Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA394759 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5833580_1.fastq.gz | Fastqsanger.gz | |||
| SRR5833580_2.fastq.gz | Fastqsanger.gz | |||
| SRR5833590_1.fastq.gz | Fastqsanger.gz | |||
| SRR5833590_2.fastq.gz | Fastqsanger.gz | |||
| SRR5833581_1.fastq.gz | Fastqsanger.gz |
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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.
2012-11-22 | GSE34207 | GEO
Project description:Eukaryotes must balance the need for gene transcription by RNA polymerase II (Pol II) against the danger of mutations caused by transposable element (TE) proliferation. In plants, these gene expression and TE silencing activities are divided between different RNA polymerases. Specifically, RNA polymerase IV (Pol IV), which evolved from Pol II, transcribes TEs to generate small interfering RNAs (siRNAs) that guide DNA methylation and block TE transcription by Pol II. While the Pol IV complex is recruited to TEs via SNF2-like CLASSY (CLSY) proteins, how Pol IV partners with the CLSYs remains unknown. Here we identified a conserved CYC-YPMF motif that is specific to Pol IV and is positioned on the complex exterior. Furthermore, we found that this motif is essential for the co-purification of all four CLSYs with Pol IV, but that only one CLSY is present in any given Pol IV complex. These findings support a “one CLSY per Pol IV” model where the CYC-YPMF motif acts as a CLSY-docking site. Indeed, mutations in and around this motif phenocopy pol iv null and clsy quadruple mutants. Together, these findings provide structural and functional insights into a critical protein feature that distinguishes Pol IV from other RNA polymerases, allowing it to promote genome stability by targeting TEs for silencing.
2024-08-22 | GSE242191 | GEO
Project description:Most human genes are loaded with promoter proximally paused RNA polymerase II (RNAP II) molecules that are poised for release into productive elongation by P-TEFb. Gdown1, a protein that renders RNAP II responsive to mediator, is involved in RNAP II elongation control. During in vitro transcription assays Gdown1 specifically blocked elongation stimulation by TFIIF, inhibited the termination activity of TTF2, and influenced pausing factors NELF and DSIF, but did not affect the function of TFIIS or the mRNA capping enzyme. Without P-TEFb, Gdown1 led to the production of stably paused polymerases in the presence of nuclear extract. ChIP-Seq data demonstrated that Gdown1 mapped over essentially all poised polymerases across the human genome. Gdown1 increases the stability of poised polymerases while maintaining their responsiveness to P-TEFb, and mediator overcomes a Gdown1-mediated block of initiation by allowing TFIIF function. 7 ChIP-Seq data for Pol II and Gdown1 in human HeLa cell. See associated publication.
2012-01-13 | E-GEOD-32442 | biostudies-arrayexpress
Project description:Termination of protein-coding gene transcription by RNA polymerase II (Pol II) depends on endonucleolytic cleavage at the poly(A) site and the activity of a 5’->3’ “torpedo” exoribonuclease. Other Pol II transcripts also undergo endonucleolytic cleavage suggesting common themes for its termination. Nevertheless, many RNA polymerases employ intrinsic/allosteric termination that directly defines transcript 3’ ends. We have analysed termination of snRNA transcription in humans, which utilises the endoribonucleolytic integrator complex. Integrator is involved, but termination continues after its depletion. This implicates additional mechanisms and shows that endo- and 5’->3’ exonuclease activities are not necessarily a basis for all Pol II termination. Although the alternative process acts as a failsafe in the absence of integrator it contributes significantly to snRNA termination in the natural situation. Long-read sequencing reveals its products to have stochastic 3’ ends that are terminated before integrator cleavage, ruling out 5’->3’ exonuclease contribution(s) and supporting an allosteric/intrinsic mechanism. Termination of some snRNA transcription occurs at T-runs further indicating common principles between this mechanism and those used by other RNA polymerases.
2020-11-04 | GSE150238 | GEO
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. We performed a methylation-sensitive amplification polymorphism analysis to search for targets of RNA-directed DNA methylation in Arabidopsis thaliana and identified several members of a gene family encoding cysteine-rich peptides (CRPs). We also examined small RNA abundance at individual CRP genes in the wild type plant, nrpd1, and rdr2 mutant plants.
