Genomics

Dataset Information

150

DDM1 represses noncoding RNA expression and RNA-directed DNA methylation in heterochromatin


ABSTRACT: In this work, we studied function of rice DDM1 in coordinating DNA methylation, expression of small (sRNA) and long noncoding (lncRNA) RNAs, and nucleosome positioning by high throughput approaches.We show that the ddm1a/1b mutation resulted in ectopic CHH methylation of transposable elements (TE) and repeats. The ectopicCHH methylationwas dependent on DRM2, a DNA methyltransferase involved in sRNA-dependent DNA-methylation (RdDM). The ddm1a/1b mutation resulted in increases of heterochromatic sRNA but decreases of euchromatic sRNA production,induced expression of a set of developmentally regulated heterochromatic lncRNA , and increased nucleosome occupancy of TE-related or silent genes including heterochromatic lncRNA loci. In particular,DDM1-mediated repression ofCentromericRetrotransposons of Rice1 (CRR1) was essential for centromere function. Overall design: BS-seq of ddm1a/1b/drm2 triple mutant; two replicates for smRNA-seq of wt and ddm1a/1b double mutant.

INSTRUMENT(S): Illumina HiSeq 2000 (Oryza sativa Japonica Group)

SUBMITTER: Feng Tan  

PROVIDER: GSE108527 | GEO | 2018-06-06

REPOSITORIES: GEO

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Publications

DDM1 Represses Noncoding RNA Expression and RNA-Directed DNA Methylation in Heterochromatin.

Tan Feng F   Lu Yue Y   Jiang Wei W   Wu Tian T   Zhang Ruoyu R   Zhao Yu Y   Zhou Dao-Xiu DX  

Plant physiology 20180524 3


C methylation of DNA, which occurs at CG, CHG, and CHH (H = A, C, or T) sequences in plants, is a hallmark for the epigenetic repression of repetitive sequences. The chromatin-remodeling factor DECREASE IN DNA METHYLATION1 (DDM1) is essential for DNA methylation, especially at CG and CHG sequences. However, its potential roles in RNA-directed DNA methylation (RdDM) and in chromatin function are not completely understood in rice (Oryza sativa). In this work, we used high-throughput approaches to  ...[more]

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