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Difference in gene expression between WT (Col-0) and atxrn4-3 mutant under non-stress and heat stress condition

ABSTRACT: Arabidopsis 5’-3’ exoribonuclease, AtXRN4, a homolog of yeast Xrn1p, functions in degradation of uncapped RNAs after de-capping step. While Xrn1p-dependent on plant XRN4’s targets for degradation is still limited. For understanding biological function of AtXRN4, we tested survivability of atxrn4 mutants under heat stress. Our results showed that atxrn4 mutants increased survival rate under short-term degradation is a main mRNA decay in yeast, knowledge heat stress compared with WT plants. Our microarray and mRNA decay assay showed that loss of AtXRN4 function caused reduction of mRNA degradation of heat shock factor A2 (HSFA2) and ethylene response factor 1 (ERF1). HSFA2 has been known as a key regulator in heat acclimation, was found as a target for AtXRN4 for degradation at non-stress condition. Heat stress applied on atxrn4-3 hsfa2 double mutant severely lacked heat tolerance phenotype of atxrn4 mutant. These results suggest that AtXRN4-mediated mRNA degradation linked to suppress heat acclimation.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE66369 | GEO | 2015/07/14

SECONDARY ACCESSION(S): PRJNA276672

REPOSITORIES: GEO

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Difference in gene expression between WT (Col-0) and atxrn4-3 mutant under non-stress and heat stress condition

Project description:Arabidopsis 5’-3’ exoribonuclease, AtXRN4, a homolog of yeast Xrn1p, functions in degradation of uncapped RNAs after de-capping step. While Xrn1p-dependent on plant XRN4’s targets for degradation is still limited. For understanding biological function of AtXRN4, we tested survivability of atxrn4 mutants under heat stress. Our results showed that atxrn4 mutants increased survival rate under short-term degradation is a main mRNA decay in yeast, knowledge heat stress compared with WT plants. Our microarray and mRNA decay assay showed that loss of AtXRN4 function caused reduction of mRNA degradation of heat shock factor A2 (HSFA2) and ethylene response factor 1 (ERF1). HSFA2 has been known as a key regulator in heat acclimation, was found as a target for AtXRN4 for degradation at non-stress condition. Heat stress applied on atxrn4-3 hsfa2 double mutant severely lacked heat tolerance phenotype of atxrn4 mutant. These results suggest that AtXRN4-mediated mRNA degradation linked to suppress heat acclimation. In the study here, 2 week-old WT and atxrn4-3 mutant plants were exposure to non-stress (22oC) and heat-stress (37oC, 1 h). Custom microarray was applied to acquire expression profile of 32788 Arabidopsis genes. 3 biological repeats of WT (non-stress), WT(heat stress), atxrn4-3 (non-stress) and atxrn4-3 (heat stress) were used for microarray analysis

2015-07-14 | E-GEOD-66369 | biostudies-arrayexpress

Transcriptomic analysis of WT and larp1 mutant 21 days old seedling at 20°C or following a heat stress (15 min at 38°C)

Project description:We report the identification of a heat-stress mediated mRNA decay in arabidopsis that is mediated by the XRN4 exonuclease and LARP1 RNA-binding protein.

2014-03-28 | GSE51879 | GEO

Transcriptomic analysis of WT and larp1 mutant 21 days old seedling at 20°C or following a heat stress (15 min at 38°C)

Project description:We report the identification of a heat-stress mediated mRNA decay in arabidopsis that is mediated by the XRN4 exonuclease and LARP1 RNA-binding protein. mRNA population in WT and larp1 mutant at 20C or 15 min at 38C

2014-03-28 | E-GEOD-51879 | biostudies-arrayexpress

HsfA2 controls the activity of developmentally and stress-regulated heat stress protection mechanisms in tomato male reproductive tissues

