Arabidopsis Retrotransposon Virus-Like Particles and Their Regulation by Epigenetically Activated Small RNA

Lee, S.C., Ernst, E., Berube, B., Borges, F., Parent, J. S., Ledon, P., Schorn, A., Martienssen, R. A. (April 2020) Arabidopsis Retrotransposon Virus-Like Particles and Their Regulation by Epigenetically Activated Small RNA. Genome Research. ISSN 1088-9051

Abstract

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.

Item Type:	Paper
Subjects:	organism description > plant > Arabidopsis bioinformatics > genomics and proteomics > genetics & nucleic acid processing > epigenetics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > epigenetics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > transposable elements bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transposons
CSHL Authors:	Martienssen, Robert A. Schorn, Andrea Ernst, Evan Borges, Filipe Parent, Jean-Sebastien Lee, Seung Cho Berube, Benjamin Ledon, Paul
Communities:	CSHL labs > Martienssen lab CSHL labs > Schorn lab CSHL Cancer Center Program > Gene Regulation and Inheritance Program
Depositing User:	Adrian Gomez
Date:	17 April 2020
Date Deposited:	22 Apr 2020 18:44
Last Modified:	29 Oct 2020 15:44
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/39248

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