Widespread imprinting of transposable elements and variable genes in the maize endosperm

Area of Science:

• Plant reproductive biology
• Genomics
• Epigenetics

Background:

• Seed development requires coordinated embryo and endosperm growth.
• Parental genomic imprinting, where only one parental allele is expressed, occurs in the endosperm of many flowering plants.
• Previous methods for studying imprinting relied on single nucleotide polymorphisms, limiting analysis to shared genomic regions.

Purpose of the Study:

• To develop a novel method for assessing genomic imprinting across both shared and variable genomic regions.
• To investigate the prevalence and patterns of imprinted gene expression in maize and other plant species.
• To explore the relationship between transposable element (TE) expression and imprinted gene expression.

Main Methods:

• Utilized whole genome assemblies from multiple maize genotypes and reciprocal crosses.
• Developed a method to analyze imprinting in both conserved and presence-absence variation regions of the genome.
• Examined transcript origins and fused transcripts at TE-gene pairs.

Main Results:

• Revealed widespread maternal expression of genes and transposable elements (TEs) with presence-absence variation in maize and across species.
• Demonstrated that most maternally expressed features are localized to the endosperm, suggesting maternal de-repression in the central cell.
• Found enrichment for maternal expression of genes nearest to maternally expressed TEs, with evidence of fused transcripts.

Conclusions:

• The new method enables comprehensive analysis of genomic imprinting, including variable genomic regions.
• Maternal imprinting is a widespread phenomenon in maize endosperm, particularly involving TEs and associated genes.
• Maternal TEs may play a role in regulating imprinted gene expression in the endosperm.