Project description:Male reproductive tissues are more sensitive to heat stress compared to vegetative tissues, however the basis of this phenomenon is poorly understood. Heat stress transcription factors (Hsfs) regulate the transcriptional changes required for protection and recovery from heat stress. HsfA2 has been characterized as co-activator of HsfA1a in tomato and is considered as one of the major Hsfs accumulating in response to elevated temperatures. The role of HsfA2 in heat stress response of different tissues was examined by exploring the composition and structure of the tissue-specific regulatory networks in transgenic tomato plants with suppressed HsfA2 expression (A2AS). Transcriptome analysis revealed that HsfA2 acts in condition- and tissue-specific manner and that only a subset of heat stress induced genes require HsfA2 for higher expression. Remarkably, although HsfA2 is not essential for thermotolerance in seedlings and flowering plants, it is required for maintenance pollen viability under stress conditions. We show that the activation of Hsf networks is important for the developmentally regulated priming of heat stress response occurring at early stages of anther and pollen development. Thereby, HsfA2 is involved in pollen thermotolerance by directly regulating heat stress responsive genes but also by stimulating the synthesis of molecular chaperones under non-stress conditions.

2016-02-22 | GSE68500 | GEO

HsfA2 controls the activity of developmentally and stress-regulated heat stress protection mechanisms in tomato male reproductive tissues

2016-02-22 | E-GEOD-68500 | biostudies-arrayexpress

Differential regulation of HSFA1s and HSFA2 after heat shock in Arabidopsis

Project description:HSFA1s are a gene family of HSFA1 with four members, HSFA1a, HSFA1b, HSFA1d, and HSFA1e. HSFA1s are the master regulators of heat shock response. As a part of the heat shock response, HSFA2 can prolong the heat shock response and amplify the heat shock response in response to repeat heat shock. To identify the heat-shock-responsive genes differentially regulated by HSFA1s and HSFA2, we compared the transcriptomic differences of plants containing only constitutively expressed HSFA1s or HSFA2 after heat stress. hsfa2 (the KO mutant of HSFA2, Col-0 background) and A2QK-10 (CaMV 35S:HSFA2 in QK mutant; QK is HSFA1a/b/d/e quadruple KO mutant) were used to compare the difference of heat shock response when plants lack HSFA1s or HSFA2. The aim is to find the HSFA1s- and HSFA2-preferred regulating genes after heat stress. As the control samples, wild type is the plant with normal heat shock response, and QK (HSFA1s KO mutant, Col-0 and Ws mixed background) is the plant that lost the heat shock response controlled by HSFA1s.

2013-04-09 | E-GEOD-44655 | biostudies-arrayexpress

Differential regulation of HSFA1s and HSFA2 after heat shock in Arabidopsis

2013-04-09 | GSE44655 | GEO

Genome-wide mapping of uncapped and cleaved transcripts reveals a role for the nuclear messenger RNA cap-binding complex in plant co-translational RNA decay

Project description:RNA turnover is necessary for controlling proper mRNA levels post-transcriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5’ end to the 3’ end, such as XRN4, or in the opposite direction by the multi-subunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of co-translational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames. This pattern of co-translational degradation is especially evident near the ends of open reading frames, where we observe accumulation of cleavage events focused 16 to 17 nucleotides upstream of the stop codon because of ribosomal pausing during translation termination. Following treatment of Arabidopsis plants with the translation inhibitor cycloheximide, cleavage events accumulate 13 to 14 nucleotides upstream of the start codon where initiating ribosomes have been stalled with these sequences in their P site. Further analysis in xrn4 mutant plants indicates that co-translational RNA decay is XRN4-dependent. Additionally, studies in plants lacking CAP-BINDING PROTEIN80/ABA HYPERSENSITIVE1, the largest subunit of the nuclear mRNA cap-binding complex, reveal a role for this protein in co-translational decay. In total, our results demonstrate the global prevalence and features of co-translational RNA decay in a plant transcriptome.

2016-09-30 | GSE71913 | GEO

Seed transcriptome of xrn4-5 and vcs-8 mutants

Project description:au14-08_xrn_vcs - seed transcriptome of xrn4-5 and vcs-8 mutants. - Role of RNA degradation in seed dormancy. - Study of the seeds regulation by the RNA-decay. Comparison between Col0 total RNA and mutants xrn4-5 and vcs-8 RNA, affected in the dormancy and in RNA metabolism. 6 dye-swap - gene knock out

2015-08-01 | E-GEOD-68268 | biostudies-arrayexpress

Seed transcriptome of xrn4-5 and vcs-8 mutants

2015-08-01 | GSE68268 | GEO

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