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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Arabidopsis rosette leaves and inflorescences from dcl1-7, rdr6-15 and dcl4-2 mutants

ABSTRACT: Rosette leaves (5-8) and inflorescence stages (1-12) from dcl1-7, rdr6-15, and dcl4-2 mutants, involved in Arabidopsis small RNA metabolism. Three biological replicates of each mutant comprising at least 9 independent plants were harvested, and the expression profiles were determined using Affymetrix ATH1 arrays. Comparisons among the sample groups allow the identification of genes regulated by small RNAs (microRNAs and trans-acting siRNAs). Experiment Overall Design: Three biological replicates of each mutant comprising at least 9 independent plants were harvested, and the expression profiles were determined using Affymetrix ATH1 arrays.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Edwards Allen

PROVIDER: E-GEOD-3011 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana.

Xie Zhixin Z Allen Edwards E Wilken April A Carrington James C JC

Proceedings of the National Academy of Sciences of the United States of America 20050829 36

Arabidopsis thaliana contains four DICER-LIKE (DCL) genes with specialized functions in small RNA biogenesis for RNA interference-related processes. A mutant with defects in DCL4 was identified and analyzed for microRNA- and endogenous, small interfering RNA (siRNA)-related functions. The dcl4-2 mutant contained normal or near-normal levels of microRNAs (21 nt) and heterochromatin-associated siRNAs (24 nt). In contrast, this mutant lacked each of three families of 21-nt trans-acting siRNAs (ta-s ...[more]

PMID: 16129836

Similar Datasets

DCL4 Functional Analysis

Project description:Rosette leaves (5-8) and inflorescence stages (1-12) from dcl1-7, rdr6-15, and dcl4-2 mutants, involved in Arabidopsis small RNA metabolism. Three biological replicates of each mutant comprising at least 9 independent plants were harvested, and the expression profiles were determined using Affymetrix ATH1 arrays. Comparisons among the sample groups allow the identification of genes regulated by small RNAs (microRNAs and trans-acting siRNAs). Keywords: other

2005-09-30 | GSE3011 | GEO

Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology

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

Transcriptome analysis of two mutants rdr6/sgs2 and sgs3 impaired in post-transcriptional gene silencing (PTGS)

Project description:Identification of new genes regulated by RDR6 and SGS3 (two genes involved in PTGS) by analysis of the transcriptome of rdr6-1 and sgs3-1 mutants compared to wild-type plants in different tissues (flower and leaves). The comparison between transcriptome of rdr6-1 and sgs3-1 mutant alleles impaired in PTGS and development (juvenile-to-adult transition) and transcriptome of rdr6-5 and sgs3-3 alleles impaired only in PTGS would allowed identification of genes involved in the developmental default (zip phenotype) of the null alleles (rdr6-1 and sgs3-1 mutants). - Transcriptome of rdr6 and sgs3 mutants will be compared to the transcriptome of wild-type plants in flower and leaves. Further-more the comparison between transcriptome of rdr6-1 and sgs3-1 mutant alleles impaired in PTGS and development (juvenile-to-adult transition) and transcriptome of rdr6-5 and sgs3-3 alleles impaired only in PTGS will be done for flowers and leaves. Keywords: gene knock in (transgenic)

2007-05-31 | GSE7936 | GEO

m6A-seq and RNA-seq in Arabidopsis dcl1 mutant

Project description:N6-methyladenosine (m6A) modification is essential for plant growth and development. Recently, a possible involvement of miRNAs in m6A modification is reported in animal. To understand a potential involvement of miRNAs in sequence-specific deposition of m6A marks in plants, in this study, we performed m6A-seq and RNA-seq for a mutant of dicer-like 1 (dcl1), a key component in miRNA biogenesis in Arabidopsis. And the difference of m6A modification was compared between Col-0 mutant and dcl1 mutant.

