The histone demethylase JMJ27 acts during the UV-induced modulation of H3K9me2 landscape and facilitates photodamage repair
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE263549 | GEO | 2024/09/05
REPOSITORIES: GEO
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Project description:The histone demethylase JMJ27 acts during the UV-induced modulation of H3K9me2 landscape and facilitates photodamage repair
| PRJNA1098035 | ENA
Project description:This project was conducted by Nitin S. Baliga of the Halobacterium group at the Institute for Systems Biology in collaboration with Jocelyne Diruggiero of University of Maryland. Halobacterium NRC-1 cell pellets were resuspended in an isotonic buffer at a low density, placed on ice and exposed to 200J/m2 of UV-C irradiation, returned to the growth medium and allowed to recover at 42oC in dark (D) or light (L). Total RNA was collected from each sample at 30 minutes (D30 and L30) and 60 minutes (L60 and D60). The control (C) was processed in a manner to identical to L60 except that it did not suffer any UV-C insult. The reference RNA was prepared from an aliquot of the same culture just prior to UV-C irradiation. Therefore the reference was also exposed to initial perturbations prior to UV-C irradiation such as change of growth medium to buffer and change of temperature from 42oC to ice. Keywords = ISB Keywords = Halobacterium NRC-1 Keywords = UV repair Keywords = ultraviolet radiation Keywords = stress response Keywords: other
2004-02-14 | GSE1040 | GEO
Project description:We report the methylation level of photodamage repair deficient plants 24h upon UV-C exposure. We determined the methlome changes genome wide and at photodamaged sites using NGS approaches.
2019-11-01 | GSE132750 | GEO
Project description:Differential expression of microRNAs was studied in maize leaves after an 8-h-exposure under UV-B light. As a control, plants were kept in the greenhouse in the absence of UV-B 4-week maize plants were grown in the greenhouse in the absence of UV-B. Then, they were divided in two groups. One group was treated with UV-B lights provided once for 8 h, starting 3 h after the beginning of the light period, using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) at a UV-B intensity of 2 W m-2, UV-A: 0.65 W m-2. The bulbs were covered with cellulose acetate to exclude wavelengths <280 nm. For the second control group, plants were exposed for 8 h under the same lamps covered with polyester film (no UV-B treatment, UV-B: 0.04 W m-2, UV-A: 0.4 W m-2). Lamp output was recorded using a UV-B/UV-A radiometer (UV203 A+B radiometer, Macam Photometrics, Ltd, Livingston, UK) to insure that both the bulbs and filters provided the designated UV dosage in all treatments. Leaf samples were collected immediately after irradiation. RNA was extracted immediately after the treatments, and used for the microRNA microarray experiments.
2013-10-31 | E-GEOD-19768 | biostudies-arrayexpress
Project description:UV-induced DNA lesions are an important contributor to mutagenesis and cancer, but it is not fully understood how the chromosomal landscape influences UV lesion formation and repair. We have used a novel high-throughput sequencing method to precisely map UV-induced cyclobutane pyrimidine dimers (CPDs) at nucleotide resolution throughout the yeast genome. Analysis of CPD formation reveals that nucleosomal DNA having an inward rotational setting is protected from CPD lesions. In strongly positioned nucleosomes, this nucleosome 'photofootprint' overrides intrinsic dipyrimidine sequence preferences for CPD formation. CPD formation is also inhibited by DNA-bound transcription factors, in effect protecting important DNA elements from UV damage. Analysis of CPD repair revealed a clear signature of efficient transcription-coupled nucleotide excision repair. Repair was less efficient at translational positions near a nucleosome dyad and at heterochromatic regions in the yeast genome. These findings define the roles of nucleosomes and transcription factors in UV damage formation and repair. UV mapping data was analyzed for yeast cells irradiated with 125J/m2 and allowed to repair for 0hr (2 samples), 20 minutes, 1 hour, or 2 hours. Data is also included for naked DNA irradiated with UV 60 or 90 J/m2
2016-08-19 | E-GEOD-79977 | biostudies-arrayexpress
Project description:Microarray technology was used to assess transcriptome changes in poplar (Populus alba L.) under a realistic simulation of increased UV-B radiation. Plants were UV-Bbe (UV-B biologically effective radiation) supplemented with a dose of 6 kJ/m2/day for 12 hours per day and allowed to recover during the night. Poplar plants were UV-B treated using a refined controlled environment able to guarantee a realistic simulation of natural conditions, especially for light parameters such as presence of background UV-B radiation for control plants and balanced PAR/UV-A/UV-B ratio. A time course experiment was planned to look both at the rapid and delayed response of poplar to UVB; two time points after 3 h (T3h) and 30 h (6th hour of the third day of treatment, T30h) were considered. 4 independent biological replicates were analysed for each time point. Competitive hybridisations were carried out using the PICME 28K microarray. Keywords: Time course experiment, stress response
