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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE26413 | GEO | 2011/01/08

SECONDARY ACCESSION(S): PRJNA136877

REPOSITORIES: GEO

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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

Transcriptome analysis of two mutants rdr6/sgs2 and sgs3 impaired in post-transcriptional gene silencing (PTGS)

Project description:Identification of new genes regulated by RDR6 and SGS3 (two genes involved in PTGS) by analysis of the transcriptome of rdr6-1 and sgs3-1 mutants compared to wild-type plants in different tissues (flower and leaves). The comparison between transcriptome of rdr6-1 and sgs3-1 mutant alleles impaired in PTGS and development (juvenile-to-adult transition) and transcriptome of rdr6-5 and sgs3-3 alleles impaired only in PTGS would allowed identification of genes involved in the developmental default (zip phenotype) of the null alleles (rdr6-1 and sgs3-1 mutants). - Transcriptome of rdr6 and sgs3 mutants will be compared to the transcriptome of wild-type plants in flower and leaves. Further-more the comparison between transcriptome of rdr6-1 and sgs3-1 mutant alleles impaired in PTGS and development (juvenile-to-adult transition) and transcriptome of rdr6-5 and sgs3-3 alleles impaired only in PTGS will be done for flowers and leaves. Keywords: gene knock in (transgenic)

2007-05-31 | GSE7936 | GEO

Transcription profiling of two Arabidopsis mutants rdr6-sgs2 and sgs3 impaired in PTGS

2006-08-01 | E-MEXP-531 | 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

rnapaths--3_02/2012-RNAPATHS-3

Project description:blanc-08-01_2012_01_rnapaths_03 - rnapaths--3_02/2012 - Identify the transcript overlap and specificity between the PTGS and decapping/exoribonuclease pathways b identifying transcripts that are significantly changed in double mutants versus single mutants, and transcripts that are commonly changed among the single and double mutants compared to WT. - Identify transcripts that are significantly changed in double mutants (L1 vcs sgs2) (xrn4-5/sgs3-11) versus their respective single mutants (L1 vcs and L1 sgs2) (xrn4-5 and sgs3-11) , and identify transcripts that are changed among the single and double mutants compared to WT (Col) reference or to mutant L1 reference.

2012-07-13 | GSE38903 | GEO

rnapaths--3_02/2012-RNAPATHS-3

2012-07-12 | E-GEOD-38903 | biostudies-arrayexpress

Genetic interactions between SUPPRESSOR OF GENE SILENCING3 and ABSCISIC ACID HYPERSENSITIVE1/CAP-BINDING PROTEIN80 affecting fertilization, embryogenesis, germination, flowering time, and powdery mildew resistance

Project description:Arabidopsis ABA HYPERSENSITIVE1 (ABH1) / CAP-BINDING-PROTEIN80 functions in cap-binding, splicing, ABA and stress response signaling and in the biogenesis of microRNAs (miRNAs). SUPPRESSOR OF GENE SILENCING3 (SGS3) plays a crucial role in post transcriptional gene silencing (PTGS). We show that abh1 sgs3 double mutant manifests pleiotropic phenotypes including altered ABA sensitivity in seed germination, fused cotyledons, delayed growth in root initiation and leaf production, accelerated juvenile-to-adult phase transition and flowering time, short and bent siliques with ectopic carpelloid tissues, reduced seed set due to altered carpel structure and pollen tube growth, and increased resistance to powdery mildew infection. A systems approach using meta-analysis of whole genome tiling microarray datasets for mutants of PTGS, RNA processing, and responses to environmental stress was taken to design a 135k feature custom microarray to probe the molecular bases of these phenotypes. Results confirmed documented effects of ABA or abh1 on precursor MIRNA expression (pre-MIR159, pre-MIR168) and identified novel miRNAs and their targets regulated by ABA (pre-MIR408, LACCASE12 and -13; pre-MIR824) or elevated in abh1 sgs3 double mutant (pre-MIR156A,C; pre-MIR164B, pre-MIR167A, pre-MIR408, At5g15845/CONSTANS-LIKE1-cis-NAT-RNA). miR156 targets SQUAMOSA-PROMOTER-BINDING-PROTEIN-LIKE genes that spawn siRNAs and control phase change; miR164 targets CUP-SHAPED-COTYLEDON1 and -2 genes; miR166 methylates target PHABULOSA genomic DNA in trans; miR167 targets AUXIN RESPONSE FACTOR 6 (ARF6) and ARF8 which regulate both female and male reproduction; miR408 targets a plantacyanin which is expressed predominantly in the transmitting tract of the pistil and affects pollen tube guidance on the stigma. We also identified sgs3 by ABA interactions on gene expression which reveal potential nodes in regulatory networks linking ABA, mRNA processing and PTGS with development.

2014-11-19 | GSE42796 | GEO

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

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

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

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