RT Journal
A1 Lee, Seung Cho
A1 Ernst, Evan
A1 Berube, Benjamin
A1 Borges, Filipe
A1 Parent, Jean-Sebastien
A1 Ledon, Paul
A1 Schorn, Andrea
A1 Martienssen, Robert A.
T1 Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA
JF Genome Research 
JO Genome Research 
YR 2020 
FD April 01 
VO 30 
IS 4 
SP 576 
OP 588 
DO 10.1101/gr.259044.119 
UL http://genome.cshlp.org/content/30/4/576.abstract 
AB 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.