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Arabis alpina

ABSTRACT: Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species

PROVIDER: PRJNA352782 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5004110_1.fastq.gz	Fastqsanger.gz
	SRR5004110_2.fastq.gz	Fastqsanger.gz
	SRR5004120_1.fastq.gz	Fastqsanger.gz
	SRR5004120_2.fastq.gz	Fastqsanger.gz
	SRR5004111_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species.

Project description:Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species.

| PRJNA353651 | ENA

Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species.

Project description:Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found the BSs that were conserved in both species, and that these contained a CArG-box that is recognised by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared to the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated genes (COR) were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared to wild-type and this correlated with reduced growth in pep1-1. Therefore FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.

2018-01-01 | GSE89889 | GEO

Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species

Project description:Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found that only 17% of their BSs were conserved in both species and that these contained a CArG-box that is recognised by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared to the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated genes (COR) were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared to wild-type and this correlated with reduced growth in pep1-1. Therefore FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.

2018-01-01 | GSE89638 | GEO

The Arabis alpina APETALA2 orthologue delays flowering by repressing floral meristem identity genes during vernalization

Project description:PEP2 regulates flowering in response to vernalization in a PEP1 -dependent and PEP1-independent pathway

2019-02-27 | GSE117977 | GEO

Analysis of TTG1 function in Arabis alpina.

Project description:BACKGROUND: In Arabidopsis thaliana (A. thaliana) the WD40 protein TRANSPARENT TESTA GLABRA1 (TTG1) controls five traits relevant for the adaptation of plants to environmental changes including the production of proanthocyanidin, anthocyanidin, seed coat mucilage, trichomes and root hairs. The analysis of different Brassicaceae species suggests that the function of TTG1 is conserved within the family. RESULTS: In this work, we studied the function of TTG1 in Arabis alpina (A. alpina). A comparison of wild type and two Aattg1 alleles revealed that AaTTG1 is involved in the regulation of all five traits. A detailed analysis of the five traits showed striking phenotypic differences between A. alpina and A. thaliana such that trichome formation occurs also at later stages of leaf development and that root hairs form at non-root hair positions. CONCLUSIONS: The evolutionary conservation of the regulation of the five traits by TTG1 on the one hand and the striking phenotypic differences make A. alpina a very interesting genetic model system to study the evolution of TTG1-dependent gene regulatory networks at a functional level.

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Arabis alpina

Project description:Genome-wide profiling of H3K4me3, H3K27me3 H3K27me1 and 5mC enrichment and mRNA levels in young leaves of Arabis alpina

| PRJNA237036 | ENA

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Project description:Whole-genome resequencing of Arabis alpina populations from Swiss Alps.