2013-12-01 | GSE9470 | 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:Differential expression of microRNAs was studied in maize leaves after an 8-h-exposure under UV-B light. As a control, plants were kept in the greenhouse in the absence of UV-B
2013-10-31 | GSE19768 | GEO
Project description:Microarray technology was used to assess transcriptome changes in poplar (Populus alba L.) under a realistic simulation of increased UV-B radiation. Plants were UV-Bbe (UV-B biologically effective radiation) supplemented with a dose of 6 kJ/m2/day for 12 hours per day and allowed to recover during the night. Poplar plants were UV-B treated using a refined controlled environment able to guarantee a realistic simulation of natural conditions, especially for light parameters such as presence of background UV-B radiation for control plants and balanced PAR/UV-A/UV-B ratio. A time course experiment was planned to look both at the rapid and delayed response of poplar to UVB; two time points after 3 h (T3h) and 30 h (6th hour of the third day of treatment, T30h) were considered. 4 independent biological replicates were analysed for each time point. Competitive hybridisations were carried out using the PICME 28K microarray. Keywords: Time course experiment, stress response Two condition experiment: UVB supplemented plants vs normal UV-B level plants. Biological replicates: 4 UVB suplemented plants, 4 control plants, two time points, one replicate per array. Dye swap between replicates.
2013-12-01 | E-GEOD-9470 | biostudies-arrayexpress
Project description:UV-B (280-320 nm) exposure causes serious damage in plants, limiting their growth and survival, effects that are partly counteracted by repair mechanisms active in plants receiving accompanying visible radiation. Though no particular UV-B receptor has been identified to date, there is strong evidence to indicate that certain aspects of UV-B perception are receptor-mediated. Investigations of down-stream signalling events have thus far indicated broad similarities to pathogen-induced defence responses in plants. In order to identify genes in Arabidopsis that may be up- or down- regulated specifically in response to UV-B exposure and compare them to genes whose expression is altered in plants challenged by an avirulent isolate of Peronospora parasitica (downy mildew), we propose to analyse the transcriptional profiles for the following treatments: 1. UV-B Responses "A-1" Columbia (Col-0) exposed to supplementary UV-B/UV-A* with a background of low photosynthetically active radiation (PAR of 20 micromol m-2 s-1) for 1.5 photoperiods (photoperiod = 12h). [UV-B treatment] "A-2" Col-0 exposed to supplementary UV-A and low PAR for 1.5 photoperiods [control for UV-B treatment] "A-3" Col-0 exposed to visible light only (low PAR) (no UV) for 1.5 photoperiods [control for UV effects in general].* There are no pure sources of UV-B light available. 2. Pathogen Responses "A-4" Col-0 spray-inoculated with P. parasitica isolate HIKS-1 (recognised by the R-gene RPP7). After spraying, plants were kept covered in plant propagators and transferred to an 18 degreeC growth chamber. !Samples for RNA extraction were taken 72h after inoculation. "A-5" The viability of spores was also checked by parallel spraying of the susceptible mutant, Col-rpp7. [pathogen treatment] "A-6" Col-0 mock treated with water, covered and transferred to an 18 degree C growth chamber, 72h prior to sampling. [control for pathogen treatment] In all experiments, we are using RNA from leaves taken at the same time of day (6 h into the 12 h photoperiod) from 4.5-week old plants grown under 12h photoperiod. All treatments were normalised against PR-1 expression levels to ensure comparability between UV-B and pathogen treatments. Due to the difficulty in distinguishing between local and systemic induced responses in UV-B treated plants, we are using RNA from whole rosettes for both the UV-B and pathogen treatment for better comparability among treatments. The degree of similarity between these two sets of transcriptional changes will complement and help interpret our experimental data on changes in resistance to pathogens in plants pre-treated with UV-B. Moreover, the data set obtained would allow for identification of UV-B specific changes in gene expression including cis-acting UV-B-responsive promoter elements. Experimenter name = Julia Brueggemann Experimenter phone = 01789 470 382 Experimenter fax = 01789 470 552 Experimenter address = Horticulture Research International Experimenter address = Wellesbourne Experimenter address = Warwickshire Experimenter zip/postal_code = CV35 9EF Experimenter country = UK Keywords: stimulus_or_stress_design
2007-01-08 | GSE5731 | GEO