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

ABSTRACT: 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

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE22159 | GEO | 2010/06/11

SECONDARY ACCESSION(S): PRJNA127723

REPOSITORIES: GEO

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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

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.

2010-07-03 | GSE22584 | GEO

Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements

Project description:Polycomb Group Proteins (PcGs) is critical in defining the epigeneticÂ blueprintÂ for animal and plant development. In plants, loss of different PcGs display both common and unique phenotypic defects, yet little is known about how these are established. Here, based on quantitative comparison of epigenomics data from mutants of key PcG components in Arabidopsis seedlings, we found that the PcG partners of CURLY LEAF (CLF), one of the major plant H3K27 trimethyltransferases, determines its selectivity in repressing gene loci involved in distinct developmental programs. The non-redundant role of CLF in determining flower development is specifically associated with HETEROCHROMATIN PROTEIN1 (LHP1). This context dependent effect of CLF corresponds well with tissue-biased target gene expression, and importantly, to differential co-occupancy of transcription factors, such as MADS box and B3-domain transcription factors. These results provide valuable insight as to the dynamic interplay between different PcGs and their collaborative control of plant development. To compare the effect of different PcGs on epigenetic structure from the genome-wide scale, we used chromatin immunoprecipitation followed by high-throughtput sequencing (ChIP-seq) to characterize the genome-wide binding profile of H3K27me3 in Col, clf-29, tfl2-2, atbmi1a/b and atring1a/b ; To investigate the functional consequence of the distinct H3K27me3 profile controlled by different combinations of PcGs, we characterized the transcriptome change in PcG mutants, including Col, clf-29, tfl2-2, lhp1-6, atbmi1a/b, atring1a/b, and clf29swn21.

2016-01-19 | E-GEOD-67322 | biostudies-arrayexpress

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

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

RNA-seq of Arabidopsis thalianal Col-0 wild type and clf-29 lhp1-4 mutant root

Project description:RNA-seq was performed in order to identify qualitative variation of transcripts in clf-29 lhp1-4 compared to WT, including SNPS, indels, splicing fidelity

2022-09-19 | E-MTAB-11263 | biostudies-arrayexpress

Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements

Project description:Polycomb Group Proteins (PcGs) is critical in defining the epigenetic blueprint for animal and plant development. In plants, loss of different PcGs display both common and unique phenotypic defects, yet little is known about how these are established. Here, based on quantitative comparison of epigenomics data from mutants of key PcG components in Arabidopsis seedlings, we found that the PcG partners of CURLY LEAF (CLF), one of the major plant H3K27 trimethyltransferases, determines its selectivity in repressing gene loci involved in distinct developmental programs. The non-redundant role of CLF in determining flower development is specifically associated with HETEROCHROMATIN PROTEIN1 (LHP1). This context dependent effect of CLF corresponds well with tissue-biased target gene expression, and importantly, to differential co-occupancy of transcription factors, such as MADS box and B3-domain transcription factors. These results provide valuable insight as to the dynamic interplay between different PcGs and their collaborative control of plant development.

2016-01-19 | GSE67322 | GEO

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

Project description:ra09-03_sgs - mutants versus wt - Identification of new genes regulated by SGS1 and SGS6/UBP5 (two genes involved in PTGS) by analysis of the transcriptomes of sgs1 and sgs6 mutants compared to wild-type plants in the shoots of seedlings. The comparison between the transcriptomes of sgs3, chr11, chr17 simple mutants impaired differently in PTGS and development (juvenile-to-adult transition and bolting), and the transcriptomes of the sgs3 chr11, sgs3 chr17 double mutants showed additive effects on development (juvenile-to-adult transition and bolting), which allows a better understanding of the genetic link existing between SGS3 and its potential partners, CHR11 (which interacts with SGS3 in a two-hybrid assay and BiFC) and CHR17, 2 homologous proteins of the SWI/SNF2 family. Transcriptome comparison between mutants and wild-type plants L1 in the shoots of seedlings. 14 dye-swaps - gene knock-in (transgenic).

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

Gene expression in clf and lhp1

Project description:Transcriptome changes in leaves of PcG protein mutants clf and lhp1. Fully expanded rosette leaf 6 was collected from 10 35-d-old plants grown in short day photoperiods.

2013-08-22 | E-MTAB-1412 | biostudies-arrayexpress

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

2011-01-08 | GSE26413 | GEO

Genome-wide small RNA abundance measured by small RNA-sequencing of Arabidopsis WT and Polycomb-group mutant clf-29 lhp1-4 under low nitrate provision

Project description:We analyzed here the genome-wide small RNAs expression changes in roots of WT and clf-29 lhp1-4 mutant. Plants were grown hydroponically under low nitrate provision (0.3 mM KNO3) and short-days conditions, and roots were collected after 5 weeks of growth.

2022-09-01 | E-MTAB-9793 | biostudies-arrayexpress

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