2023-06-11 | GSE222644 | GEO

Transcription profiling of two Arabidopsis mutants rdr6-sgs2 and sgs3 impaired in PTGS

2006-08-01 | E-MEXP-531 | biostudies-arrayexpress

Dicer-like proteins and their role in plant-herbivore interactions in Nicotiana attenuata

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

Novel DICER-LIKE1 siRNAs Bypass the Requirement for DICER-LIKE4 in Maize Development

Project description:Dicer enzymes function at the core of RNA silencing to defend against exogenous RNA, or as an endogenous mechanism of gene regulation. Plant DICER-LIKE4 (DCL4) performs dual functions, acting in antiviral defense, as well as in development via the biogenesis of tasiR-ARFs. These small RNAs play an essential role in the grasses and act to spatially define the expression domain of AUXIN RESPONSE FACTOR3 (ARF3) transcription factors. However, contrary to tasiR-ARFs’ essential function in development, DCL4 proteins exhibit strong evidence of recurrent adaptation typical of host factors involved in antiviral immunity. Here, we address how DCL4 balances its role in development with pressures to diversify in response to viral attack. We show that, in contrast to other tasiR-ARF biogenesis mutants, dcl4 null alleles condition an uncharacteristically mild phenotype, correlated with normal expression of select arf3 targets. Loss of DCL4 activity yields a class of 22-nt tasiR-ARF variants associated with the processing of arf3 transcripts into 22-nt secondary siRNAs by DCL1. Our findings uncover the presence of a novel DCL1-dependent siRNA pathway that bypasses the otherwise adverse developmental effects of DCL4 mutations. This novel pathway is predicted to have important implications for DCL4’s role in antiviral defense by reducing the selective constraints on DCL4 and allowing it to diversify in response to viral suppressors. Examination of small RNAs isolated from dcl4, dcl1 and double mutants in imbibed kernels of maize

2015-09-01 | E-GEOD-66986 | biostudies-arrayexpress

Analysis of the RDR6-dependent small RNA profile in ein5 ski2 in Arabidopsis

Project description:Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3’-5’ mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5’-3’ exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). A number of endogenous genes, including many miRNA target genes, manifest transitive 21-22 nt siRNA production and compromised gene expression in ein5 ski2 in an RDR6-dependent manner. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5’-3’ and 3’-5’ cytoplasmic mRNA decay pathways.

2016-11-15 | GSE52408 | GEO

Expression data of wild-type and dcl1-15 torpedo-staged embryos

Project description:Severe loss-of-function alleles of DCL1 are embryonic lethal. Defects in cell division were seen as early as the globular stage in the strong loss-of-function allele dcl1-15. Phenotypic work with dcl1-15 and the null allele dcl1-5 suggested that, in addition to the severe patterning defects, the mutants were maturing earlier than wild-type embryos. We performed global gene expression analysis of dcl1-15 and wild-type torpedo staged embryos to examine this maturation phenotype further. The results suggested that DCL1 is a heterochronic gene. Comparisons to a time series of embryo development (http://www.seedgenenetwork.net/arabidopsis) showed that the genes differentially expressed in dcl1-15 embryos behaved more like green-cotyledon stage embryos than torpedo embryos. Seeds of a DCL1/dcl1-15 plant were sown. For each wild-type sample, 300 torpedo stage embryos were selected from wild-type siblings. For each mutant replicate, 300 dcl1-15/dcl1-15 embryos were selected from the siliques of DCL1/dcl1-15 where the wild-type embryos were at the torpedo stage.

2011-02-17 | E-GEOD-24887 | biostudies-arrayexpress

Characterization of DCL4 missense alleles provides novel insights into its ability to process distinct classes of dsRNA substrates

Project description:In the model plant Arabidopsis thaliana, four Dicer-like proteins (DCL1-4) mediate the production of various classes of small RNAs (sRNAs). Among these four proteins, DCL4 is by far the most versatile RNaseIII-like enzyme and previously identified dcl4 missense alleles were shown to uncouple the production of the various classes of DCL4-dependent sRNAs. Yet, little is known about the molecular mechanism pertaining this uncoupled production. Here, by studying the subcellular localization, interactome and binding to the sRNA precursors of three distinct dcl4 missense alleles, we simultaneously highlight the absolute requirement of its helicase domain for efficient production of all DCL4-dependent sRNAs, and identify an important determinant of DCL4 versatility within its PAZ domain that is mandatory for efficient processing of intramolecular foldback dsRNA precursors but dispensable for the production of siRNAs from RDR-dependent dsRNA susbtrates. This study not only provides novel insights into DCL4 mode of action in plants but also delineates interesting tools to further study the complexity of plant RNA silencing pathways.

2018-04-24 | GSE106383 | GEO

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