Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA103627 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gene expression analysis of 7d-old Arabidopsis seedlings exposed to short term (2 h) hypoxia, long term (9 h) hypoxia, and 1 h reoxygenation after long term (9 h) hypoxia to evaluate the regulation of gene expression at the level of translation. Experiment Overall Design: 30 samples, 5 conditions (2 hr hypoxia stress, 2hr non-stress, 9 hr hypoxia stress , 9 hr non-stress, 9 hr hypoxia with 1 hr recovery), 2 RNA pools (Total mRNA and polysomal mRNA), 3 replicates
2008-10-20 | E-GEOD-9719 | biostudies-arrayexpress
Project description:Gene expression analysis of 7d-old Arabidopsis seedlings exposed to short term (2 h) hypoxia, long term (9 h) hypoxia, and 1 h reoxygenation after long term (9 h) hypoxia to evaluate the regulation of gene expression at the level of translation. Keywords: Time Course, hypoxia recovery, polysomal mRNA, IP RNA, polysomes, hypoxia stress, reoxygenation, translational control.
2008-07-22 | GSE9719 | GEO
Project description:Dynamics of mRNA abundance and translation in response to darkness and reillumination
| PRJNA149791 | ENA
Project description:Previous studies towards reduced oxygen availability mostly focused on changes in total mRNA expression neglecting underlying transcriptional and post-transcriptional events. Therefore, we generated a comprehensive overview of hypoxia-induced changes in total mRNA expression, global de novo transcription, and mRNA stability in monocytic THP-1 cells. Since hypoxic epi-sodes often persist for prolonged periods, we further compared adaptations to acute and chronic hypoxia. While total mRNA changes correlated well with enhanced transcription during short term hypoxia, mRNA destabilization gained importance under chronic conditions. Reduced mRNA stability not only added to compensatory attenuation of immune responses, but most no-tably to the reduction of nuclear-encoded mRNAs associated with various mitochondrial func-tions. These changes may prevent the futile production of new mitochondria under conditions where mitochondria cannot exert their full metabolic function and are indeed actively removed by mitophagy. The post-transcriptional mode of regulation might further allow for rapid recov-ery of mitochondrial capacities upon reoxygenation. Our results provide a comprehensive re-source of functional mRNA expression dynamics and underlying transcriptional and post-transcriptional regulatory principles during the adaptation to hypoxia. Furthermore, we specifically uncover mitochondrial functions controlled by RNA stability regulation in the con-text of hypoxia.
2022-06-01 | GSE199947 | GEO
Project description:Post-transcriptional gene regulation plays a significant role in the response to oxygen deprivation. Here, we utilized advances in next-generation sequencing technology to examine changes in transcriptional control, mRNA loading on to polysome, and regulation of ribosome activity during mRNA translation in 7-day-old Arabidopsis seedlings subjected to 2 hour hypoxia treatment.
2013-11-23 | GSE50597 | GEO
Project description:High-altitude pulmonary hypertension (HAPH) is a severe and progressive disease caused by chronic hypoxia and subsequent pulmonary vascular remodeling. No cure is currently available owing to an incomplete understanding about vascular remodeling. It is believed that hypoxia-induced diseases can be prevented by treating hypoxia. Thus, this study aimed to determine whether daily short-duration reoxygenation at sea level attenuates pulmonary hypertension under high-altitude hypoxia. To this end, a simulated 5,000-m hypoxia rat model was used to evaluate the effect of short-duration reoxygenation. Results show that intermittent, not continuous, short-duration reoxygenation effectively attenuates hypoxia-induced pulmonary hypertension. The mechanisms underlining the protective effects involved that intermittent, short-duration reoxygenation prevented functional and structural remodeling of pulmonary arteries and proliferation, migration, and phenotypic conversion of pulmonary artery smooth muscle cells under hypoxia. The specific genes or potential molecular pathways responsible for mediating the protective effects were also characterised by RNA sequencing.This study is novel in revealing a new potential method in preventing high-altitude pulmonary hypertension. It gives insights into the selection and optimisation of oxygen supply schemes in high-altitude areas.
2020-11-06 | GSE160926 | GEO
Project description:Post-transcriptional gene regulation plays a significant role in the response to oxygen deprivation. Here, we utilized advances in next-generation sequencing technology to examine changes in transcriptional control, mRNA loading on to polysome, and regulation of ribosome activity during mRNA translation in 7-day-old Arabidopsis seedlings subjected to 2 hour hypoxia treatment. 14 samples, 2 conditions (2 hr hypoxia and 2 hr normoxia), 2 bioreplicates of 3 RNA pools (total mRNA, immunopurified (TRAP) polysomal mRNA, ribosome footprints), 1 bioreplicate of 1 RNA pool (immunopurified (TRAP)-ribosome footprints).
2013-11-23 | E-GEOD-50597 | biostudies-arrayexpress
Project description:Low oxygen stress dynamically regulates the translation of cellular mRNAs as a means of energy conservation in seedlings of Arabidopsis thaliana. Most of the highly hypoxia-induced mRNAs are recruited to polysomes and actively translated, whereas other cellular mRNAs become translationally inactive and are either targeted for stabilization or degradation. Here we identify the involvement of OLIGOURIDYLATE BINDING PROTEIN 1 (UBP1), a triple RNA Recognition Motif protein, in dynamic and reversible aggregation of translationally repressed mRNAs during hypoxia. Mutation or downregulation of UBP1C interferes with seedling establishment and reduces survival of low oxygen stress. By use of messenger ribonucleoprotein immunopurification, we show that UBP1C constitutively binds a subpopulation of mRNAs characterized by U-rich 3M-bM-^@M-^Y-untranslated regions under normoxic conditions. During hypoxia, UBP1C association with non-U-rich mRNAs is enhanced concomitant with its aggregation into microscopically visible cytoplasmic foci, referred to as UBP1 stress granules (SGs). This UBP1C-mRNA association occurs as global levels of protein synthesis decline. Upon reoxygenation, rapid UBP1 SG disaggregation coincides with the return of the stabilized mRNAs to polysomes. The mRNAs that are highly induced and translated during hypoxia largely circumvent UBP1C sequestration. Thus, UBP1 is established as a component of dynamically assembled cytoplasmic mRNPs that sequester mRNAs that are poorly translated during a transient low energy stress. Immunoprecipated RNA associated with Arabidopsis UBP1C (IP) was compared with total cellular RNA from light (L), mock dark (D), 2 h hypoxia, and 2 h hypoxia + 20 min reoxygenation treated samples with duplicate hybridizations to the Affymetrix ATH1 Genechip array.
2014-01-13 | E-GEOD-49411 | biostudies-arrayexpress
Project description:Preceding hypoxia by an ethylene treatment improves root tip survival. To identify key players and processes mediating ethylene enhanced tolerance, the transcriptomic response of root tips was investigated directly after ethylene or control pretreatment, 2 and 4 hours of subsequent hypoxia, and 1 hour of reoxygenation. Seedlings were 4 days or 7 days old and grown on MS plates without added sugar. Only the root tips were harvested
2022-02-01 | E-MTAB-11231 | biostudies-arrayexpress
Project description:Increased sucrose levels mediate selective mRNA translation in Arabidopsis
| PRJNA255000 | ENA