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siRNAs and RNA-directed DNA Methylation during seed development

Seeds are the bedrock of agriculture – they form the majority of food for humans and livestock, and are necessary to grow nearly all of our remaining food. Understanding seed development is therefore a critical component how we feed our growing population with less land, fewer inputs, and diminished environmental impact.


Seed development in flowering plants is similar to reproduction in mammals – the embryo grows and develops within the maternal body, interacting with Mom via a transient nutritive tissue that is also a product of fertilization (placenta in mammals, endosperm in plants). This interaction provides an opportunity for maternal-filial communication after fertilization, potentially in the form of small RNAs that direct chemical modification of DNA. Indeed, small RNA mediated DNA methylation (RdDM) is required for successful reproduction in many plant species.


Research in the Mosher lab is focused on understanding how RdDM influences seed development and whether mothers transmit small RNAs to the endosperm to modify development. Understanding how mothers influence seed development could lead to increased yield or improved nutritional composition of seed crops. Understanding communication between the maternal tissue and the endosperm might also uncover paradigms for maternal-fetal communication during mammalian development.

"The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but 'That's funny...' "

Isaac Asimov

Project 1: How do maternal siRNAs impact seed development?

Seed development requires the careful coordination of three genetically distinct tissues – embryo, endosperm, and seed coat. We have demonstrated that small RNA-directed DNA Methylation (RdDM) is required for seed development in some Brassicaceae, but not in others (Grover JW, et al. 2018). Loss of RdDM causes seed abortion after fertilization, most likely through failure of endosperm development. It is therefore surprising that RdDM in the endosperm is not required. Rather, maternal siRNA production is necessary for seed development after fertilization (Grover JW, et al. 2018).


Maternal tissue surrounding the development endosperm produces abundant siRNAs from a small number of genomic loci (known as “siren loci”) and siRNA production from these loci is required for seed development (Grover JW, et al. 2020; Burgess D, et al. 2022). Siren loci overlap pseudogenes and gene fragments and can target DNA methylation at homologous protein-coding genes in trans (Burgess D, et al. 2022). Production of siren siRNAs is sometimes associated with expression changes of target genes, providing a mechanism linking siRNA production to development. Using molecular biology, genetics, and high throughput sequencing approaches, we will explore this mechanism.

Project 2: Do siren siRNAs move from maternal to filial tissues?

Although seeds lacking RdDM fail to develop endosperm appropriately, RdDM in the endosperm is neither required nor sufficient for seed development. Instead, maternal somatic RdDM is required for endosperm development (Grover JW, et al. 2018). Siren siRNAs, which are produced abundantly in the maternal seed coat, also accumulate in the endosperm, where they are maternal-specific, suggesting that siren siRNAs might move from maternal to filial tissues. We are currently developing microscopic and molecular approaches to directly test this hypothesis.

Project 3: What is the role of Pol VI in grasses?

RdDM requires two plant-specific polymerases, RNA Pol IV and V. The unique functions of these polymerases are encoded in duplicate copies of the largest and second-largest subunits, which are present in all land plants (Huang Y, et al. 2015). We discovered additional duplications of these subunits in the critically-important grass family, and provide evidence that these subunits might represent a novel sixth polymerase (Trujillo JT, et al. 2018). These subunits are expressed specifically during reproduction, and ongoing projects will interrogate the assembly and molecular function of this new polymerase.

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