Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Genome Res. 2020 Apr;30(4):576-588. doi: 10.1101/gr.259044.119. Epub 2020 Apr 17.
In , LTR retrotransposons are activated by mutations in the chromatin gene (), 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 and 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 element revealed multiple central polypurine tracts (cPPTs), a feature shared with HIV in which cPPTs promote nuclear localization. For one member of the subfamily (), cPPT intermediates were not observed, but abundant circular DNA indicated transposon "suicide" by auto-integration within the VLP. easiRNA targeted genomic RNA, polysome association of () 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.
在中，染色质基因（）的突变激活长末端重复转座子（LTR retrotransposons），导致依赖 RNA 依赖性 RNA 聚合酶 6（RDR6）的 21-22nt 表观遗传激活 siRNA（easiRNA）。我们从和中纯化了病毒样颗粒（VLPs），其中基因组 RNA 被逆转录成互补 DNA。VLPs DNA （VLP DNA-seq）的高通量短读和长读测序揭示了一个全面的活跃 LTR 转座子目录，而不需要映射转座，也不需要依赖基因组拷贝数。功能完整的元件的线性复制中间体揭示了多个中央多嘧啶序列（cPPTs），这与 HIV 共享，其中 cPPTs 促进核定位。对于 亚家族的一个成员（），没有观察到 cPPT 中间体，但丰富的环状 DNA 表明转座子在 VLPs 内通过自动整合进行“自杀”。easiRNA 靶向基因组 RNA，亚基因组 RNA 的多核糖体关联，以及通过组蛋白 H3 赖氨酸-9 二甲基化进行转录。VLP DNA-seq 提供了 LTR 转座子及其在转录、转录后和逆转录水平上的控制的全面景观。
