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Microarray analysis of gene expression in the Arabidopsis rlt1-1 rlt2-1 mutant

ABSTRACT: The Arabidopsis thaliana Imitation Switch (AtISWI) subfamily of ATP-dependent chromatin remodeling factors play essential roles in plant development. Here we show that the DDT domain transcription factor RINGLET (RLT) form a complex with AtISWI. RLT1 physically interacts with CHR11 in yeast cells. Single mutants rlt1-1 and rlt2-1 show no obvious developmental defects, while the rlt1-1 rlt2-1 double mutant phenocopies the AtISWI mutant chr11-1 chr17-1. In addtion, the RLT-ISWI complex selectively represses SEPALLATA, FRUITFULL and SUPPRESSOR OF OVEREXPRESSION OF CO 1, but not AGAMOUS and PISTILLATA in leaves.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE22584 | GEO | 2010/07/03

SECONDARY ACCESSION(S): PRJNA128403

REPOSITORIES: GEO

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Microarray analysis of gene expression in the Arabidopsis rlt1-1 rlt2-1 mutant

Project description:The Arabidopsis thaliana Imitation Switch (AtISWI) subfamily of ATP-dependent chromatin remodeling factors play essential roles in plant development. Here we show that the DDT domain transcription factor RINGLET (RLT) form a complex with AtISWI. RLT1 physically interacts with CHR11 in yeast cells. Single mutants rlt1-1 and rlt2-1 show no obvious developmental defects, while the rlt1-1 rlt2-1 double mutant phenocopies the AtISWI mutant chr11-1 chr17-1. In addtion, the RLT-ISWI complex selectively represses SEPALLATA, FRUITFULL and SUPPRESSOR OF OVEREXPRESSION OF CO 1, but not AGAMOUS and PISTILLATA in leaves. Leaves from 15-day-old seedlings of wild-type Col-0 and rlt1-1 rlt2-1 were used for RNA preparation.In the experiment data,3a3b refers to rlt1-1 rlt2-1.

2010-07-29 | E-GEOD-22584 | biostudies-arrayexpress

Micro-array analysis of gene expression in the Arabidopsis chr11-1 chr17-1 mutant

Project description:Chromatin remodeling factors of the Imitation Switch (ISWI) family play important roles in epigenetic regulations of gene expression in yeast and animals, whereas their function in plants remains elusive. Here we report characterization of the Arabidopsis ISWI genes CHR11 and CHR17. Double mutant chr11 chr17 displayed a dramatically reduced plant size with early flowering. In addition, epidermis of the double mutant leaves showed cell characteristics seen only in floral organs. These phenotypes resemble, at least partially, those of the Polycomb mutants curly leaf (clf) and like heterochromatin protein1 (lhp1). Microarray analysis revealed that a number of targets of the Polycomb pathway were derepressed in chr11 chr17 leaves. Furthermore, triple mutants combining chr11 chr17 with clf-29 or lhp1-6 both greatly enhanced clf-29 and lhp1-6 phenotypes, respectively. All these results strongly suggest that the ISWI family genes in Arabidopsis may function in gene silencing via the Polycomb pathway Leaves from 15-day-old seedlings of wild-type Col-0 and chr11-1 chr17-1 were used for RNA preparation.In the experiment data,A refers to Col-0, and B refers to chr11-1 chr17-1.

2010-06-23 | E-GEOD-22159 | biostudies-arrayexpress

Micro-array analysis of gene expression in the Arabidopsis chr11-1 chr17-1 mutant

