Imprinted regulatory networks reveal the molecular cross-talk between paternal and maternal genomes in the endosperm of Arabidopsis arenosa

Summary paragraphImprinted genes do not act alone to shape seed development, but as a complex network -- just like any other gene. Yet, the molecular context in which they are embedded, i.e. their gene network, remains largely understudied. To address this knowledge gap, we characterized the imprintome of Arabidopsis arenosa at the species-level and used gene regulatory network analyses. We show that genomic imprinting preferentially affects only a few pathways, offering candidates for dosage sensitive processes and the molecular arena of parental conflict. In these pathways, some imprinted genes act as hub genes, among which NRPE1, highlighting the importance of epigenetics in endosperm development. The interaction between parental genomes was rather one-sided: paternally expressed regulators preferentially targeted PEGs, while maternally expressed regulators targeted both PEGs and MEGs indiscriminately. This aligns with a self-promoting paternal influence and a maternal buffer under a parental conflict scenario. Shared paternal and maternal regulation of downstream targets was nevertheless common, and we reveal novel molecular interactions between imprinted regulators. Overall, our work shows how genomic imprinting may act as a molecular means for parental conflict, but also highlights the importance of parental molecular coordination in endosperm development.