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RNA Polymerase IV sensitises the chromatin via histone modifications modulating protein coding genes [RNA-Seq]

ABSTRACT: Knock down of RNA polymerase IV in rice caused pleiotropic reproductive defects. We investigated the molecular effects of loss of pol IV in different rice tissues by profiling sRNA and mRNA transcriptomes, DNA methylomes, histone modifications and degradome sequencing. These analyses revealed the multifaceted roles of RNA polymerase IV in bringing about regulation of protein coding genes.

ORGANISM(S): Oryza sativa

PROVIDER: GSE180335 | GEO | 2023/02/28

REPOSITORIES: GEO

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RNA Polymerase IV sensitizes the chromatin via histone modifications modulating protein coding genes [Degradome]

Project description:Knock down of RNA polymerase IV in rice caused pleiotropic reproductive defects. We investigated the molecular effects of loss of pol IV in different rice tissues by profiling sRNA and mRNA transcriptomes, DNA methylomes, histone modifications and degradome sequencing. These analyses revealed the multifaceted roles of RNA polymerase IV in bringing about regulation of protein coding genes.

2023-02-28 | GSE180312 | GEO

RNA Polymerase IV sensitises the chromatin via histone modifications modulating protein coding genes [MethylC-Seq]

2023-02-28 | GSE180333 | GEO

RNA Polymerase IV sensitizes the chromatin via histone modifications modulating protein coding genes [ChIP-Seq]

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RNA Polymerase IV sensitises the chromatin via histone modifications modulating protein coding genes [sRNA-Seq]

2023-02-28 | GSE180456 | GEO

Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5M-bM-^@M-^Y rapid amplification of cDNA ends (RLM 5M-bM-^@M-^Y-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice. The degradome sequence of Young inflorescences from Oryza sativa L. ssp. indica (93-11) was sequenced

2010-01-01 | E-GEOD-19050 | biostudies-arrayexpress

Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5’ rapid amplification of cDNA ends (RLM 5’-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice.

2010-01-01 | GSE19050 | GEO

Polymerase IV Plays a Crucial Role in Pollen Development in Capsella

Project description:In Arabidopsis thaliana, DNA-dependent RNA polymerase IV (Pol IV) is required for the formation of transposable element (TE)-derived small RNA (sRNA) transcripts. These transcripts are processed by DICER-LIKE3 into 24-nt small interfering RNAs (siRNAs) that guide RNA-directed DNA methylation. In the pollen grain, Pol IV is also required for the accumulation of 21/22-nt epigenetically activated siRNAs (easiRNAs), which likely silence TEs via post-transcriptional mechanisms. Despite this proposed role of Pol IV, its loss of function in Arabidopsis does not cause a discernable pollen defect. Here, we show that the knockout of NRPD1, encoding the largest subunit of Pol IV in the Brassicaceae species Capsella rubella, caused post-meiotic arrest of pollen development at the microspore stage. As in Arabidopsis, all TE-derived siRNAs were 2 depleted in Capsella nrpd1 microspores. In the wild-type background, the same TEs produced 21/22-nt and 24-nt siRNAs; these processes required Pol IV activity. Arrest of Capsella nrpd1 microspores was accompanied by the deregulation of genes targeted by Pol IV-dependent siRNAs. TEs were much closer to genes in Capsella rubella compared to Arabidopsis thaliana, perhaps explaining the essential role of Pol IV in pollen development in Capsella. Our discovery that Pol IV is functionally required in Capsella microspores emphasizes the relevance of investigating different plant models.

2020-01-23 | GSE136847 | GEO

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

Pol IV-RDR2 protein interaction study

Project description:Protein-protein interaction between DNA dependent RNA polymerase IV and RNA dependent RNA polymerase2. The coupled activities of the physically associated polymerases lead to the biogenesis of dsRNAs that serve as precursors of 24nt siRNAs.

2020-09-14 | PXD020170 | Pride

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

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 | GSE95824 | GEO

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