Dataset Information

Transcription profiling by array of serrate-1 mutant Arabidopsis seedlings

ABSTRACT: microRNAs function as sequence-specific guides to regulate genes by post-transcriptional gene silencing. Many miRNAs are involved in the control plant development by regulating the accumulation of transcripts encoding transcription factors. This causes pleiotropic developmental phenotypes of mutants defective in miRNA accumulation, such as dcl1, hen1, hyl1 and ago1. The serrate-1 (se-1) mutant of Arabidopsis also exhibits a highly pleiotropic phenotype which overlaps with phenotypes of mutants defective in miRNA accumulation. It has been proposed that SE functions specifically in miRNA-mediated repression of the leaf polarity genes PHABULOSA and PHAVOLUTA. Microarray analysis of transcript levels in se-1 compared to wild-type however revealed upregulation of many genes known to be targets of miRNA regulation. We show that SE is a general regulator of miRNA levels probably controlling processing of pri-miRNA to miRNA.

REANALYSIS of: E-MEXP-838

ORGANISM(S): Arabidopsis thaliana

PROVIDER: E-MEXP-838 | ExpressionAtlas | 2015-11-17

REPOSITORIES: ExpressionAtlas

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Dataset's files

Source:

			Action	DRS
	E-MEXP-838-analysis-methods.tsv	Tabular
	E-MEXP-838-atlasExperimentSummary.Rdata	Rdata
	E-MEXP-838-configuration.xml	Xml
	E-MEXP-838-percentile-ranks.tsv	Tabular
	E-MEXP-838.condensed-sdrf.tsv	Tabular

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Publications

SERRATE: a new player on the plant microRNA scene.

Lobbes Dajana D Rallapalli Ghanasyam G Schmidt Dominik D DD Martin Cathie C Clarke Jonathan J

EMBO reports 20060915 10

MicroRNAs (miRNAs) function as sequence-specific guides that control gene expression by post-transcriptional gene silencing. Many miRNAs influence plant development by regulating the accumulation of transcripts that encode transcription factors. Mutants defective in miRNA accumulation, such as dcl1, hen1, hyl1 and ago1, have pleiotropic developmental phenotypes. The serrate-1 (se-1) mutant of Arabidopsis also shows a highly pleiotropic phenotype, which overlaps with the phenotypes of mutants def ...[more]

PMID: 16977334

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Project description:Several genes encoding transcription factors (TFs) were indicated to have a key role in the induction of somatic embryogenesis (SE), which is triggered in the somatic cells of plants. In order to further explore the genetic regulatory network that is involved in the embryogenic transition induced in plant somatic cells, micro-RNA (miRNAs) molecules, the products of MIRNA (MIR) genes and the common regulators of TF transcripts, were analyzed in an embryogenic culture of Arabidopsis thaliana. In total, the expression of 190 genes of the 114 MIRNA families was monitored during SE induction and the levels of the primary (pri-miRNAs) transcripts vs. the mature miRNAs were investigated. The results revealed that the majority (98%) of the MIR genes were active and that most of them (64%) were differentially expressed during SE. A distinct attribute of the MIR expression in SE was the strong repression of MIR transcripts at the early stage of SE followed by their significant up-regulation in the advanced stage of SE. Comparison of the mature miRNAs vs. pri-miRNAs suggested that the extensive post-transcriptional regulation of miRNA is associated with SE induction. Candidate miRNA molecules of the assumed function in the embryogenic response were identified among the mature miRNAs that had a differential expression in SE, including miR156, miR157, miR159, miR160, miR164, miR166, miR169, miR319, miR390, miR393, miR396, and miR398. Consistent with the central role of phytohormones and stress factors in SE induction, the functions of the candidate miRNAs were annotated to phytohormone and stress responses. To confirm the functions of the candidate miRNAs in SE, the expression patterns of the mature miRNAs and their presumed targets were compared and regulatory relation during SE was indicated for most of the analyzed miRNA-target pairs. The results of the study contribute to the refinement of the miRNA-controlled regulatory pathways that operate during embryogenic induction in plants and provide a valuable platform for the identification of the genes that are targeted by the candidate miRNAs in SE induction.