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MiRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE52952 | GEO | 2014/03/18

SECONDARY ACCESSION(S): PRJNA230526

REPOSITORIES: GEO

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miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis.

Project description:In plants, post-transcriptional gene silencing (PTGS) is mediated by DICER-LIKE 1 (DCL1)-dependent microRNAs (miRNAs), which also trigger 21-nucleotide secondary short interfering RNAs (siRNAs) via RNA-DEPENDENT RNA POLYMERASE 6 (RDR6), DCL4 and ARGONAUTE 1 (AGO1), whereas transcriptional gene silencing (TGS) of transposons is mediated by 24-nucleotide heterochromatic (het)siRNAs, RDR2, DCL3 and AGO4 (ref. 4). Transposons can also give rise to abundant 21-nucleotide 'epigenetically activated' small interfering RNAs (easiRNAs) in DECREASED DNA METHYLATION 1 (ddm1) and DNA METHYLTRANSFERASE 1 (met1) mutants, as well as in the vegetative nucleus of pollen grains and in dedifferentiated plant cell cultures. Here we show that easiRNAs in Arabidopsis thaliana resemble secondary siRNAs, in that thousands of transposon transcripts are specifically targeted by more than 50 miRNAs for cleavage and processing by RDR6. Loss of RDR6, DCL4 or DCL1 in a ddm1 background results in loss of 21-nucleotide easiRNAs and severe infertility, but 24-nucleotide hetsiRNAs are partially restored, supporting an antagonistic relationship between PTGS and TGS. Thus miRNA-directed easiRNA biogenesis is a latent mechanism that specifically targets transposon transcripts, but only when they are epigenetically reactivated during reprogramming of the germ line. This ancient recognition mechanism may have been retained both by transposons to evade long-term heterochromatic silencing and by their hosts for genome defence.

| S-EPMC4074602 | biostudies-literature

miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-03-18 | E-GEOD-52952 | biostudies-arrayexpress

miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis [Affymetrix]

Project description:Utilizing Affymetrix ATH1 microarrays to analyze transposon expression in DNA methylation mutants, and RNAi mutants, compared to wildtype.

2014-03-18 | GSE52067 | GEO

miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis [Affymetrix]

Project description:Utilizing Affymetrix ATH1 microarrays to analyze transposon expression in DNA methylation mutants, and RNAi mutants, compared to wildtype. Total RNA extracted from plant inflorescence tissue.

2014-03-18 | E-GEOD-52067 | biostudies-arrayexpress

miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis (bisulfite-seq)

Project description:Utilizing whole-genome BIS-seq to analyze transposon methylation in DNA methylation mutants, and RNAi mutants, compared to wildtype.

2014-03-18 | GSE52346 | GEO

miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis [PARE-seq]

2014-03-18 | GSE52342 | GEO

miRNAs trigger widespread epigenetically-activated siRNAs from transposons inÂ Arabidopsis [PARE-seq]

Project description:Utilizing whole-genome Parallele Analysis of RNA Ends (PARE)-seq to analyze the degradome to assess miRNA-binding of transposons in DNA methylation mutants, and RNAi mutants, compared to wildtype. Genome-wide small RNA profiling was done by Illumina TruSeq sample preparation followed by high-throughput sequencing with Illumina HiSeq 2000 platform.Â

2014-03-18 | E-GEOD-52342 | biostudies-arrayexpress

miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis (small RNA-seq)

Project description:Utilizing whole-genome sRNA-seq to analyze transposon derived siRNAs in DNA methylation mutants, and RNAi mutants, compared to wildtype.

2014-03-18 | GSE52951 | GEO

miRNAs trigger widespread epigenetically-activated siRNAs from transposons inM-BM- Arabidopsis (bisulfite-seq)

Project description:Utilizing whole-genome BIS-seq to analyze transposon methylation in DNA methylation mutants, and RNAi mutants, compared to wildtype. DNA extracted from plant inflorescence tissue, bisulphite-treated and libraries sequenced Illumina HiSEq, mapped by BiSMark.

2014-03-18 | E-GEOD-52346 | biostudies-arrayexpress

miRNAs trigger widespread epigenetically-activated siRNAs from transposons in Arabidopsis (small RNA-seq)

Project description:Utilizing whole-genome sRNA-seq to analyze transposon derived siRNAs in DNA methylation mutants, and RNAi mutants, compared to wildtype. Total RNA extracted from plant inflorescence tissue, small RNA sequenced Illumina HiSeq, read size 18-nt to 26-nt, mapping with Bowtie (Tuxedo)

2014-03-18 | E-GEOD-52951 | biostudies-arrayexpress

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