DNA demethylation is important for imprinted gene expression in maize endosperm but may do more

Gent et al. characterize a classical maize mutant and find insights into genomic imprinting and DNA methylation in endosperm

Jonathan I. Gent, Department of Plant Biology, University of Georgia, Athens, GA 30602, USA

 Background:

In 1970, Jerry Kermicle reported that maize kernels could have dramatically different pigmentation depending on which parent the r1 gene is inherited from. This was the first discovery of many genomically imprinted genes that are selectively expressed from the maternal genome in endosperm. Later, Kermicle also discovered a mutant with poor maternal r1 expression. He hypothesized that the normal function of the mutated gene would be to derepress maternal r1; hence the name maternal depression of r1 (mdr1). The identify of mdr1 has remained unknown since then, but studies using Arabidopsis thaliana have revealed that DNA demethylation by enzymes called DNA glycosylases is important for expression of some maternally inherited genes in endosperm.

Question:

We wanted to identify the mdr1 gene. We hypothesized that mdr1 would reveal insights into molecular mechanisms of genomic imprinting in maize.

Findings:

We discovered that mdr1 encodes one of two DNA glycosylases with high expression in endosperm. We found that at least one of the two must be functional for endosperm to develop normally, but the one encoded by mdr1 is expressed higher. Surprisingly, most of the genes the mdr1 DNA glycosylase demethylates do not appear to be genomically imprinted, and about half the DNA it demethylates is not even near genes. These findings suggest that DNA glycosylases also have an undiscovered function unrelated to genomic imprinting in endosperm.

Next steps:

We want to know how specific regions in the genome are targeted for demethylation. What distinguishes these regions from other regions in endosperm? And what keeps them from being demethylated in other tissues? On the flip side, little is known about the effect of demethylation in endosperm, other than genomic imprinting. We want to know what affect DNA demethylation by DNA glycosylases has on chromatin structure and why it is important.

Reference:

Jonathan I. Gent, Kaitlin M. Higgins, Kyle W. Swentowsky, Fang-Fang Fu, Yibing Zeng, Dong won Kim, R. Kelly Dawe, Nathan M. Springer, and Sarah N. Anderson (2022). The maize gene maternal derepression of r1 encodes a DNA glycosylase that demethylates DNA and reduces siRNA expression in the endosperm. Plant Cell. https://doi.org/10.1093/plcell/koac199