IlTorAlte1
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB58747 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Tortricodes alternella (winter shade) genome assembly, ilTorAlte1, alternate haplotype
| PRJEB58748 | ENA
Project description:Tortricodes alternella (winter shade), genomic and transcriptomic data
| PRJEB57277 | ENA
Project description:Shade can trigger the shade avoidance syndrome (SAS) in shade-intolerant species, which cause exaggerated growth and affect crop yield. We report that Arabidopsis transcription factors bZIP59 negatively regulate SAS. To identify direct targets of bZIP59 at the genome-wide level, we performed ChIP-Seq using ProbZIP59::bZIP59-GFP/bzip59 transgenic plants under white light or transferred to shade conditions for 2 hours. Our results indicated shade light dramatically increased the DNA binding ability of bZIP59, and shade-enhanced binding of bZIP59 majorly located around transcriptional start site (TSS) of genes.
2024-08-18 | GSE236101 | GEO
Project description:The transcriptome of a light sensitive tea cultivar ‘Huangjinya’ plants exposed to sunlight and shade were analyzed by high-throughput sequencing followed by de novo assembly.
2017-06-23 | GSE97659 | GEO
Project description:Accessible chromatin regions host DNA regulatory motives and are highly accessible to the transcription factors and transcriptional machinery. In Arabidopsis, responses to light are heavily regulated at the transcriptional level. Shade, for example, can limit photosynthesis and is rapidly perceived by phytochromes as a reduction of red to far-red light ratio. Under shade, phytochromes inactivate and allow PHYTOCHROME INTERACTING FACTORs (PIFs) to promote a wide scale genome reprogramming. A strong and fast initial regulation of shade responsive genes is followed by an attenuation of this response under prolonged shade. We wanted to determine if transcriptional response pattern to shade depends on chromatin accessibility. For this we used ATAC-seq to profile the chromatin of seedlings exposed to short (1h) and long (25h) simulated shade. Transcription pattern of most acute shade responsive genes correlates with the rapid increase in PIF levels/activity at 1h, and its decrease at 25h of shade exposure. For a set of acute responding genes, PIFs also modulate chromatin accessibility at their binding sites in response to shade. Our results suggest that permanent state of open chromatin conformation allows PIFs to easily access and recognize their binding motifs, rapidly initiating a burst in gene expression triggered by shade. This transcriptional response primarily depends on a transient increase in stability of PIFs and gene occupancy and is followed by a moderate change of chromatin accessibility.
2025-11-06 | GSE283129 | GEO
Project description:Shade avoidance helps plants maximize their access to light for growth under crowding. It is unknown, however, whether a priming shade avoidance mechanism exists that allows plants to respond more effectively to successive shade conditions. Here, we show that the shade-intolerant plant Arabidopsis can remember a first experienced shade event and respond more efficiently to the next event on hypocotyl elongation. The transcriptional regulator PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) and the histone H3K27-demethylase RELATIVE OF EARLY FLOWERING 6 (REF6) were identified as being required for this shade avoidance memory. RNA-sequencing analysis revealed that shade induction of shade memory-related genes was impaired in the pif7 and ref6 mutants. Based on the enrichments of H3K27me3, REF6 and PIF7, we found that priming shade treatment induced PIF7 accumulation, which further recruited REF6 to demethylate H3K27me3 on the chromatin of certain memory-related genes, leading to a state poised for their transcription. Upon the second shade treatment, enhanced shade-mediated induction of these genes resulted in stronger hypocotyl growth responses. We conclude that the transcriptional memory mediated by epigenetic modification plays a key role in the ability of primed plants to remember previously experienced shade and acquire enhanced responses to recurring shade conditions.
2024-07-29 | GSE268785 | GEO
Project description:Accessible chromatin regions host DNA regulatory motives and are highly accessible to the transcription factors and transcriptional machinery. In Arabidopsis, responses to light are heavily regulated at the transcriptional level. Shade, for example, can limit photosynthesis and is rapidly perceived by phytochromes as a reduction of red to far-red light ratio. Under shade, phytochromes inactivate and allow PHYTOCHROME INTERACTING FACTORs (PIFs) to promote a wide scale genome reprogramming. A strong and fast initial regulation of shade responsive genes is followed by an attenuation of this response under prolonged shade. We wanted to determine if transcriptional response pattern to shade depends on chromatin accessibility. For this we used ATAC-seq to profile the chromatin of seedlings exposed to short (1h) and long (25h) simulated shade. Transcription pattern of most acute shade responsive genes correlates with the rapid increase in PIF levels/activity at 1h, and its decrease at 25h of shade exposure. For a set of acute responding genes, PIFs also modulate chromatin accessibility at their binding sites in response to shade. Our results suggest that permanent state of open chromatin conformation allows PIFs to easily access and recognize their binding motifs, rapidly initiating a burst in gene expression triggered by shade. This transcriptional response primarily depends on a transient increase in stability of PIFs and gene occupancy and is followed by a moderate change of chromatin accessibility.
2025-11-06 | GSE283133 | GEO
Project description:Coping of evergreen conifers of boreal forests with freezing temperatures on bright winter days puts the photosynthetic machinery in great risk of oxidative damage. To survive harsh winter conditions, conifers have evolved a unique but poorly characterised photoprotection mechanism, a sustained form of non-photochemical quenching (sustained NPQ). Here we focused on functional properties and underlying molecular mechanisms related to the development of sustained NPQ in Norway spruce (Picea abies). Data was collected during four consecutive years (2016-19) from trees growing in sun and shade habitats. When day temperatures dropped below -4°C, specific N-terminally triply phosphorylated LHCB1 isoform (3p-LHCII) and phosphorylated PSBS (p-PSBS) were detected in the thylakoid membrane. Development of sustained NPQ coincided with the highest level of 3p-LHCII and p-PSBS, occurring after prolonged combination of bright winter days and temperature close to -10°C. Artificial induction of both the sustained NPQ and recovery from naturally induced sustained NPQ provided information on differential dynamics and light-dependence of 3p-LHCII and p-PSBS accumulation and dephosphorylation as essential prerequisites of sustained NPQ. Data obtained collectively suggest three novel components related to sustained NPQ in spruce. (i) Freezing temperatures induce 3p-LHCII accumulation independently of light, which is suggested to initiate de-stacking of appressed thylakoid membranes due to increased electrostatic repulsion of adjacent membranes. (ii) p-PSBS accumulation is both light- and temperature-dependent and closely linked to the initiation of sustained NPQ, which (iii) in concert with PSII photoinhibition is likely to trigger sustained NPQ in spruce.
2020-07-27 | PXD018941 | Pride