Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding [Arabidopsis]
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE99396 | GEO | 2017/06/26
SECONDARY ACCESSION(S): PRJNA388384
REPOSITORIES: GEO
Similar Datasets
Project description:BackgroundRetrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanisms have evolved to repress retrotransposon mobility. Even though retrotransposons fully depend on transcriptional activity of the host RNA polymerase II (Pol II) for their mobility, it was so far unclear whether Pol II is directly involved in repressing their activity.ResultsHere we show that plants defective in Pol II activity lose DNA methylation at repeat sequences and produce more extrachromosomal retrotransposon DNA upon stress in Arabidopsis and rice. We demonstrate that combined inhibition of both DNA methylation and Pol II activity leads to a strong stress-dependent mobilization of the heat responsive ONSEN retrotransposon in Arabidopsis seedlings. The progenies of these treated plants contain up to 75 new ONSEN insertions in their genome which are stably inherited over three generations of selfing. Repeated application of heat stress in progeny plants containing increased numbers of ONSEN copies does not result in increased activation of this transposon compared to control lines. Progenies with additional ONSEN copies show a broad panel of environment-dependent phenotypic diversity.ConclusionsWe demonstrate that Pol II acts at the root of transposon silencing. This is important because it suggests that Pol II can regulate the speed of plant evolution by fine-tuning the amplitude of transposon mobility. Our findings show that it is now possible to study induced transposon bursts in plants and unlock their use to induce epigenetic and genetic diversity for crop breeding.
| S-EPMC5501947 | biostudies-literature
Project description:We report the application of a high-throughput sequencing approach that is specifically designed to analyze the active mobilome of eukaryotes after simultaneous inhibition of RNA polymerase II and/or DNA methylation in O. sativa japonica. We found that the simultaneous inhibition of Pol II and DNA-methylation activated the evolutionary young Houba-Retrotransposon in O. sativa suggesting a crucial role of Pol II in regulating retrotransposition in plants.
2017-06-26 | GSE90484 | GEO
Project description:A new paradigm has emerged proposing that the crosstalk between nuclear transcription and cytoplasmic mRNA stability keeps robust mRNA levels in cells under steady-state conditions. A key piece in this crosstalk is the highly conserved 5'-3' RNA exonuclease Xrn1, which degrades most cytoplasmic mRNAs but also associates with nuclear chromatin to activate transcription by not well-understood mechanisms. Here, we investigated the role of Xrn1 in the transcriptional response of Saccharomyces cerevisiae cells to osmotic stress. We show that a lack of Xrn1 results in much lower transcriptional induction of the upregulated genes but in similar high levels of their transcripts because of parallel mRNA stabilization. Unexpectedly, lower transcription in xrn1 occurs with a higher accumulation of RNA polymerase II (RNAPII) at stress-inducible genes, suggesting that this polymerase remains inactive backtracked. Xrn1 seems to be directly implicated in the formation of a competent elongation complex because Xrn1 is recruited to the osmotic stress-upregulated genes in parallel with the RNAPII complex, and both are dependent on the mitogen-activated protein kinase Hog1. Our findings extend the role of Xrn1 in preventing the accumulation of inactive RNAPII at highly induced genes to other situations of rapid and strong transcriptional upregulation.
| S-EPMC8489925 | biostudies-literature
Project description:RNA polymerase (Pol) II promoter-proximal pausing is a common regulatory step to initiate RNA synthesis and it is coordinated by a ribonucleoprotein complex scaffolded containing the noncoding RNA Rn7sk. However, how this transcriptional mechanism modulates gene expression programs in adult tissues is largely unknown. Here, we released paused RNA Pol II by depleting Rn7sk during mouse and human epidermal stem cell differentiation. Unexpectedly, the forced release of transcription robustly repressed RNA levels including numerous cell cycle regulators leading to cell cycle exit and differentiation. The repression of genes occurred in the absence of chromatin remodelling at promoters and enhancers. Instead, it was caused by splicing defects and co-transcriptional RNA degradation. However, rather than acting globally, Rn7sk modulated transcription gene-specifically. Genes that required Rn7sk for efficient transcription contained highly accessible promoters, lower guanosine and cytosine (GC) content, shorter introns, and weaker 3’ splice sites. In the absence of a tightly controlled Pol II pause release complex, these intrinsic gene properties cumulated in impaired splicing leading to RNA decay. Thus, 7SK-regulated transcriptional pausing is an essential step to coordinate transcription with splicing to permit productive transcription of a distinct set of genes.
