mechanism is involved in diverse biological processes including seed development and dormancy (Gehring et al ; Zhu et al ), fruit ripening (Liu et al ; Lang et al ), stomata formation (Yamamuro et al ), and nodule development (Satge et al ), suggesting biological significance of the active DNA demethylation mechanism. Although ROS1 is a major ubiquitously expressed 5‐mC DNA glycosylase involved in DNA demethylation, the loss‐of‐function mutant of ROS1 was not observed to show obvious developmental defects except for enhancement of seed dormancy and overproduction of stomatal lineage cells (Yamamuro et al ; Zhu et al ). We predict that, in addition to active DNA demethylation, there may exist a distinct mechanism which is important for protecting genes from potentially harmful DNA methylation and transcriptional silencing.…”