2010-06-11 | GSE22159 | GEO

MNase-seq analysis of Col-0 and chr11-1 chr17-1

Project description:Chromatin has a highly organized structure with the repeating nucleosome subunits. The position of nucleosomes on the chromatin is dynamically regulated by ATP-dependent chromatin remodeling factors (remodelers), therefore providing specific epigenetic information. However, the in vivo nucleosome distribution pattern in plants and how plant remodelers control the pattern formation are not yet clear. Here we use the Micrococcal Nuclease digestion followed by deep sequencing (MNase-seq) assay to show the genome-wide nucleosome pattern in plants and the role of the Arabidopsis thaliana Imitation Switch (AtISWI) subfamily remodelers in the pattern formation. Our data revealed three patterns in wild-type plants: 1) Promoters have a relative low nucleosome density compared with gene bodies; 2) Nucleosome density is negatively associated with gene expression levels; 3) The evenly and periodically spaced nucleosomes in gene bodies are positively associated with gene expression levels. Double mutations in the AtISWI genes CHROMATIN REMODELING 11 (CHR11) and CHR17 resulted in loss of the evenly-spaced-nucleosome pattern in gene bodies, but did not affect nucleosome density, suggesting that the primary role of AtISWI is to slide nucleosomes in gene bodies for promotion of transcription. The overall design of the experiment: (1) Nuclear extraction from Col-0 and chr11-1 chr17-1. (2) MNase treatment. (3) DNA purification. (4) Library construction. (5) Deep sequencing. (6) Data analysis.

2014-03-30 | E-GEOD-50242 | biostudies-arrayexpress

mutants versus wt - Transcriptome analysis of mutants impaired in post-transcriptional gene silencing (PTGS)

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2011-01-08 | E-GEOD-26413 | biostudies-arrayexpress

mutants versus wt - Transcriptome analysis of mutants impaired in post-transcriptional gene silencing (PTGS)

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ChIP-Chip tiling array for H3k27ac in mouse MV+ (lens epithelium) and RAG cells ( renal adenocarcinoma) over panel of genes including Pax6, Sox2, Otx2, Sox9.

Project description:Enhancer identification using H3k27ac ChIP-ChIP in mouse MV+ and RAG, using custom tilling array covering a 66 Mb region around Pax6 (Chr2:75,000,000-141,000,000) mm9. Additional loci and regions, Sox2 (chr3:32,000,000-37,000,000), Otx2 (chr14:48,500,000-50,500,000), Rax (chr18:65,500,000-68,000,000), Hba a-globin (chr11:32,050,000-32,450,000), Six3 (chr17:85,200,000-86,700,000), Sox1 (chr8:11,800,000-12,800,000), Mab21L2 (chr3:85,850,000-86,850,000), Bmp4 (chr14:46,500,000-47,500,000), NeuroD1 (chr2:79,050,000-79,600,000), Prox1 (chr1:191,700,000-192,700,000), Hmx1 (chr5:34,700,000-36,200,000), H19-Igf2 (chr7:149500000-150500000), Sox9 (chr11:110000000-116000000).

2018-10-18 | GSE119659 | GEO

ChIP-Chip tiling array for H3k27ac in mouse β-TC3 cells over panel of genes including Pax6, Sox2, Otx2, Sox9.

Project description:Enhancer identification using H3k27ac ChIP-ChIP in mouse β-TC3 cells, using custom tilling array covering a 66 Mb region around Pax6 (Chr2:75,000,000-141,000,000) mm9. Additional loci and regions, Sox2 (chr3:32,000,000-37,000,000), Otx2 (chr14:48,500,000-50,500,000), Rax (chr18:65,500,000-68,000,000), Hba a-globin (chr11:32,050,000-32,450,000), Six3 (chr17:85,200,000-86,700,000), Sox1 (chr8:11,800,000-12,800,000), Mab21L2 (chr3:85,850,000-86,850,000), Bmp4 (chr14:46,500,000-47,500,000), NeuroD1 (chr2:79,050,000-79,600,000), Prox1 (chr1:191,700,000-192,700,000), Hmx1 (chr5:34,700,000-36,200,000), H19-Igf2 (chr7:149500000-150500000), Sox9 (chr11:110000000-116000000).

2018-08-01 | GSE116805 | GEO

Arabidopsis thaliana

Project description:MNase-seq analysis of Col-0 and chr11-1 chr17-1

| PRJNA217328 | ENA

Gene expression profiling of Arabidopsis floral homeotic mutants

Project description:The gene expression profiles of inflorescences of the floral homeotic mutants apetala1, apetala2, apetala3, pistillata, and agamous were compared to wild-type inflorescences using a flower-specific cDNA array (GSM21001-21015) and a "whole-genome" oligonucleotide array (Operon) (GSM21016-21035). All experiments were performed at least in triplicate. This SuperSeries is composed of the SubSeries listed below.

2004-05-02 | GSE1275 | GEO

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