Resetting of the 24-nt siRNA landscape in rice zygotes

Abstract

The zygote, a totipotent stem cell, is crucial to the life cycle of sexually reproducing organisms. It is produced by the fusion of two differentiated cells - the egg and sperm, which in plants have radically different siRNA transcriptomes from each other, and from multicellular embryos. Due to technical challenges, the epigenetic changes that accompany the transition from differentiated gametes to totipotent zygote are poorly understood. Since siRNAs serve as both regulators and outputs of the epigenome, we performed here the successful characterization of small RNA transcriptomes of zygotes from rice. Zygote small RNAs exhibited extensive maternal carryover and an apparent lack of paternal contribution, indicated by absence of sperm signature siRNAs. Zygote formation was accompanied by widespread redistribution of 24-nt siRNAs relative to gametes, such that ~70% of the zygote siRNA loci did not overlap any egg cell siRNA loci. Newly-detected siRNA loci in zygote are gene proximal and not associated with centromeric heterochromatin, similar to canonical siRNAs, in sharp contrast to gametic siRNA loci which are gene-distal and heterochromatic. In addition, zygote but not egg siRNA loci were associated with high DNA methylation in the mature embryo. Thus, the zygote begins transitioning before the first embryonic division to an siRNA profile that is associated with future RdDM in embryogenesis. These findings indicate that in addition to changes in gene expression, the transition to totipotency in the plant zygote is accompanied by resetting of the epigenetic reprogramming that occurred during gamete formation.

Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat

“…Similarly, activation of TEs such as LINE is detected at the 2-cell stage of early embryos in mice, which was highly marked by open chromatin and is essential for ZGA [50,51]. In Arabidopsis, the expression of 24-nt sRNAs reached a peak at the midembryonic stage, which further promoted cell-autonomous TE silencing [52,53]. Further analysis of DNA methylome and small RNA profiling around the transition stage would give a better conclusion of the functional consequence of such dACR eruptions in wheat.…”

Plant Small RNAs: Their Biogenesis, Regulatory Roles, and Functions

“…A few research groups have described a set of 24-nt siRNAs named siRNAs in endosperm (aka sirens), which are generated from a relatively small number of loci but are highly abundant in ovules and seeds (25,63,100,157,244). Sirens that accumulate in endosperm are maternally biased and have been suggested to move from the seed coat into filial tissues (the endosperm and embryo/zygote) to mediate DNA methylation of protein-coding genes in trans (25, 63).…”

“…Therefore, sirens appear to mediate RdDM specifically in ovule and seed tissues, while hc-siRNAs are responsible for RdDM in other tissues. Sirens have so far only been reported in Arabidopsis, Brassica rapa, and rice (63,100,157,244), so the extent of conservation of these 24-nt siRNAs in the angiosperms needs further investigation.…”

DNA methylation dynamics during germline development

“…CLSY3 is highly expressed in the early ovary and ovules ( Long et al, 2021 ; Zhou et al, 2022b ), and it is yet unclear which cell types in the ovule express these siRNAs and are subject to trans ‐induced methylation. However, a recent study of rice egg and zygote siRNA landscapes shows that the egg cell accumulates abundant 24‐nt siRNAs from siren loci that are distinct from the source loci in sperm ( Li et al, 2022 ), indicating that DNA methylation reprogramming occurs in the female germline, at distinct loci from those in the male germline, and methylation reprogramming is likely a conserved phenomenon among flowering plants.…”