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Transcriptome profiling of Arabidopsis roots upon lateral root induction in WT and TOR knock down [dataset1]

ABSTRACT: To get a genome wide picture of the effects of TOR knockdown during the early phase of lateral root formation, we compared by RNA-seq the transcriptomes of roots 6h after the synchronous induction of lateral formation by auxin treatment (Himanen et al, 2002 - http://dx.doi.org/10.1105/tpc.004960) in the inducible UB10pro>>amiR-TOR background.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE199202 | GEO | 2022/03/23

REPOSITORIES: GEO

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Profiling of bulk and ribosome associated mRNA of Arabidopsis roots upon lateral root induction upon TOR activity inhibition with AZD8055 [dataset2]

Project description:We performed targeted purification of polysomal mRNA (TRAP-Seq, Vragović et al, 2015 - http://dx.doi.org/10.1073/pnas.1417947112) using a transgenic line ubiquitously expressing a GFP-tagged RPL18 (Mustroph et al, 2009 - https://doi.org/10.1073/pnas.0906131106) 6h after the synchronous induction of lateral root formation by auxin treatment (IAA) upon inhibition of TOR activity (AZD8055 treatment, AZD). To correct for abundance of mRNA, bulk RNA-Seq was performed on the same samples and used to normalise the reads purified with the ribosomes.

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Project description:Using Western blot, we found the level of H3K27me3, but not H3K4me3, H3K9me2 and H3K36me3, was specifically reduced in the tor-es mutant. To gain a genome-wide view of the effects of TOR activity on H3K27me3 distribution, we performed quantitative chromatin immunoprecipitation with an exogenous reference genome (ChIP-Rx) followed by deep-sequencing. We find a global reduction of H3K27me3 occupancy in tor-es, whereas the H3K9me2 level was largely unaffected. These results suggest that TOR may be a specific and direct regulator of global deposition of H3K27me3. To investigate the function of TOR phosphorylation of FIE, we complemented the heterozygous fie/+ plants with GFP-FIE or the phosphorylation site mutant (SSTS/AAAA) under the control of the FIE promoter. To provide a parallel comparison with SSTS/AAAA/fie, we generated estradiol-inducible fie-amiR-es transgenic lines, that eliminated FIE protein. Quantitative ChIP-seq analyses revealed greatly reduced H3K27me3 levels across the genome in SSTS/AAAA and fie-amiR-es mutants. And transcriptome profiling by RNA-Seq was conducted to globally identify thousands of genes coordinately dysregulated in the shoots of SSTS/AAAA and fie-amiR-es plants. Furthermore, gene Ontology analysis of 986 TOR-FIE-PRC2 target genes revealed significant enrichment for transcription factors/regulators controlling a broad spectrum of developmental programs.

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2013-01-31 | GSE38878 | GEO

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