21-nt phasiRNAs direct target mRNA cleavage in rice male germ cells

Abstract

In grasses, phased small interfering RNAs (phasiRNAs), 21- or 24-nucleotide (nt) in length, are predominantly expressed in anthers and play a role in regulating male fertility. However, their targets and mode of action on the targets remain unknown. Here we profile phasiRNA expression in premeiotic and meiotic spikelets as well as in purified male meiocytes at early prophase I, tetrads and microspores in rice. We show that 21-nt phasiRNAs are most abundant in meiocytes at early prophase I while 24-nt phasiRNAs are more abundant in tetrads and microspores. By performing highly sensitive degradome sequencing, we find that 21-nt phasiRNAs direct target mRNA cleavage in male germ cells, especially in meiocytes at early prophase I. These targets include 435 protein-coding genes and 71 transposons that show an enrichment for carbohydrate biosynthetic and metabolic pathways. Our study provides strong evidence that 21-nt phasiRNAs act in a target-cleavage mode and may facilitate the progression of meiosis by fine-tuning carbohydrate biosynthesis and metabolism in male germ cells.

miRador: a fast and precise tool for the prediction of plant miRNAs

“…This may have resulted in reduced precision, particularly in the case of Arabidopsis in which most tools performed their worst in terms of precision. In the case of rice, however, we utilized well staged low-input sRNA and PARE sequencing libraries generated in triplicates from small amounts of tissue (Jiang et al, 2020). These tissue-specific datasets may provide cleaner results with less noise in the PARE data than what was found in the Arabidopsis and maize libraries resulting in the best predictions for all tools.…”

Oxygen, secreted proteins and small RNAs: mobile elements that govern anther development

“…One study in pummelo predicted and verified targets in trans with gene ontologies of broad terms but also including PCD and pollen development (Fang et al 2020). By now, two pioneering study in rice meiocytes finally found indeed RNA degradation of target genes of reproductive 21nt-phasiRNAs (Jiang et al 2020;Zhang et al 2020c). In rice meiocytes, target genes were enriched for carbohydrate biosynthesis and metabolism, and also included OsDMC1B, a meiotic gene (Jiang et al 2020).…”

“…By now, two pioneering study in rice meiocytes finally found indeed RNA degradation of target genes of reproductive 21nt-phasiRNAs (Jiang et al 2020;Zhang et al 2020c). In rice meiocytes, target genes were enriched for carbohydrate biosynthesis and metabolism, and also included OsDMC1B, a meiotic gene (Jiang et al 2020). Another study gained insight on genes targeted for degradation in rice anthers through degradome data from whole rice spikelets of WT and of mutants in MEL1, the rice AGO5 which binds phasiRNA.…”

“…The second part needs further examination. • Q4: What are the functions of genes targeted by phasi RNAs for degradation, as identified now in rice (Jiang et al 2020;Zhang et al 2020c)? Are there further targets in other cells, at other times?…”

“…Common to both photoperiod and temperature changes is the modification of developmental timing-higher temperature as well as long-day conditions lead to faster anther development, meiosis and microsporogenesis (Zhang et al 2020a;Zhu et al 2020;Teng et al 2020). One hypothesis regarding the biological function of phasiRNAs is a role in destabilization of mRNA that are not needed anymore, as by animal piRNAs (Gou et al 2014 (Jiang et al 2020).…”