Small RNAs within the developing seed of Arabidopsis thaliana

Abstract

The developing seed of Arabidopsis thaliana exhibits a wide range of dynamic epigenetic phenomena, but relatively little is known about the small RNA (sRNA) populations found within the tissues composing the seed. We set out to profile the sRNA complement found within whole seeds and the embryo and endosperm tissues within the seed. In whole seeds, variation in sRNA activity at TEs near genes is shown to correspond with variation in parental biases in gene expression. In addition, regions exhibiting differential methylation between embryo and endosperm are enriched for whole seed sRNA expression. We also discovered sRNA enrichment upstream of both maternally and paternally expressed imprinted genes. When analyzing sRNA populations within the embryo and endosperm, we defined differential sRNA regions (DSRs) with tissue-enriched sRNA expression patterns. Embryo DSRs were strongly associated with heterochromatic regions of the genome, while endosperm DSRs showed strong overlap with gene bodies and Polycomb-associated regions of the genome. Using seeds derived from FI crosses, we were able to assay the parent-of-origin for sRNAs within the seed tissues. Although sRNA parent-of-origin genome-wide reflects the overall genomic complement from the parents, there are regions of the genome with strong parental bias in sRNA expression, and endosperm DSRs are enriched for maternally-biased sRNA expression. Furthermore, imprinted genes are associated with parentally-biased sRNAs in the endosperm - paternally biased gene expression is associated with maternally biased sRNA expression, and vice versa. Surprisingly, the loss of a Pol IV, a key component in the sRNA biogenesis pathway, does not directly lead to a reduction in the magnitude of imprinted gene expression, but rather leads to a genome-wide increase in maternal gene expression. We also assayed the ability of sRNAs to move between the central cell and the egg cell of the unfertilized female gametophyte, finding preliminary evidence that sRNAs might move between these cells, as has been previously hypothesized. This work contributes to our understanding of the role of sRNAs within the developing seed and their relationship with other characterized epigenetic marks and changes.