Back-spliced RNA from retrotransposon binds to centromere and regulates centromeric chromatin loops in maize
Back-spliced RNA from retrotransposon binds to centromere and regulates centromeric chromatin loops in maize
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来自反转录转座子的反向剪接 RNA 与着丝粒结合并调节玉米的着丝粒染色质环
DOI：
10.1371/journal.pbio.3000582
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发表时间：
2020-01-01
期刊：
影响因子：
9.8
通讯作者：
Han, Fangpu
中科院分区：
文献类型：
--
作者：
Liu, Yalin;Su, Handong;Han, Fangpu
在大多数植物中，着丝粒DNA含有高度重复的序列，包括串联重复序列和反转录转座子；然而，这些序列在着丝粒结构和功能中的作用尚不清楚。在这里，我们发现着丝粒反转录转座子(CRM)的多个RNA序列富含在玉米(Zea Mays)着丝粒中，并且CRM1产生了反向剪接的RNA。根据反向剪接序列，我们鉴定了3种类型的CRM1衍生的具有相同反向剪接位点的环状RNA。这些环状RNA通过R-环与着丝粒结合。一个环状RNA中的两个R环位置促进了CRM1区染色质环的形成。当RNA干扰(RNAi)用于靶向CRM1环状RNA的后剪接位点时，这些环状RNA形成的R环和染色质环的水平降低，而具有相似结合位点的线性RNA产生的R环水平上升。只有一个R环的线形RNA不能促进染色质环的形成。在RNAi植物的CRM1区域，高水平的R环和低水平的染色质环导致着丝粒H3变体(CENH3)的定位减少。我们的工作揭示了CRM1RNA通过R环和染色质环形成的着丝粒组织，这表明CRM1元件可能有助于在着丝粒进化过程中建立合适的染色质环境。这些结果表明，R环是着丝粒染色质的组成部分，正确的着丝粒结构是CENH3定位的关键。
In most plants, centromeric DNA contains highly repetitive sequences, including tandem repeats and retrotransposons; however, the roles of these sequences in the structure and function of the centromere are unclear. Here, we found that multiple RNA sequences from centromeric retrotransposons (CRMs) were enriched in maize (Zea mays) centromeres, and back-spliced RNAs were generated from CRM1. We identified 3 types of CRM1-derived circular RNAs with the same back-splicing site based on the back-spliced sequences. These circular RNAs bound to the centromere through R-loops. Two R-loop sites inside a single circular RNA promoted the formation of chromatin loops in CRM1 regions. When RNA interference (RNAi) was used to target the back-splicing site of the circular CRM1 RNAs, the levels of R-loops and chromatin loops formed by these circular RNAs decreased, while the levels of R-loops produced by linear RNAs with similar binding sites increased. Linear RNAs with only one R-loop site could not promote chromatin loop formation. Higher levels of R-loops and lower levels of chromatin loops in the CRM1 regions of RNAi plants led to a reduced localization of the centromeric H3 variant (CENH3). Our work reveals centromeric chromatin organization by circular CRM1 RNAs via R-loops and chromatin loops, which suggested that CRM1 elements might help build a suitable chromatin environment during centromere evolution. These results highlight that R-loops are integral components of centromeric chromatin and proper centromere structure is essential for CENH3 localization.