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GenomicsDDM1 and RdDM are the major regulators of transposon DNA methylation in Arabidopsis
Eukaryotic DNA methylation is found in silent transposable elements and active genes. Nucleosome remodelers of the DDM1/Lsh family are thought to be specifically required to maintain transposon methylation, but the reason for this is unknown. Here, we find that a chromatin gradient that extends from...
ORGANISM(S): Arabidopsis thaliana 
2013-04-17 | E-GEOD-41302 | biostudies-arrayexpress
TranscriptomicsMethyl DIP-chip from self-pollinated ddm1 mutant and ddm1 kyp double mutant
Methylation of histone H3 lysine 9 (H3K9me) and small RNA are associated with constitutively silent chromatin in diverse eukaryotes including plants. In plants, silent transposons are also marked by cytosine methylation, especially at non-CpG sites. The transposon-specific non-CpG methylation in pla...
ORGANISM(S): Arabidopsis thaliana 
2011-12-25 | E-GEOD-34222 | biostudies-arrayexpress
TranscriptomicsTranscriptome analysis of ddm1 Arabidopsis mutant, epiRIL98 and epiRIL202
Transcriptome analysis of ddm1 Arabidopsis mutant, epiRIL98 and epiRIL202 Transcriptome analysis of ddm1 Arabidopsis mutant, epiRIL98 and epiRIL202
ORGANISM(S): Arabidopsis thaliana 
2012-09-03 | E-GEOD-37106 | biostudies-arrayexpress
TranscriptomicsHigh-throughput pyrosequencing of endogenous small RNAs from Arabidopsis thaliana wild-type and ddm1 mutant.
DNA methylation is essential for silencing transposable elements and some genes in higher eukaryotes, implying that this modification must be tightly controlled. However, accidental changes in DNA methylation can be transmitted through mitosis, as in cancer, or meiosis, leading to epiallelic variati...
ORGANISM(S): Arabidopsis thaliana 
2009-02-02 | E-GEOD-13419 | biostudies-arrayexpress
GenomicsRNA-seq for Col-0 WT, ddm1(-/-) and Col-0 X ddm1 (F1) to evaluate transposon expression in F1 Col-0Xddm1 and ddm1
RNA-seq for Col-0 WT, ddm1(-/-) and Col-0 X ddm1 (F1) to evaluate transposon expression in F1 Col-0Xddm1 and ddm1
PRJNA632034 | ENA
TranscriptomicsMapping regulatory elements using signatures of open chromatin in Arabidopsis thaliana
Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We reported genome-wide h...
ORGANISM(S): Arabidopsis thaliana 
2012-07-05 | E-GEOD-34318 | biostudies-arrayexpress
GenomicsRNA-seq for WT and ddm1(-/-) to evaluate transposon expression in ddm1 1st generation
RNA-seq for WT and ddm1(-/-) to evaluate transposon expression in ddm1 1st generation
PRJNA632031 | ENA
GenomicsWGBS of 169 ddm1-derived epiRILs
WGBS of 169 ddm1-derived epiRILs
PRJNA719410 | ENA
Genomicslong-read transcriptomic analysis of ddm1
long-read ONT transcriptomic analysis of ddm1
PRJEB49338 | ENA
UnknownDDM1 guards against telomere truncation in Arabidopsis.
Not available
S-EPMC5880217 | biostudies-literature
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