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Assessment of the Pol IV largest subunit, NRPD1, DeCL domain deletion construct to rescue Pol IV-dependent siRNAs in the nrpd1-3 mutant (sRNA).

ABSTRACT: The Arabidopsis thaliana multi-subunit RNA Polymerase IV largest subunit DeCL domain was functionally assessed with an NRPD1 DeCL domain deletion construct.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE95824 | GEO | 2017/07/17

SECONDARY ACCESSION(S): PRJNA378529

REPOSITORIES: GEO

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Assessment of the Pol IV largest subunit, NRPD1, DeCL domain deletion construct to rescue Pol IV-dependent DNA methylation in the nrpd1-3 mutant (Bisulfite-Seq).

Project description:The Arabidopsis thaliana multi-subunit RNA Polymerase IV largest subunit DeCL domain was functionally assessed with an NRPD1 DeCL domain deletion construct.

2017-07-17 | GSE95823 | GEO

sRNA expression in the Pol V largest subunit mutant, nrpe1-11

Project description:RNA Polymerase V transcription recruits siRNA-Argonaute protein complexes to chromatin, thereby specifying sites of RNA-directed DNA methylation (RdDM) and transcriptional gene silencing in plants. The Pol V largest subunit, NRPE1, has an extensive carboxyl-terminal domain (CTD) that is dispensable for catalytic activity in vitro, yet essential in vivo. A CTD subdomain, DeCL, named for its similarity to a chloroplast protein, DEFECTIVE CHLOROPLASTS AND LEAVES, is required for Pol V function at virtually all loci, similar to mutants defective for Pol V recruitment. Deletions removing three other CTD subdomains affect overlapping subsets of loci, similar to mutants lacking proteins that bind Pol V or its transcripts. A yeast two-hybrid screen for CTD-interactors identified the 3-prime -> 5-prime exoribonuclease, RRP6L1 as an interactor with the DeCL subdomain and the adjacent QS subdomain, named for its numerous glutamine-serine (QS) repeats. These RRP6L1-binding subdomains immediately follow the Argonaute-binding subdomain. Experimental evidence indicates that RRP6L1 trims the 3-prime ends of Pol V transcripts sliced by ARGONAUTE 4 (AGO4), suggesting a model whereby the adjacent CTD subdomains enable the spatial and temporal coordination of AGO4 and RRP6L1 RNA processing activities.

2017-02-25 | GSE93355 | GEO

Functional analysis of the Pol IV DeCL domain

Project description:Functional analysis of the Pol IV DeCL domain

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Functional analysis of the Arabidopsis thaliana Pol V largest subunit, NRPE1, carboxy-terminal domain by whole genome bisulfite sequencing

2017-02-25 | GSE93358 | GEO

MethlyC-Seq of nrpd1-3, nrpd1-12, and nrpe1-11

Project description:Using MethylC-Seq to provide single-base resolution of DNA methylation status in nrpd1-3, nrpd1-12, and nrpe1-11 mutants

2015-02-05 | GSE64499 | GEO

MethlyC-Seq of nrpd1-3, nrpd1-12, and nrpe1-11

Project description:Using MethylC-Seq to provide single-base resolution of DNA methylation status in nrpd1-3, nrpd1-12, and nrpe1-11 mutants MethylC-Seq: 3 mutants examined, nrpd1-3, nrpd1-12, and nrpe1-11

2015-02-05 | E-GEOD-64499 | biostudies-arrayexpress

Epigenomic profiles of Brachypodium distachyon mutants deficient in RNA polymerase IV (Pol IV)

Project description:Monocot grass species (Poaceae) express a diverse set of multisubunit RNA polymerase enzymes, including Pol II, Pol IV and Pol V. To better understand this functional diversity, we have charted Pol IV function in the model Brachypodium distachyon. Intriguingly, pol IV null mutations in Poaceae crops disrupt growth, reproductive development and seed set. In order to investigate how Pol IV controls vegetative growth and TE activity in these grasses, we have isolated B. distachyon mutant alleles for Pol IV’s largest subunit, NRPD1. We obtained the germplasm in which to screen for these pol IV mutations from the B. distachyon community's sodium azide (NaN) and T-DNA insertion collections.

2024-03-04 | GSE243693 | GEO

The NRPD1 N-terminus contains a Pol IV-specific motif that is critical for genome surveillance in Arabidopsis.

Project description:RNA-guided surveillance systems constrain the activity of transposable elements (TEs) in host genomes. In plants, RNA polymerase IV (Pol IV) transcribes TEs into primary transcripts from which RDR2 synthesizes double-stranded RNA precursors for small interfering RNAs (siRNAs) that guide TE methylation and silencing. How the core subunits of Pol IV, homologs of RNA polymerase II subunits, diverged to support siRNA biogenesis in a TE-rich, repressive chromatin context is not well understood. Here we studied the N-terminus of Pol IV's largest subunit, NRPD1. Arabidopsis lines harboring missense mutations in this N-terminus produce wild-type (WT) levels of NRPD1, which co-purifies with other Pol IV subunits and RDR2. Our in vitro transcription and genomic analyses reveal that the NRPD1 N-terminus is critical for robust Pol IV-dependent transcription, siRNA production and DNA methylation. However, residual RNA-directed DNA methylation observed in one mutant genotype indicates that Pol IV can operate uncoupled from the high siRNA levels typically observed in WT plants. This mutation disrupts a motif uniquely conserved in Pol IV, crippling the enzyme's ability to inhibit retrotransposon mobilization. We propose that the NRPD1 N-terminus motif evolved to regulate Pol IV function in genome surveillance.

| S-EPMC6753494 | biostudies-literature

Arabidopsis thaliana

Project description:Assessment of the Pol IV largest subunit, NRPD1, DeCL domain deletion construct to rescue Pol IV-dependent siRNAs in the nrpd1-3 mutant (sRNA).

| PRJNA378529 | ENA

Transcriptomics of Arabidopsis thaliana nrpd1-3 and nrpd1-3 plant 2L under control or heat stress

Project description:The intent of the experiment was to infer differential heat-induced transncriptional disturbance of genes in a background with novel insertions of ONSEN/Copia78 LTR retrotransposon. For this, we performed Illumina 150 bp pair-end RNA-seq, in RdDM mutant nrpd1-3 and a line with numerous ONSEN neo-insertions (nrpd1-3 plant 2L); under control and heat stress.

2019-03-16 | E-MTAB-5884 | biostudies-arrayexpress

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