Gene Imprinting

For some loci, DNA demethylation establishes gene imprinting in the endosperm, an epigenetic phenomenon found in flowering plants and animals whereby alleles of a gene are expressed differently depending on whether they are inherited from the male or female parent. Several known imprinted genes are essential for seed development. Our genome-wide DNA methylation profiling and subsequent RNA-seq analysis has identified many new imprinted genes. The function of most of these genes is unknown, but many encode putative transcription factors and chromatin-related proteins and thus could be important for directing the endosperm developmental program. We seek to understand the function of these genes during seed development, the molecular mechanism of their imprinting, and whether imprinting of these genes is conserved within the species and in related species. Transposable elements (TEs) vary as lineages diverge, and DNA methylation and small RNAs have been shown to be polymorphic within A. thaliana. Our finding that DNA demethylation occurs at repeated sequences that correspond to remnants of TEs suggested that the set of imprinted genes could vary within the species. We have recently defined a set of variably imprinted genes within Arabidopsis and shown that this is correlated with methylation variation of proximal TEs. We are also defining the set of imprinted genes in the related outcrossing species A. lyrata to test evolutionary theories about the origins and function of imprinting.