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Arabidopsis thaliana

ABSTRACT: Epigenetic and biochemical determinants of Pol IV-dependent genome surveillance in plants

PROVIDER: PRJNA510791 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8357240.fastq.gz	Fastqsanger.gz
	SRR8357250_1.fastq.gz	Fastqsanger.gz
	SRR8357250_2.fastq.gz	Fastqsanger.gz
	SRR8357260.fastq.gz	Fastqsanger.gz
	SRR8357270_1.fastq.gz	Fastqsanger.gz

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Arabidopsis thaliana

Project description:Pol-IV dependent transcripts in Arabidopsis

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Project description:In plants, transposons and non-protein-coding repeats are epigenetically silenced by CG and non-CG methylation. This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, Pol IV and Pol V, in a process called RNA-directed DNA methylation. By contrast, many protein-coding genes transcribed by Pol II contain in their gene bodies exclusively CG methylation that is independent of small RNAs and Pol IV/Pol V activities. It is unclear how the different methylation machineries distinguish between transposons and genes. Here we report on a group of atypical genes that display in their coding region a transposon-like methylation pattern, which is associated with gene silencing in sporophytic tissues.

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Project description:In plants, heterochromatin is maintained by a small RNA-based gene silencing mechanism known as RNA-directed DNA methylation (RdDM). RdDM requires the non-redundant functions of two plant-specific DNA-dependent RNA polymerases (Pol) Pol IV and Pol V. Pol IV plays a major role in siRNA biogenesis, while Pol V may recruit DNA methylation machinery to target endogenous loci for silencing. Although small RNA-generating regions which are dependent on both Pol IV and Pol V have been identified previously, the genomic loci targeted Pol V for siRNA accumulation and silencing have not been described extensively. To characterize the Pol V-dependent, heterochromatic siRNA-generating regions in the Arabidopsis genome, we deeply sequenced the small RNA populations of wild-type and Pol V mutant plants. Furthermore, we characterized the siRNA-generating regions which were dependent on RdDM effectors and examined their dependency on Pol V. Small RNA libraries were generated and deeply sequenced from mutant alleles dms4-1, drd1-1, dms3-1, and rdm1-4, along with their control library (“Wt(T+S)”) which has been described previously (Kanno et al. 2004 Current Biology). More than 2,000 small RNA-generating loci were identified which were greatly suppressed in Pol V mutants.

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Arabidopsis thaliana cultivar:Columbia-0

Project description:Pol IV and RDR2-dependent precursors of 24 nt siRNAs

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Characterization of small RNA-generating regions targeted by RNA polymerase V in Arabidopsis

2012-06-11 | E-GEOD-36424 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:Structural Variant of a Tandem Repeat-containing Silencer Locus Reveals Distinct Pol II and Pol IV-dependent Pathways of siRNA Biogenesis

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RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm [PareSeq]

Project description:Gene expression in endosperm – a seed tissue that mediates transfer of maternal resources to offspring – is under complex epigenetic control. We show here that plant-specific RNA Polymerase IV mediates parental control of endosperm gene expression. Pol IV is required for the production of small interfering RNAs that typically direct DNA methylation. We compared small RNAs, DNA methylation, and mRNAs in A. thaliana endosperm from reciprocal heterozygotes produced by crossing wild-type plants to Pol IV mutants. We find that maternally and paternally acting Pol IV have divergent effects on endosperm. Losses of maternal and paternal Pol IV impact sRNAs and DNA methylation at distinct genomic sites. Strikingly, maternally and paternally-acting Pol IV have antagonistic impacts on gene expression at some loci, divergently promoting or repressing endosperm gene expression. Antagonistic parent-of origin effects have only rarely been described and are consistent with a gene regulatory system evolving under parental conflict

2022-03-04 | GSE197715 | GEO

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