Repetitive sequences in parasitic plants
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB34450 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3528104_1.fastq.gz | Fastqsanger.gz | |||
| ERR3528104_2.fastq.gz | Fastqsanger.gz | |||
| ERR3528105_1.fastq.gz | Fastqsanger.gz | |||
| ERR3528105_2.fastq.gz | Fastqsanger.gz | |||
| ERR3528106_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
Project description:Background: Epigenetic processes play an important role in the plant response to adverse environmental conditions. A role for DNA hypomethylation has recently been suggested in the pathogenic interaction between bacteria and plants, yet it remains unclear whether this phenomenon reflects a conserved and general plant immunity response. We therefore investigated the role of DNA methylation in the plant defence against damaging parasitic nematodes. Methods and results: Treatment of roots of rice (monocot plant) and tomato (dicot plant) by a nematode-associated molecular pattern (NAMP) from different parasitic nematodes revealed global DNA hypomethylation using ELISA based quantification, suggesting conservation among plants. Focusing on root-knot induced gall tissue in rice, the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon 5-Azacitidine treatment. Whole genome bisulfite sequencing revealed that hypomethylation was massively present in the CHH context, while absent for CpG or CHG nucleotide contexts. CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point, but rather showed a delayed effect on transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA-directed DNA methylation pathway (RdDM) and DDM1, which are known to be steering DNA methylation in CHH context. Conclusions: We demonstrated that DNA hypomethylation confers enhanced defence in rice towards root-parasitic nematodes and is likely to be part of the basal NAMP-triggered immunity response in plants.
2020-07-07 | GSE130064 | GEO
Project description:Small RNAs recognize, bind, and regulate other complementary cellular RNAs. The introduction of small RNAs to eukaryotic cells frequently results in unintended silencing of related, but not identical, RNAs: a process termed off-target gene silencing. Off-target gene silencing is one of the major concerns during the application of small RNA-based technologies for gene discovery and the treatment of human disease. Off-target gene silencing is commonly thought to be due to inherent biochemical limitations of the RNAi machinery. Here we show that, following the introduction of exogenous sources of dsRNA, the nuclear RNAi pathway, but not its cytoplasmic counterparts, is the primary source of off-target silencing in C. elegans. In addition, we show that during the normal course of growth and development the nuclear RNAi pathway regulates repetitive gene families. Therefore, we speculate that RNAi off-target effects might not be “mistakes” but, rather, an intentional and genetically programmed aspect of small RNA-mediated gene silencing, which might allow small RNAs to silence rapidly evolving parasitic nucleic acids. Finally, reducing off-target effects by manipulating the nuclear RNAi pathway in vivo might improve the efficacy of small RNA-based technologies. (The Zhou X, Xu F, Mao H, Ji J, Meng Y, Feng X, and Shouhong Guang (2014) Nuclear RNAi Contributes to the Silencing of Off-Target Genes and Repetitive Sequences in Caenorhabditis elegans. Genetics 2014 May;197(1):121-32. doi: 10.1534/genetics.113.159780.)
2016-12-14 | GSE92307 | GEO
Project description:Histone H3K9 trimethylation (H3K9me3) plays a pivotal role in the establishment and maintenance of heterochromatin and is essential for facilitating epigenetic inheritance. H3K9me3 is often biasedly deposited and associated with repetitive sequence region, although the underlying mechanism remain poorly understood. In this study, we identify two proteins, SECP-1 and SECP-2, as crucial cofactors for the genome-wide deposition of H3K9me3 in Caenorhabditis elegans. SECP-1 interacts directly with SECP-2 and the primary H3K9me3 methyltransferase, SET-25, forming a protein complex that bridges SECP-2 with SET-25. This complex assembles in the cytoplasm and is transported into the nucleus through SET-25. Once in the nucleus, the complex is recruited to and concentrated at SET-25’s genomic targets in an interdependent manner. The accumulation of this complex correlates with the formation of condensates at repetitive sequences, the perinuclear localization of heterochromatin, and the epigenetic inheritance of small RNA-mediated gene silencing. The introduction of transgenic arrays leads to the redistribution of the SECP-1/SECP-2/SET-25 complex to the transgene locus, a genome-wide decrease in H3K9me3 levels, and an increase in repetitive sequence expression. We propose that repetitive sequences drive the formation of condensates containing H3K9me3 methyltransferase complexes, which in turn causes a biased deposition of H3K9me3 at these genomic regions.
