Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA105607 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:rs06-06_mirna - flagellin experiment in dcl2-dcl3-dcl4 mutant background - Time course : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? miRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants? siRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants? - What are the genes (including primary miRNA transcripts) that are differentially regulated upon flg22 treatment? 14-day old seedlings (Col-0 and dcl2-dcl3-dcl4) treated with flg22 (flagellin- derived peptide). Keywords: treated vs untreated comparison
2008-06-02 | GSE10354 | GEO
Project description:rs06-06_mirna - flagellin experiment in dcl2-dcl3-dcl4 mutant background - Time course : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? miRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants? siRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants? - What are the genes (including primary miRNA transcripts) that are differentially regulated upon flg22 treatment? 14-day old seedlings (Col-0 and dcl2-dcl3-dcl4) treated with flg22 (flagellin- derived peptide). Keywords: treated vs untreated comparison 8 dye-swap - CATMA arrays
2008-06-01 | E-GEOD-10354 | biostudies-arrayexpress
Project description:rs06-06-mirna_camv_treatment - camv treatment - Which genes (including miRNA genes) are differentially regulated by CaMV? Requirement of 21nt, 22nt, 24nt virus-derived siRNAs in this differential gene regulation? - 4/5 weeks old seedlings (Col-0, dcl2/dcl3, dcl2/dcl4, dcl3/dcl4, dcl2/dcl3/dcl4) infected with CaMV and harvested 21 days post infection.
2012-03-21 | GSE36457 | GEO
Project description:DICER-like proteins produce small RNAs that silence genes involved in development and defenses against viruses and pathogens. Which DCLs participate in plant-herbivore interactions remains unstudied. We identified four distinct DCL genes and stably silenced their expression by RNAi in Nicotiana attenuata, a model system for the study of plant-herbivore interactions. Silencing DCL1 expression was lethal to the plants. Manduca sexta larvae performed significantly better on ir-dcl3and ir-dcl4 plants, but not on ir-dcl2 plants compared to wild type plants. Phytohormones, defense metabolites and microarray analyses revealed that when DCL3 and DCL4 were silenced separately, herbivore resistance traits were regulated in distinctly different ways. Crossing of the lines revealed complex interactions in the patterns of regulation. Single ir-dcl4 and double ir-dcl2/ ir-dcl3 plants were impaired in JA accumulation, while JA-Ile was increased in ir-dcl3 plants. Ir-dcl3 and ir-dcl4 plants were impaired in nicotine accumulation; silencing DCL2 in combination with either DCL3 or DCL4 restored nicotine levels to those of WT. Trypsin proteinase inhibitor activity and transcripts were only silenced in ir-dcl3 plants. We conclude that DCL2/3/4 interact in a complex manner to regulate anti-herbivore defenses and that these interactions significantly complicate the already challenging task of understanding smRNA function in the regulation of biotic interactions.
2013-12-24 | GSE30124 | GEO
Project description:rs06-06-mirna_camv_treatment - camv treatment - Which genes (including miRNA genes) are differentially regulated by CaMV? Requirement of 21nt, 22nt, 24nt virus-derived siRNAs in this differential gene regulation? - 4/5 weeks old seedlings (Col-0, dcl2/dcl3, dcl2/dcl4, dcl3/dcl4, dcl2/dcl3/dcl4) infected with CaMV and harvested 21 days post infection. 7 dye-swap - gene knock out,normal vs disease comparison
2012-03-21 | E-GEOD-36457 | biostudies-arrayexpress
Project description:DICER-like proteins produce small RNAs that silence genes involved in development and defenses against viruses and pathogens. Which DCLs participate in plant-herbivore interactions remains unstudied. We identified four distinct DCL genes and stably silenced their expression by RNAi in Nicotiana attenuata, a model system for the study of plant-herbivore interactions. Silencing DCL1 expression was lethal to the plants. Manduca sexta larvae performed significantly better on ir-dcl3and ir-dcl4 plants, but not on ir-dcl2 plants compared to wild type plants. Phytohormones, defense metabolites and microarray analyses revealed that when DCL3 and DCL4 were silenced separately, herbivore resistance traits were regulated in distinctly different ways. Crossing of the lines revealed complex interactions in the patterns of regulation. Single ir-dcl4 and double ir-dcl2/ ir-dcl3 plants were impaired in JA accumulation, while JA-Ile was increased in ir-dcl3 plants. Ir-dcl3 and ir-dcl4 plants were impaired in nicotine accumulation; silencing DCL2 in combination with either DCL3 or DCL4 restored nicotine levels to those of WT. Trypsin proteinase inhibitor activity and transcripts were only silenced in ir-dcl3 plants. We conclude that DCL2/3/4 interact in a complex manner to regulate anti-herbivore defenses and that these interactions significantly complicate the already challenging task of understanding smRNA function in the regulation of biotic interactions. Gene expression in leaves of Nicotiana attenuata wild type, irDCL3 and irDCL4 plants was measured at 1 hour after elicitation with oral secretions of Manduca sexta larvae. Three independent experiments were performed with wild type plants and three independent experiments were performed with irDCL3 and irDCL4 plants. A total of 811 genes were identified as differentially regulated in irDCL3 and irDCL4 compared to wild type plants.
