wide range of pathways allowing for gene expression regulation exist: these range from pre-transcriptional to post-transcriptional processes and take place to regulate certain developmental transitions, responses to environmental conditions, among others. In this study we investigate how gene expression mechanisms have evolved to establish a dominance hierarchy in a complex multiallelic locus – the self-incompatibility system of Arabidopsis. In this unique system, dozens of alleles co-exist in a dominance continuum and the reproductive success of a diploid individual greatly depends on the ability of the dominant allele to repress the activity of the recessive allele. The peculiar evolutionary dynamics at the self-incompatibility locus entails that any given dominant allele must robustly control the expression of numerous other recessive alleles, as well as have the flexibility to accommodate frequent loss and gain of alleles in the population. This complex gene regulatory network relies on the activity of miRNA-like elements that are believed to function through DNA methylation. Here, we explore the characteristics of these elements and their potential participation in pre- and post-transcriptional gene silencing pathways, such as RdDM. Our results show that these miRNA-like elements have unusual molecular properties, likely function independently of DNA methylation, but are nevertheless very robust in controlling transcript levels of targeted alleles, challenging our current understanding of canonical gene regulatory pathways and their evolution.
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