2021-08-12 | GSE132782 | GEO
Project description:The switch from cellular proliferation to differentiation occurs to a large extend through specific programs of gene expression. In fission yeast, the high-mobility-group transcription factor Ste11 is the master regulator of sexual differentiation. ste11 is induced by environmental conditions, mostly nitrogen starvation, leading to mating and meiosis 1. We have used ChIP-chip and gene expression profiling to show that CDK-dependent phosphorylation of serine 2 in the C-terminal domain (CTD) of the largest subunit of the RNA polymerase II (PolII) holoenzyme plays a critical role in the induction of ste11 transcription during sexual differentiation while it has a minor impact on gene expression during vegetative growth. Moreover, we demonstrate that both the recruitment of the CTD serine 2 kinase and the phosphorylation event initiate at the promoter region of ste11 in contrast to the classical case where serine 2 phosphorylation occurs across the coding region 2. In the absence of CTD serine 2 phosphorylation, both PolII occupancy at the ste11 locus, and ste11 expression are impaired. This results in sterility that is rescued when ste11 is expressed from the canonical adh promoter. We conclude that a modification of the RNA polymerase II holoenzyme plays a specific and pivotal role in the sexual differentiation. For the ChIP-chip experiments, 3-4 biological replicates were performed for each tagged protein of interest. For the expression experiments, two biological samples were hybridized for each mutant strain (replicates 1 and 2), with two dye-swap technical replicates per sample (replicates 3 and 4).
2010-01-01 | E-GEOD-16498 | biostudies-arrayexpress
Project description:In eukaryotes, transcription of protein-encoding genes is strongly regulated by posttranslational modifications of histones that affect the accessibility of the DNA by RNA polymerase II (RNAPII). The Elongator complex was originally identified in yeast as a histone acetyltransferase (HAT) complex that activates RNAPII-mediated transcription. In Arabidopsis thaliana, the Elongator mutants elo1, elo2, and elo3 with decreased leaf and primary root growth due to reduced cell proliferation identified homologs of components of the yeast Elongator complex, Elp4, Elp1, and Elp3, respectively. Here we show that the Elongator complex was purified from plant cell cultures as a six-component complex. The role of plant Elongator in transcription elongation was supported by colocalization of the HAT enzyme, ELO3, with euchromatin and the phosphorylated form of RNAPII, and reduced histone H3 lysine 14 acetylation at the coding region of the SHORT HYPOCOTYL 2 auxin repressor and the LAX2 auxin influx carrier gene with reduced expression levels in the elo3 mutant. Additional auxin-related genes were down-regulated in the transcriptome of elo mutants but not targeted by the Elongator HAT activity showing specificity in target gene selection. Biological relevance was apparent by auxin-related phenotypes and marker gene analysis. Ethylene and jasmonic acid signaling and abiotic stress responses were up-regulated in the elo transcriptome and might contribute to the pleiotropic elo phenotype. Thus, although the structure of Elongator and its substrate are conserved, target gene selection has diverged, showing that auxin signaling and influx are under chromatin control.
