In Arabidopsis, LTR retrotransposons are activated by mutations in the chromatin gene DECREASE in DNA METHYLATION 1 (DDM1), giving rise to 21- to 22-nt epigenetically activated siRNA (easiRNA) that depend on RNA DEPENDENT RNA POLYMERASE 6 (RDR6). We purified virus-like particles (VLPs) from ddm1 and ddm1rdr6 mutants in which genomic RNA is reverse transcribed into complementary DNA. High-throughput short-read and long-read sequencing of VLP DNA (VLP DNA-seq) revealed a comprehensive catalog of active LTR retrotransposons without the need for mapping transposition, as well as independent of genomic copy number. Linear replication intermediates of the functionally intact COPIA element EVADE revealed multiple central polypurine tracts (cPPTs), a feature shared with HIV in which cPPTs promote nuclear localization. For one member of the ATCOPIA52 subfamily (SISYPHUS), cPPT intermediates were not observed, but abundant circular DNA indicated transposon "suicide" by auto-integration within the VLP. easiRNA targeted EVADE genomic RNA, polysome association of GYPSY (ATHILA) subgenomic RNA, and transcription via histone H3 lysine-9 dimethylation. VLP DNA-seq provides a comprehensive landscape of LTR retrotransposons and their control at transcriptional, post-transcriptional, and reverse transcriptional levels.

中文翻译：

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拟南芥逆转录转座子病毒样颗粒及其通过表观遗传激活的小 RNA 的调控。

在拟南芥中，LTR 反转录转座子被 DNA 甲基化 1 (DDM1) 中染色质基因减少的突变激活，从而产生依赖于 RNA 依赖性 RNA 聚合酶 6 (RDR6) 的 21 至 22 nt 表观遗传激活的 siRNA (easiRNA)。我们从 ddm1 和 ddm1rdr6 突变体中纯化了病毒样颗粒 (VLP)，其中基因组 RNA 被逆转录为互补 DNA。VLP DNA 的高通量短读和长读测序 (VLP DNA-seq) 揭示了活性 LTR 反转录转座子的综合目录，无需映射转座，并且与基因组拷贝数无关。功能完整的 COPIA 元素 EVADE 的线性复制中间体揭示了多个中央聚嘌呤束 (cPPT)，这是与 HIV 共有的一个特征，其中 cPPT 促进核定位。对于 ATCOPIA52 亚家族 (SISYPHUS) 的一名成员，未观察到 cPPT 中间体，但丰富的环状 DNA 表明转座子通过 VLP 内的自动整合“自杀”。easiRNA 靶向 EVADE 基因组 RNA、GYPSY (ATHILA) 亚基因组 RNA 的多核糖体结合，以及通过组蛋白 H3 赖氨酸 9 二甲基化进行的转录。VLP DNA-seq 提供了 LTR 反转录转座子及其在转录、转录后和逆转录水平上的控制的全面概况。