Widespread occurrence of microRNA-mediated target cleavage on membrane-bound polysomes.
Widespread occurrence of microRNA-mediated target cleavage on membrane-bound polysomes.
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DOI：
10.1186/s13059-020-02242-6
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发表时间：
2021-01-05
期刊：
影响因子：
12.3
通讯作者：
Chen X
中科院分区：
文献类型：
--
作者：
Yang X;You C;Wang X;Gao L;Mo B;Liu L;Chen X
小分子RNA（small RNA，sRNA）包括microRNA（microRNA，miRNAs）和小干扰RNA（small interfering RNA，siRNAs），在植物基因沉默中起着重要作用，但它们的亚细胞定位尚未得到很好的研究，这限制了我们对sRNA作用机制的理解。我们研究了玉米（Zea mays，近交系“B73”）和水稻（Oryza sativa，cv.“Nipponbare”）通过对多核糖体相关sRNA和3′切割片段进行高通量测序，发现miRNA和21-核苷酸（nt）/22-nt siRNA的子集在不同组织中相对于总多核糖体（TP）在膜结合多核糖体（MBP）上富集。大多数siRNA是由转座因子（TE）产生的，与DNA转座子相反，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。在MBP上观察到广泛发生的miRNA介导的靶切割，并且这些切割事件中的大部分是MBP独特的。通常被认为是非编码RNA的生殖性21-nt phasiRNA-generating（21-nt phasiRNA-generating）和24-nt phasiRNA-generating（24-nt phasiRNA-generating）前体被多核糖体结合，并且在MBP上进一步检测到miR 2118对21 PHAS前体和miR 2275对24 PHAS前体的高频切割。与TP相反，生殖性21-nt phasiRNA在MBP上富集，而24-nt phasiRNA几乎完全没有多核糖体占据。MBP过度积累是sRNA在细胞质中分配的保守模式，内质网（ER）结合的核糖体作为玉米和水稻中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。
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.
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DOI：
10.1073/pnas.1314749110
发表时间：
2013-11-26
影响因子：
11.1
作者：
Deng, Yan;Srivastava, Renu;Howell, Stephen H.
通讯作者：
Howell, Stephen H.
影响因子：
9.2
作者：
Addo-Quaye, Charles;Eshoo, Tifani W.;Axtell, Michael J.
通讯作者：
Axtell, Michael J.
影响因子：
14.9
作者：
Dalmadi, Agnes;Gyula, Peter;Havelda, Zoltan
通讯作者：
Havelda, Zoltan
影响因子：
11.6
作者：
Howell, Miya D.;Fahlgren, Noah;Carrington, James C.
通讯作者：
Carrington, James C.
影响因子：
5.8
作者：
Addo-Quaye, Charles;Miller, Webb;Axtell, Michael J.
通讯作者：
Axtell, Michael J.