Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptomic analysis of regulatory gene expression profiles by NF-YCs, and RGL2 under paclobutrazol (PAC) condition

ABSTRACT: To understand how the NF-YC-RGL2 complex functions in repressing seed germination, a genome-wide transcriptomic analysis was carried out using germinating seeds of rgl2, nf-ycT and the wild-type (Col) grown on the medium containing 5 uM PAC and Col grown on mock treatment. Basing on the criteria of 1.5-fold cutoff for the genes with 5% false discovery rate, we first identified the differentially expressed genes in Col_PAC vs Col_mock, nf-ycT_PAC vs Col_PAC, and rgl2_PAC vs Col_PAC subsets, which are referred to as PAC-, NF-YC-, and RGL2-regulated genes.These data reveal that NF-YCs and RGL2 co-target a set of common genes in response to phytohormone signals, strongly supporting the role of NF-YC-RGL2 in seed germination regulation. Digital gene expression tag profiles of wild type (Col), nf-ycT mutant, and rgl2 mutant germinating seed for 12 h after stratification were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Xu Liu

PROVIDER: E-GEOD-84753 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The NF-YC-RGL2 module integrates GA and ABA signalling to regulate seed germination in Arabidopsis.

Liu Xu X Hu Pengwei P Huang Mingkun M Tang Yang Y Li Yuge Y Li Ling L Hou Xingliang X

Nature communications 20160914

The antagonistic crosstalk between gibberellic acid (GA) and abscisic acid (ABA) plays a pivotal role in the modulation of seed germination. However, the molecular mechanism of such phytohormone interaction remains largely elusive. Here we show that three Arabidopsis NUCLEAR FACTOR-Y C (NF-YC) homologues NF-YC3, NF-YC4 and NF-YC9 redundantly modulate GA- and ABA-mediated seed germination. These NF-YCs interact with the DELLA protein RGL2, a key repressor of GA signalling. The NF-YC-RGL2 module t ...[more]

PMID: 27624486

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Project description:In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development. In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development. Three biological replicates for 4-d-old seedlings grown under dark or red-light and long-day (0.5 ?mole m-2 sec-1) contitions.

Dataset Information

Transcriptomic analysis of regulatory gene expression profiles by NF-YCs, and RGL2 under paclobutrazol (PAC) condition

Publications

The NF-YC-RGL2 module integrates GA and ABA signalling to regulate seed germination in Arabidopsis.

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