2012-11-22 | E-GEOD-34207 | biostudies-arrayexpress
Project description:RNA polymerases IV and V (Pol IV and Pol V) are plant-specific polymerases required for the generation of noncoding RNAs in RNA-directed DNA methylation (RdDM) and transcriptional gene silencing. Their subunit compositions largely resemble that of Pol II. However, the mechanism and accessory factors involved in their assembly remain largely unknown. In this study, we performed a forward genetic screen and identified novel mutant alleles of MINIYO (IYO), QUATRE-QUART 2 (QQT2) and NUCLEAR RNA POLYMERASE B/D/E 11 (NRPB/D/E11) that are defective in RdDM. We found that Pol IV-dependent small interfering RNAs (siRNAs) and Pol V-dependent transcripts were greatly reduced in the mutants. NRPE1, the largest subunit of Pol V, dissociated from other Pol V subunits in the iyo and qqt2 mutants, suggesting the involvement of IYO and QQT2 in Pol V assembly. Furthermore, we found that IYO and QQT2 were mutually dependent for their binding to the NRPE3 subassembly to facilitate the assembly of Pol V holoenzyme. Our findings reveal IYO and QQT2 as cofactors for Pol V assembly and provide mechanistic insights into how RNA polymerases are assembled in Arabidopsis.
2018-04-09 | GSE103326 | GEO
Project description:Intronic transposon elements (TEs) comprise a large proportion in eukaryotic genomes, but how they regulate the host genes remains to be explored. Our forward genetic screen disclosed the plant specific RNA polymerases IV and V in suppressing intronic TE-mediated cryptic transcription initiation of a chimeric transcripts at FLC (FLCTE). Initiation of FLCTE transcription is blocked by the locally formed intronic heterochromatin, and RNA Pol V direct associates and establishes intronic heterochromatin, thus inhibits the entry of RNA Pol II Ser5p and the occupancy of H3K4 methylation for promoting initiation. Genome-wide Pol II Ser5p native elongation transcription sequencing revealed that this is a common mechanism among intronic heterochromatin-containing genes. This study sheds light on deeply understanding the function of intronic heterochromatin on host genes expression in eukaryotic genome.
2019-11-01 | GSE125096 | GEO
Project description:In Arabidopsis thaliana two nuclear 5'-3' exonucleases, XRN2 & 3, are involved in the degradation and processing of several classes of nuclear RNAs and in transcription termination of RNA polymerase II. The role of XRN3 in Pol II transcription termination is investigated by combining two different types of RNA-seq data for Col-0 background WT and xrn3-8 mutant A. thaliana seedlings. The data for the experiment comprises single molecule Direct RNA Sequencing of unamplified RNA (3x WT, 4x xrn3-8 mutant) and high-depth Illumina strand-specific short read sequencing of PCR amplified ribosomal-RNA depleted RNA (Illumina TruSeq stranded ribozero Plant kit, 3x WT, 3x xrm3-8 mutant). In the xrn3 mutant, these data reveal a widespread accumulation of non-coding intergenic transcripts (xrn3-associated transcripts - XATs) generated by Pol II read-through transcription that are usually polyadenylated and lack the 5' cap structure. This data highlights the important role of exoribonucleases in the torpedo mechanism of Pol II transcription termination and show that a global disturbance in this process significantly impacts both gene expression and transcriptome integrity.
2019-09-02 | E-MTAB-5137 | biostudies-arrayexpress
Project description:Transcription termination determines the ends of transcriptional units and thereby ensures integrity of gene regulation. Here we perform genome-wide investigation of RNA polymerase II (Pol II) transcription termination in Caenorhabditis elegans and observe two distinct modes of termination. Whereas a subset of genes requires the exoribonuclease XRN2, a known termination factor, termination of other genes appears independent of, and refractory to, XRN2. Unexpectedly, promoters instruct the choice of termination mode, but XRN2-independent termination additionally requires a compatible region downstream of the 3’ end cleavage site. Hence, different termination mechanisms may affect different configurations of Pol II complexes dictated by promoters.
2018-02-05 | GSE97775 | GEO
Project description:Control of transcription speed, which influences many co-transcriptional processes, is poorly understood. We report that PNUTS-PP1 phosphatase is a negative regulator of RNA pol II elongation rate. The PNUTS W401A mutation, which disrupts PP1 binding, causes genome-wide acceleration of transcription associated with hyper-phosphorylation of the Spt5 elongation factor. Immediately downstream of poly(A) sites, pol II decelerates from >2kb/min to <1 kb/min, which correlates with Spt5 dephosphorylation. Pol II deceleration and Spt5 dephosphorylation require poly(A) site recognition and the PNUTS-PP1 complex, which is in turn necessary for transcription termination. These results lead to a new model for termination, the “sitting duck torpedo” mechanism, where poly(A) site-dependent deceleration caused by PNUTS-PP1 and Spt5 dephosphorylation is required to convert pol II into a viable target for the Xrn2 terminator exonuclease. Spt5 and its bacterial homologue NusG therefore have related functions controlling kinetic competition between RNA polymerases and the termination factors that pursue them.
2019-10-30 | GSE134198 | GEO