Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
Genome Biol. 2021 Jan 5;22(1):15. doi: 10.1186/s13059-020-02242-6.
Small RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) serve as core players in gene silencing at transcriptional and post-transcriptional levels in plants, but their subcellular localization has not yet been well studied, thus limiting our mechanistic understanding of sRNA action.
We investigate the cytoplasmic partitioning of sRNAs and their targets globally in maize (Zea mays, inbred line "B73") and rice (Oryza sativa, cv. "Nipponbare") by high-throughput sequencing of polysome-associated sRNAs and 3' cleavage fragments, and find that both miRNAs and a subset of 21-nucleotide (nt)/22-nt siRNAs are enriched on membrane-bound polysomes (MBPs) relative to total polysomes (TPs) across different tissues. Most of the siRNAs are generated from transposable elements (TEs), and retrotransposons positively contributed to MBP overaccumulation of 22-nt TE-derived siRNAs (TE-siRNAs) as opposed to DNA transposons. Widespread occurrence of miRNA-mediated target cleavage is observed on MBPs, and a large proportion of these cleavage events are MBP-unique. Reproductive 21PHAS (21-nt phasiRNA-generating) and 24PHAS (24-nt phasiRNA-generating) precursors, which were commonly considered as noncoding RNAs, are bound by polysomes, and high-frequency cleavage of 21PHAS precursors by miR2118 and 24PHAS precursors by miR2275 is further detected on MBPs. Reproductive 21-nt phasiRNAs are enriched on MBPs as opposed to TPs, whereas 24-nt phasiRNAs are nearly completely devoid of polysome occupancy.
MBP overaccumulation is a conserved pattern for cytoplasmic partitioning of sRNAs, and endoplasmic reticulum (ER)-bound ribosomes function as an independent regulatory layer for miRNA-induced gene silencing and reproductive phasiRNA biosynthesis in maize and rice.
小 RNA（sRNA）包括 microRNA（miRNA）和 small interfering RNA（siRNA），在植物中作为转录和转录后水平基因沉默的核心分子发挥作用，但它们的亚细胞定位尚未得到很好的研究，因此限制了我们对 sRNA 作用的机制理解。
我们通过高通量测序多核糖体相关 sRNA 和 3' 切割片段，在玉米（Zea mays，自交系“B73”）和水稻（Oryza sativa，cv. “Nipponbare”）中全面研究了 sRNA 及其靶标的细胞质分配，发现 miRNA 和一小部分 21 核苷酸（nt）/22-nt siRNA 相对于总多核糖体（TP）在不同组织中都在膜结合多核糖体（MBP）上富集。大多数 siRNA 是由转座元件（TE）产生的，反转录转座子对 22-nt TE 衍生的 siRNA（TE-siRNA）的 MBP 过度积累有积极贡献，而 DNA 转座子则没有。在 MBP 上观察到广泛发生的 miRNA 介导的靶标切割，并且这些切割事件中的很大一部分是 MBP 特有的。普遍认为 21PHAS（21-nt phasiRNA 生成）和 24PHAS（24-nt phasiRNA 生成）前体是非编码 RNA，但它们也与多核糖体结合，并且进一步在 MBP 上检测到 miR2118 对 21PHAS 前体和 miR2275 对 24PHAS 前体的高频切割。生殖 21-nt phasiRNA 在 MBP 上相对于 TPs 富集，而 24-nt phasiRNA 几乎完全缺乏多核糖体占据。
MBP 过度积累是 sRNA 细胞质分配的一种保守模式，内质网（ER）结合核糖体在玉米和水稻中作为 miRNA 诱导的基因沉默和生殖 phasiRNA 生物合成的独立调控层发挥作用。
