Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Identification of RVE8 target genes

ABSTRACT: The goal of this study is to identify the targets of RVE8, a MYB-like transcription factor involved in the circadian clock in Arabidopsis. Analysis of 7 days old rve8-1 RVE8::RVE8:GR and rve8-1 seedlings treated with dexamethasone or mock identified genes responsive to RVE8 induction.The RVE8 up-regulated genes are enriched for evening-phased genes while the down-regulated genes are enriched for a morning phase. This study reveals that RVE8 is a master regulator of circadian gene expression in Arabidopsis. Transgenic line rve8-1 RVE8::RVE8:GR and rve8-1 treated with DEX or mock with three biological replicates each, 12 samples in total.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Polly Hsu

PROVIDER: E-GEOD-38879 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Accurate timekeeping is controlled by a cycling activator in Arabidopsis.

Hsu Polly Yingshan PY Devisetty Upendra K UK Harmer Stacey L SL

eLife 20130430

Transcriptional feedback loops are key to circadian clock function in many organisms. Current models of the Arabidopsis circadian network consist of several coupled feedback loops composed almost exclusively of transcriptional repressors. Indeed, a central regulatory mechanism is the repression of evening-phased clock genes via the binding of morning-phased Myb-like repressors to evening element (EE) promoter motifs. We now demonstrate that a related Myb-like protein, REVEILLE8 (RVE8), is a dire ...[more]

PMID: 23638299

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Project description:Small RNAs (sRNAs) are hypothesized to contribute to hybrid vigor because they maintain genome integrity, contribute to genetic diversity, and control gene expression. We used Illumina sequencing to assess how sRNA populations vary between two maize inbred lines (B73, Mo17) and their hybrid. We sampled sRNAs from the seedling shoot apex and the developing ear, two rapidly growing tissues that program the greater growth of maize hybrids. We found that parental differences in siRNAs primarily originate from repeat regions. Although the maize genome contains greater number and complexity of repeats compared to Arabidopsis or rice, we confirmed that like these simpler plant genomes, 24-nt siRNAs whose abundance differs between maize parents also show a trend of downregulation following hybridization. Surprisingly, hybrid vigor is fully maintained when 24-nt siRNAs are globally reduced by mutation of the RNA-dependent RNA polymerase2 (RDR2) encoded by modifier of paramutation1 (mop1). We also discovered that 21-22nt siRNAs derived from a number of distinct retrotransposon families differentially accumulate between B73 and Mo17 as well as their hybrid. Thus, maize possesses a novel source of genetic variation for regulating both transposons and genes at a genomic scale, which may contribute to its high degree of observed heterosis. sRNA libraries were derived from RNA isolated from the seedling shoot apex and developing ear tissues from B73, Mo17, B73xMo17 and Mo17xB73. The shoot apex was chosen because it is enriched for meristematic tissue where cell proliferation occurs, rates of organ initiation are determined, and organ size is specified. The developing ear was examined because it is enriched in meristematic tissue and is undergoing rapid growth, and also because the mature ear shows the highest degree of heterosis. Total RNA was isolated and separated on a 15% TBE-Urea polyacrylamide gel. Using a 10-bp ladder, the sRNA fraction representing 10-40-bp was excised. sRNA libraries were prepared according to Lu et al. (2007) or manufacturer's instructitions (Illumina). A combination of Perl scripts and FASTX toolkit scripts were used to remove adapters, collapse identical sequences and count reads per sequence. Supplementary processed data text files contain the distinct sRNA sequences for all of the genotypes analyzed in that experiment. Abundance (reads per million) was calculated for each distinct sequence by dividing the number of reads of distinct sRNA in a library by the total number of sRNA reads for that library and multiplying this by 1 million. Genome builds: B73 genome, maizesequence.org release 4a.53 (October, 2009); Mo17 whole genome shotgun clones.

Dataset Information

Identification of RVE8 target genes

Publications

Accurate timekeeping is controlled by a cycling activator in Arabidopsis.

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