2013-12-24 | E-GEOD-30124 | biostudies-arrayexpress
Project description:Experiment 1<br> Gene profiling upon biotic stress treatment<br> Biological question : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment?<br> Experiment description : 14-day old seedlings (Col-0 and fls2 KO) treated with 10uM of flg22 (flagellin- derived peptide) over a one hour timecourse.<br> <br> Experiment 2<br> Gene profiling in microRNA mutants<br> Biological question : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants?<br> Experiment description : Ler, dcl1-9, hen1-1 and hasty were grown for 12-day on MS solid medium ,seedlings were then transferred in MS liquid medium and harvested 2 days after.<br> <br> Experiment 3<br> Gene profiling in siRNA mutants<br> Biological question : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants?<br> Experiment description : Col-0, dcl2-1, dcl3-1 and rdr2-1 were grown for 12-day on MS solid medium ,seedlings were then transferred in MS liquid medium and harvested 2 days after.<br> <br> Experiment 4<br> Gene profiling in Agrobacterium-induced tumors and auxin-induced calli.<br> Biological question : What are the genes (including miRNA precursors) that are differentially regulated in an Agrobacterium-induced tumors compared to auxin-induced calli?<br> Experiment description : Col-0 plants were infected with wt Agrobacterium tumefaciens (strain A208) by stabbing the emerging stems. 18 days later, growing tumors were harvested as were the non-infected part of the stabbed-stem.In parallel, Col-0 seeds were germinated on Callus Induction Media (CIM) and 18 days later, calli were harvested.<br> <br> Experiment 5<br> Gene profiling in tasiRNA mutants<br> Biological question : What are the genes (including miRNA precursors) that are differentially regulated in a set of tasiRNA mutants?<br> Experiment description : Col-0, dcl4-1, rdr6-1 were grown for 12-day on MS solid medium ,seedlings were then transferred in MS liquid medium and harvested 2 days after.<br> <br> Experiment 6<br> Gene profiling upon biotic stress treatment<br> Biological question : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment?<br> Experiment description : 14-day old seedlings (Col-0 and fls2 KO) treated with 10uM of flg22 (flagellin- derived peptide) over a one hour timecourse.<br> <br> <br>
2006-12-20 | E-MEXP-517 | biostudies-arrayexpress
Project description:Small RNAs play essential regulatory roles in genome stability, development and stress responses in most eukaryotes. Plants encode DICER-LIKE (DCL) RNaseIII enzymes, including DCL1, which produces miRNAs, and DCL2, DCL3 and DCL4, which produce diverse size classes of siRNA. Plants also encode RNASE THREE-LIKE (RTL) enzymes that lack DCL-specific domains and whose function is largely unknown. Small RNA sequencing in plants over-expressing RTL1 or RTL2 or lacking RTL2 revealed that RTL1 over-expression inhibits the accumulation of all types of small RNAs produced by DCL2, DCL3 and DCL4, indicating that RTL1 is a general suppressor of plant siRNA pathways. By contrast, RTL2 plays minor, if any, role in the small RNA repertoire. In vivo and in vitro assays revealed that RTL1 prevents siRNA production by degrading dsRNA before they are processed by DCL2, DCL3 and DCL4. The substrate of RTL1 cleavage is likely long perfect (or near-perfect) dsRNA, consistent with the RTL1-insensitivity of miRNAs, which derive from short imperfect dsRNA. RTL1 is naturally expressed only weakly in roots, but virus infection strongly induces its expression in leaves, suggesting that RTL1 induction is a general strategy used by viruses to counteract the siRNA-based plant antiviral