Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA326659 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3713530.fastq.gz | Fastqsanger.gz | |||
| SRR3713540.fastq.gz | Fastqsanger.gz | |||
| SRR3713521.fastq.gz | Fastqsanger.gz | |||
| SRR3713531.fastq.gz | Fastqsanger.gz | |||
| SRR3713522.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 20 |
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Project description:Translational landscape of photomorphogenic Arabidopsis
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Project description:We used profiling of Arabidopsis small RNA populations present in the mature ovules to define the potential genome targets of small RNAs during reproductive development. Defining the contributions and interactions of paternal and maternal genomes during embryo development is critical to understand the fundamental processes involved in hybrid vigor, hybrid sterility, and reproductive isolation. To determine the parental contributions and their regulation during Arabidopsis embryogenesis we combined deep-sequencing-based RNA profiling and genetic analyses. At the 2-4 cell stage there is a strong, genome-wide dominance of maternal transcripts, although transcripts are contributed by both parental genomes. At the globular stage the relative paternal contribution is higher, largely due to a gradual activation of the paternal genome. We identified two antagonistic maternal pathways that control these parental contributions. Paternal alleles are initially down-regulated by the chromatin siRNA pathway, linked to DNA and histone methylation, while transcriptional activation requires maternal activity of the histone chaperone complex CAF1. Our results define maternal epigenetic pathways controlling the parental contributions in plant embryos, which are distinct from those regulating genomic imprinting. Profiling of small RNAs in wild type ovules of Arabidopsis
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Project description:Thermoresponive small RNAs in Arabidopsis thalinana
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Project description:Small RNAs in Arabidopsis hybrid siliques
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Project description:Small RNAs play important regulatory roles in most eukaryotes but only a small proportion of these molecules have been identified. We sequenced more than two million small RNAs from seedlings and the inflorescence of the model plant Arabidopsis thaliana. Known and new miRNAs were among the most abundant of the non-redundant set of more than 75,000 sequences, whereas more than half represented lower abundance small-interfering RNAs (siRNAs) that match repetitive sequences, intergenic regions, and genes. Individual or clusters of highly-regulated small RNAs were readily observed. Targets of antisense RNA or miRNA did not appear to be preferentially associated with siRNAs. Many genomic regions previously considered featureless were found to be sites of numerous small RNAs. Keywords: small RNA identification , modified MPSS
2005-09-02 | GSE3008 | GEO
Project description:Ouyang2014 - photomorphogenic UV-B signalling
network
This model is described in the article:
Coordinated photomorphogenic
UV-B signaling network captured by mathematical modeling.
Ouyang X, Huang X, Jin X, Chen Z,
Yang P, Ge H, Li S, Deng XW.
Proc. Natl. Acad. Sci. U.S.A. 2014 Aug;
111(31): 11539-11544
Abstract:
Long-wavelength and low-fluence UV-B light is an
informational signal known to induce photomorphogenic
development in plants. Using the model plant Arabidopsis
thaliana, a variety of factors involved in UV-B-specific
signaling have been experimentally characterized over the past
decade, including the UV-B light receptor UV resistance locus
8; the positive regulators constitutive photomorphogenesis 1
and elongated hypocotyl 5; and the negative regulators cullin4,
repressor of UV-B photomorphogenesis 1 (RUP1), and RUP2.
Individual genetic and molecular studies have revealed that
these proteins function in either positive or negative
regulatory capacities for the sufficient and balanced
transduction of photomorphogenic UV-B signal. Less is known,
however, regarding how these signaling events are
systematically linked. In our study, we use a systems biology
approach to investigate the dynamic behaviors and correlations
of multiple signaling components involved in Arabidopsis
UV-B-induced photomorphogenesis. We define a mathematical
representation of photomorphogenic UV-B signaling at a temporal
scale. Supplemented with experimental validation, our
computational modeling demonstrates the functional interaction
that occurs among different protein complexes in early and
prolonged response to photomorphogenic UV-B.
This model is hosted on
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BIOMD0000000545.
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2024-09-02 | BIOMD0000000545 | BioModels
Project description:Arabidopsis thaliana Col-0 inflorescence small RNAs
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Project description:Low oxygen responsive small RNAs in Arabidopsis
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Project description:Profiling of small RNAs in Arabidopsis ovules
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Project description:Small RNA sequences from Arabidopsis thaliana Col-0 inflorescence tissues of three biological replicates. The data were analyzed to identify non-templated nucleotides in Arabidopsis small RNAs.
2016-05-18 | GSE79119 | GEO