| S-EPMC2824411 | biostudies-literature
Project description:BackgroundThe centromeric and pericentromeric regions of plant chromosomes are colonized by Ty3/gypsy retrotransposons, which, on the basis of their reverse transcriptase sequences, form the chromovirus CRM clade. Despite their potential importance for centromere evolution and function, they have remained poorly characterized. In this work, we aimed to carry out a comprehensive survey of CRM clade elements with an emphasis on their diversity, structure, chromosomal distribution and transcriptional activity.ResultsWe have surveyed a set of 190 CRM elements belonging to 81 different retrotransposon families, derived from 33 host species and falling into 12 plant families. The sequences at the C-terminus of their integrases were unexpectedly heterogeneous, despite the understanding that they are responsible for targeting to the centromere. This variation allowed the division of the CRM clade into the three groups A, B and C, and the members of each differed considerably with respect to their chromosomal distribution. The differences in chromosomal distribution coincided with variation in the integrase C-terminus sequences possessing a putative targeting domain (PTD). A majority of the group A elements possess the CR motif and are concentrated in the centromeric region, while members of group C have the type II chromodomain and are dispersed throughout the genome. Although representatives of the group B lack a PTD of any type, they appeared to be localized preferentially in the centromeres of tested species. All tested elements were found to be transcriptionally active.ConclusionsComprehensive analysis of the CRM clade elements showed that genuinely centromeric retrotransposons represent only a fraction of the CRM clade (group A). These centromeric retrotransposons represent an active component of centromeres of a wide range of angiosperm species, implying that they play an important role in plant centromere evolution. In addition, their transcriptional activity is consistent with the notion that the transcription of centromeric retrotransposons has a role in normal centromere function.
| S-EPMC3059260 | biostudies-literature
Project description:The C-terminal domain (CTD) of RNA polymerase II regulates transcription through spatially and temporally coordinated events. Previous work had established that the CTD binds DNA but the significance of this interaction has not been determined. The present work shows that the CTD binds DNA in its unphosphorylated form, the form in which it is present in the pre-initiation complex. The CTD/DNA complex is recognized by and is phosphorylated by Cdk7 but not by Cdk9. Model-building studies indicate the structural mechanism underlying such specificity involves interaction of Cdk7 with DNA in the context of the CTD/DNA complex. The model has been tested by mutagenesis experiments. CTD dissociates from DNA following phosphorylation by Cdk7, allowing transcription initiation. The CTD then becomes accessible for further phosphorylation by Cdk9 that drives the transition to transcription elongation.
| S-EPMC2651791 | biostudies-literature
Project description:Perception of microbe-associated molecular patterns (MAMPs) elicits host transcriptional reprogramming as part of the immune response. Although pathogen perception is well studied, the signaling networks orchestrating immune gene expression remain less clear. In a genetic screen for components involved in the early immune gene transcription reprogramming, we identified Arabidopsis RNA polymerase II C-terminal domain (CTD) phosphatase-like 3 (CPL3) as a negative regulator of immune gene expression. MAMP perception induced rapid and transient cyclin-dependent kinase C (CDKC)-mediated phosphorylation of Arabidopsis CTD. The CDKCs, which are in turn phosphorylated and activated by a canonical MAP kinase (MAPK) cascade, represent a point of signaling convergence downstream of multiple immune receptors. CPL3 directly dephosphorylated CTD to counteract MAPK-mediated CDKC regulation. Thus, modulation of the phosphorylation dynamics of eukaryotic RNA polymerase II transcription machinery by MAPKs, CTD kinases, and phosphatases constitutes an essential mechanism for rapid orchestration of host immune gene expression and defense upon pathogen attacks.
| S-EPMC4268009 | biostudies-literature
Project description:Fruit firmness is crucial for storability, making cultivating varieties with higher firmness a key target in tomato breeding. In recent years, tomato varieties primarily rely on hybridizing ripening mutants to produce F1 hybrids to enhance firmness. However, the undesirable traits introduced by these mutants often lead to a decline in the quality of the varieties. CRISPR/Cas9 has emerged as a crucial tool in accelerating plant breeding and improving specific target traits as technology iterates. In this study, we used a CRISPR/Cas9 system to simultaneously knock out two genes, FIS1 and PL, which negatively regulate firmness in tomato. We generated single and double gene knockout mutants utilizing the tomato genetic transformation system. The fruit firmness of all knockout mutants exhibited a significant enhancement, with the most pronounced improvement observed in the double mutant. Furthermore, we assessed other quality-related traits of the mutants; our results indicated that the fruit quality characteristics of the gene-edited lines remained statistically comparable to those of the wild type. This approach enabled us to create transgenic-free mutants with diverse genotypes across fewer generations, facilitating rapid improvements in tomato firmness. This study offers significant insights into molecular design breeding strategies for tomato.
| S-EPMC11763693 | biostudies-literature