defense. Accordingly, transgenic plants over-expressing RTL1 are more sensitive to TYMV infection than wild-type plants, likely because RTL1 prevents the production of antiviral siRNAs. However, TCV, TVCV and CMV, which encode stronger suppressors of RNA silencing (VSR) than TYMV, are insensitive to RTL1 over-expression. Indeed, TCV VSR inhibits RTL1 activity, suggesting that inducing RTL1 expression and dampening RTL1 activity is a dual strategy used by viruses to establish a successful infection. These results reveal another level of complexity in the evolutionary battle between viruses and plant defenses. Flower sRNA profiles in diverse conditions involving RTL1 and RTL2
2013-09-10 | E-GEOD-49866 | biostudies-arrayexpress
Project description:To determine the extent to which the major small RNA pathways functions across the Arabidopsis thaliana genome, small RNA populations from several tissues of wild-type (wt) and mutant plants were amplified by RT-PCR and sequenced using high-throughput 454 sequencing technology. Keywords: small RNAs, high-throughput sequencing Amplicons were prepared by 5' and 3' adaptor ligation and RT-PCR using small RNA fractions from inflorescence tissue (containing stage 1-12 flowers) of wt Col-0 plants, mutants with defects in each DCL gene (dcl1-7, dcl2-1, dcl3-1, dcl4-2), and mutants with defects in each RDR gene for which a function has been established (rdr1-1, rdr2-1, rdr6-15). Amplicons from whole seedlings (3 day post-germinations) were prepared from Col-0 and rdr6-15 plants. Small RNA preparations from leaf samples of Col-O that were either uninoculated or inoculated by Pseudomonas syringae pv tomato (DC3000hrcC) for 1 hr and 3 hr were also sequenced.
2007-02-01 | E-GEOD-6682 | biostudies-arrayexpress
Project description:Small RNAs play essential regulatory roles in genome stability, development and stress responses in most eukaryotes. Plants encode DICER-LIKE (DCL) RNaseIII enzymes, including DCL1, which produces miRNAs, and DCL2, DCL3 and DCL4, which produce diverse size classes of siRNA. Plants also encode RNASE THREE-LIKE (RTL) enzymes that lack DCL-specific domains and whose function is largely unknown. Small RNA sequencing in plants over-expressing RTL1 or RTL2 or lacking RTL2 revealed that RTL1 over-expression inhibits the accumulation of all types of small RNAs produced by DCL2, DCL3 and DCL4, indicating that RTL1 is a general suppressor of plant siRNA pathways. By contrast, RTL2 plays minor, if any, role in the small RNA repertoire. In vivo and in vitro assays revealed that RTL1 prevents siRNA production by degrading dsRNA before they are processed by DCL2, DCL3 and DCL4. The substrate of RTL1 cleavage is likely long perfect (or near-perfect) dsRNA, consistent with the RTL1-insensitivity of miRNAs, which derive from short imperfect dsRNA. RTL1 is naturally expressed only weakly in roots, but virus infection strongly induces its expression in leaves, suggesting that RTL1 induction is a general strategy used by viruses to counteract the siRNA-based plant antiviral defense. Accordingly, transgenic plants over-expressing RTL1 are more sensitive to TYMV infection than wild-type plants, likely because RTL1 prevents the production of antiviral siRNAs. However, TCV, TVCV and CMV, which encode stronger suppressors of RNA silencing (VSR) than TYMV, are insensitive to RTL1 over-expression. Indeed, TCV VSR inhibits RTL1 activity, suggesting that inducing RTL1 expression and dampening RTL1 activity is a dual strategy used by viruses to establish a successful infection. These results reveal another level of complexity in the evolutionary battle between viruses and plant defenses.
2013-09-10 | GSE49866 | GEO