Study : Arabidopsis retrotransposon virus-like-particles and their regulation by epigenetically activated small RNA

Identification

Name

Arabidopsis retrotransposon virus-like-particles and their regulation by epigenetically activated small RNA

Identifier

dXJuOkVWQS9zdHVkeS9QUkpOQTUyOTM5MQ==

Source

Data link

Link to this study on EBI European Nucleotide Archive

Description

We report polysomal RNA sequencing data (RNAseq), small RNAseq, and virus-like-particle (VLP) DNA sequencing (DNAseq) and ChIPseq data. Arabidopsis ddm1 mutants produce LTR retrotransposon transcripts that are processed into 21-22 nt easiRNAs by RNA-Dependent RNA polymerase 6 (RDR6). To test if 21-22 nt easiRNAs regulate transcription, translation and reverse transcription of LTR retrotransposons, we compared ddm1 and ddm1rdr6 in polysomal RNAseq, VLP DNAseq and ChIPseq data. We found a handful of ATHILA elements were differentially regulated in ddm1rdr6 for polysomal RNAseq, VLP DNAseq, and ChIPseq datasets. Using short read and long read technologies, we also profiled functional LTR retrotransposons that made full-length DNA by reverse transcription inside VLPs. Small RNAseq data were obtained in pollen and inflorescence tissues in wild-type and ddm1. Overall design: Polysomal RNAseq from total extract and microsome fraction with each 3 biological replicates of ddm1 and ddm1rdr6; Small RNAseq data from pollen and inflorescence tissues of wild-type and ddm1 with one replicate; VLP DNAseq using short read with 2-3 biological replicates and long read technologies with one replicate from wild-type, ddm1 and ddm1rdr6. ChIPseq was performed with 2 biological replicates from wild-type, rdr6, ddm1, and ddm1rdr6.

Data files

Genotype

Accession number	Name	Taxon