Abundant expression of maternal siRNAs is a conserved feature of seed development

Abstract

<jats:p>Small RNAs are abundant in plant reproductive tissues, especially 24-nucleotide (nt) small interfering RNAs (siRNAs). Most 24-nt siRNAs are dependent on RNA Pol IV and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and establish DNA methylation at thousands of genomic loci in a process called RNA-directed DNA methylation (RdDM). In<jats:italic>Brassica rapa</jats:italic>, RdDM is required in the maternal sporophyte for successful seed development. Here, we demonstrate that a small number of siRNA loci account for over 90% of siRNA expression during<jats:italic>B. rapa</jats:italic>seed development. These loci exhibit unique characteristics with regard to their copy number and association with genomic features, but they resemble canonical 24-nt siRNA loci in their dependence on RNA Pol IV/RDR2 and role in RdDM. These loci are expressed in ovules before fertilization and in the seed coat, embryo, and endosperm following fertilization. We observed a similar pattern of 24-nt siRNA expression in diverse angiosperms despite rapid sequence evolution at siren loci. In the endosperm, siren siRNAs show a marked maternal bias, and siren expression in maternal sporophytic tissues is required for siren siRNA accumulation. Together, these results demonstrate that seed development occurs under the influence of abundant maternal siRNAs that might be transported to, and function in, filial tissues.</jats:p>

The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis

“…S2A, and Fig. 4C), and work from Grover et al in B. rapa 37 , demonstrate that, at least in these species, siren 24nt-siRNAs target high levels of DNA methylation via the RdDM pathway. Thus, by this metric, they behave similarly to other 24nt-siRNAs.…”

“…This distinct pattern of 24nt-siRNAs was initially observed in the endosperm of rice, where they were designated as siren loci 36 . Subsequently, the small RNA patterns leading to this designation have been detected in other plant species and have been shown to arise prior to formation of the endosperm, in ovule tissues 37,39,40 . Regarding their function, our work in Arabidopsis ( Fig.…”

“…Thus, by this metric, they behave similarly to other 24nt-siRNAs. However, given their locations near genes 36,37 and findings that mutations in Pol-IV components result in severe fertility defects in B. rapa 41 and rice 42 , and subtle defects in Arabidopsis 41 , it has been suggested that siren loci could play roles in regulating genes important for seed development and/or for controlling imprinting in the endosperm 36,37 . Although examination of the 24nt-siRNA, DNA methylation, and gene expression profiles at siren loci using our Arabidopsis ovule data did not show any clear candidates in support of these hypotheses, such roles may be more evident in species with stronger fertility defects.…”

“…2B and Table S5). Given the similarity of these ovule loci to those described in rice 36 and Brassica 37 , they are hereafter referred to by their initial designation as siren (small-interfering RNA in endosperm) loci 36 . Second, the expression profiles in Class 1, Class 2, and to a lesser extent Class 3, are similar in flower, rosette, and leaf tissues ( Fig.…”

Developmental and genomic architecture of plant embryogenesis: from model plant to crops

“…During B. rapa seed development, 90% of 24-nt siRNAs are produced from fewer than 200 loci that are highly expressed in the ovule and seed coat, accumulate in the endosperm, and at low levels in embryos. These siRNAs remain expressed throughout embryogenesis, indicating that they are likely involved in regulating their target genes throughout seed development ( Grover et al., 2020 ).…”