2025-05-28 | GSE297992 | GEO
Project description:Histone H3K9 trimethylation (H3K9me3) plays a pivotal role in the establishment and maintenance of heterochromatin and is essential for facilitating epigenetic inheritance. H3K9me3 is often biasedly deposited and associated with repetitive sequence region, although the underlying mechanism remain poorly understood. In this study, we identify two proteins, SECP-1 and SECP-2, as crucial cofactors for the genome-wide deposition of H3K9me3 in Caenorhabditis elegans. SECP-1 interacts directly with SECP-2 and the primary H3K9me3 methyltransferase, SET-25, forming a protein complex that bridges SECP-2 with SET-25. This complex assembles in the cytoplasm and is transported into the nucleus through SET-25. Once in the nucleus, the complex is recruited to and concentrated at SET-25’s genomic targets in an interdependent manner. The accumulation of this complex correlates with the formation of condensates at repetitive sequences, the perinuclear localization of heterochromatin, and the epigenetic inheritance of small RNA-mediated gene silencing. The introduction of transgenic arrays leads to the redistribution of the SECP-1/SECP-2/SET-25 complex to the transgene locus, a genome-wide decrease in H3K9me3 levels, and an increase in repetitive sequence expression. We propose that repetitive sequences drive the formation of condensates containing H3K9me3 methyltransferase complexes, which in turn causes a biased deposition of H3K9me3 at these genomic regions.
2025-05-28 | GSE297991 | GEO
Project description:Little is known about plant pathogenic response to parasitic plants, although some parasitic plants affect crop production in certain areas. To study this, we chose Glycine max as the model host plant and investigated changes in expression patterns after parasitization by Cuscuta using microarrays.
2014-06-27 | GSE51328 | GEO
Project description:DNA hypomethylation confers enhanced immunity against parasitic nematodes in plants
| PRJNA533778 | ENA
Project description:Replication gaps that persist into mitosis likely represent important threats to genome stability, but experimental identification of these gaps has proved challenging. We have developed a technique that allows us to explore the dynamics by which genome replication is completed prior to mitosis. Using this approach, we demonstrate that excessive allocation of replication resources to origins within repetitive regions, induced by SIR2 deletion, leads to persistent replication gaps and genome instability. Conversely, the weakening of replication origins in repetitive regions suppresses these gaps. Given known age- and cancer-associated changes in chromatin accessibility at repetitive sequences, we suggest that replication gaps resulting from misallocation of replication resources underlie age- and disease-associated genome instability.
2017-02-13 | GSE90151 | GEO
Project description:Parasitism is a successful life strategy that has evolved independently in several families of Higher Plants. In parasitic plants, nutrients and water are obtained from their hosts through specifically adapted haustoria. The genera Cuscuta and Orobanche represent examples for the two profoundly different groups of parasites, one parasitizing host shoots and the other infecting host roots. In this study, we sequenced and described the overall repertoire of small RNAs (sRNome) from Cuscuta campestris and compared it to an exploratory sRNome from Orobanche aegyptiaca. Because they regulate the genomic information by mechanisms like RNA interference, these sRNomes add important bricks to our understanding of the success of the parasitic lifestyle. We could show that Cuscuta campestris contains a number of novel microRNAs (miRNAs) in addition to a conspicuous retention of miRNAs that are typically lacking in other Solanales, while several typically conserved miRNAs seem to have become obsolete in the parasite. One new miRNA appears to be derived from a horizontal gene transfer event, a process never reported in plants for the acquisition of new miRNA sequences. The exploratory miRNome (exploratory due to the absence of a full genomic sequence for reference) from the root parasitic Orobanche aegyptiaca also revealed a loss of a number of miRNAs compared to established miRNomes of photosynthetic species from the same order. In summary, our study shows for both parasites partly similar evolutionary signatures in the RNA silencing machinery. Our data bear proof for the dynamism of this regulatory mechanism in parasitic plants.
2022-07-22 | GSE181576 | GEO
Project description:A long-distance inhibitory system regulates haustoria numbers in parasitic plants
| PRJNA1066823 | ENA
Project description:Little is known about plant pathogenic response to parasitic plants, although some parasitic plants affect crop production in certain areas. To study this, we chose Glycine max as the model host plant and investigated changes in expression patterns after parasitization by Cuscuta using microarrays. Transcriptional change of Glycine max stem with and without Cuscuta at 2 different stages were compared
2014-06-27 | E-GEOD-51328 | biostudies-arrayexpress