TE-like DNA methylation of highly expressed endosperm genes in maize

Unlike CG methylation alone, which is associated with stable and moderate levels of transcription, gene body methylation in both CG and CHG contexts is associated with poorly transcribed and missanotated genes. Recent results show that removal of this TE-like methylation from a set of maize pollen specific genes promotes high-level transcription. Here we report that TE-like methylated genes that are maternally demethylated are expressed toward the extreme high end of the spectrum in endosperm. As with their pollen counterparts, they have few exons, and are enriched for short, secreted proteins. Nearly half encode zeins, the major seed storage proteins of maize. When methylation is high in promoters as well as in gene bodies, their paternal copies are silenced in endosperm, resulting in genomic imprinting. These findings reveal that sporophytic TE-like methylation in gene bodies can be a signature of nearly-constitutive silencing but high and specific expression in endosperm or pollen.