Transcriptomics

Dataset Information

62

Genome-wide identification of mis-spliced/intron-retained transcripts in Arabidopsis thaliana rcf1-1 mutant plants under cold stress as determined by tiling array analysis.


ABSTRACT: Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regulators of CBF genes. We used whole genome tiling array analysis under cold stress to identify transcripts which are mis-spliced/intron-retained in rcf1-1. Fourteen-day-old wild type and rcf1-1 seedlings grown on MS agar medium (1x MS salts, 2% sucrose, 0.6% agar, pH 5.7) were subjected to cold stress at 4°C for 12 h. Total RNA was extracted with Trizol reagent (Invitrogen) and synthesized into double-stranded DNA that was hybridized to whole genome tiling arrays (Affymetrix Arabidopsis Tiling1.0R). All hybridizations were performed with 3 biological replicates.

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Jianhua Zhu   Renyi Liu  Changhua Jiang  Chenglin Chai  Qingmei Guan  Yanyan Zhang  Jianmin Wu  Jianhua Zhu 

PROVIDER: E-GEOD-41378 | ArrayExpress | 2013-02-25

SECONDARY ACCESSION(S): GSE41378PRJNA176718

REPOSITORIES: GEO, ArrayExpress

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Publications

A DEAD box RNA helicase is critical for pre-mRNA splicing, cold-responsive gene regulation, and cold tolerance in Arabidopsis.

Guan Qingmei Q   Guan Qingmei Q   Wu Jianmin J   Zhang Yanyan Y   Jiang Changhua C   Liu Renyi R   Chai Chenglin C   Zhu Jianhua J  

The Plant cell 20130131 1


Cold stress resulting from chilling and freezing temperatures substantially reduces crop production worldwide. To identify genes critical for cold tolerance in plants, we screened Arabidopsis thaliana mutants for deregulated expression of a firefly luciferase reporter gene under the control of the C-REPEAT BINDING FACTOR2 (CBF2) promoter (CBF2:LUC). A regulator of CBF gene expression1 (rcf1-1) mutant that is hypersensitive to cold stress was chosen for in-depth characterization. RCF1 encodes a c  ...[more]

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