Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of Arabidopsis arf2 and wild type dark grown seedlings treated with brassinazole

ABSTRACT: While the close relationship between BRs and auxin has been widely reported, the molecular mechanism for combinatorial control of shared target genes has remained elusive. In this work, we demonstrate that BRs synergistically increase seedling sensitivity to auxin and show that combined treatment with both hormones can increase the magnitude and duration of gene expression. arf2 mutants are less sensitive to changes in endogenous BR levels, while a large number of genes affected in an arf2 background are returned to near wild-type levels by altering BR biosynthesis. Together, these data suggest a model where BIN2 increases expression of auxin-induced genes by directly inactivating repressor ARFs, leading to synergistic increases in transcription. Experiment Overall Design: Total RNA was extracted from 4-day-old, etiolated Arabidopsis seedlings grown on 0.5 ÂµM BRZ or mock treatments and used to probe ATH1 microarrays (Affymetrix), according to manufacturerâ??s protocols. There are three independent biological replicates for each genotype and treatment, except for arf2 mutants with BRZ where only two arrays passed quality control. We performed standard Affymetrix quality-control procedures using the BioConductor packages simpleaffy. Expression was normalized and estimated using the gcRMA package of BioConductor.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Jennifer Nemhauser

PROVIDER: E-GEOD-11216 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Integration of auxin and brassinosteroid pathways by Auxin Response Factor 2.

Vert Grégory G Walcher Cristina L CL Chory Joanne J Nemhauser Jennifer L JL

Proceedings of the National Academy of Sciences of the United States of America 20080703 28

Plant form is shaped by a complex network of intrinsic and extrinsic signals. Light-directed growth of seedlings (photomorphogenesis) depends on the coordination of several hormone signals, including brassinosteroids (BRs) and auxin. Although the close relationship between BRs and auxin has been widely reported, the molecular mechanism for combinatorial control of shared target genes has remained elusive. Here we demonstrate that BRs synergistically increase seedling sensitivity to auxin and sho ...[more]

PMID: 18599455

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Project description:Brassinosteroids (BRs) are a class of class of phytohormones with important roles in regulating physiological and developmental processes. Small RNAs, including small interfering RNAs and microRNAs (miRNAs), are non-protein coding RNAs that regulate gene expression at the transcriptional and post-transcriptional levels. However, the roles of small RNAs in BR response have not been studied well. In this study, we aimed to identify BR-responsive small RNA clusters and miRNAs in Arabidopsis. In addition, the effect of BR-responsive small RNAs on their transcripts and target genes were examined. Small RNA libraries were constructed from control and epibrassinolide-treated seedlings. After sequencing the small RNA libraries, differentially expressed small RNA clusters were identified by examining the expression levels of small RNAs in 100-nt bins of Arabidopsis genome. To identify the BR-responsive miRNAs, the expression levels of all the annotated mature miRNAs, registered in miRBase, were analyzed. Previously published RNA-seq data were utilized to monitor the BR-responsive expression patterns of differentially expressed small RNA clusters and miRNA target genes. In results, 38 BR-responsive small RNA clusters, including 30 down-regulated and eight up-regulated clusters, were identified. These differentially expressed small RNA clusters were from miRNA loci, transposons, protein-coding genes, pseudo genes and others. Of these, a transgene, BRI1, accumulates small RNAs, which are not found in the wild type. Small RNAs in this transgene are up-regulated by BRs while BRI1 mRNA is down-regulated by BRs. By analyzing the expression patterns of mature miRNAs, we have identified BR-repressed miR398a-5p and BR-induced miR156g. Although miR398a-5p is down-regulated by BRs, its predicted targets were not responsive to BRs. However, SPL3, a target of BR-inducible miR156g, is down-regulated by BRs. BR-responsive small RNAs and miRNAs identified in this study will provide an insight into the role of small RNAs in BR responses in plants. Especially, we suggest that miR156g/SPL3 module might play a role in BR-mediated growth and development in Arabidopsis.

Dataset Information

Transcription profiling of Arabidopsis arf2 and wild type dark grown seedlings treated with brassinazole

Publications

Integration of auxin and brassinosteroid pathways by Auxin Response Factor 2.

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