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

ABSTRACT: 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)

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE7936 | GEO | 2007/05/31

SECONDARY ACCESSION(S): PRJNA100103

REPOSITORIES: GEO

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

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

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

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

2011-01-08 | GSE26413 | GEO

Arabidopsis thaliana

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

| PRJNA100103 | ENA

Analysis of the RDR6-dependent small RNA profile in ein5 ski2 in Arabidopsis

Project description:Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3’-5’ mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5’-3’ exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). A number of endogenous genes, including many miRNA target genes, manifest transitive 21-22 nt siRNA production and compromised gene expression in ein5 ski2 in an RDR6-dependent manner. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5’-3’ and 3’-5’ cytoplasmic mRNA decay pathways.

2016-11-15 | GSE52408 | GEO

Analysis of the RDR6-dependent small RNA profile in ein5 ski2 in Arabidopsis with biological replications and increased sequencing depth

Project description:Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3 -5 mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5 -3 exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). A number of endogenous genes, including many miRNA target genes, manifest transitive 21-22 nt siRNA production and compromised gene expression in ein5 ski2 in an RDR6-dependent manner. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5 -3 and 3 -5 cytoplasmic mRNA decay pathways. In this experiment, we did three replicates in sequencing that help increase the power in identify the differentially represented genes.The sequencing depth was also increased. Therefore we identified more siRNA-generating loci than that in previous study (GSE52408) (441 vs. 200 loci).

2015-04-13 | GSE57936 | GEO

Analysis of the RDR6-dependent small RNA profile in ein5 ski2 in Arabidopsis with biological replications and increased sequencing depth

Project description:Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3 -5 mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5 -3 exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). A number of endogenous genes, including many miRNA target genes, manifest transitive 21-22 nt siRNA production and compromised gene expression in ein5 ski2 in an RDR6-dependent manner. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5 -3 and 3 -5 cytoplasmic mRNA decay pathways. In this experiment, we did three replicates in sequencing that help increase the power in identify the differentially represented genes.The sequencing depth was also increased. Therefore we identified more siRNA-generating loci than that in previous study (GSE52408) (441 vs. 200 loci). Examination of small RNA profiles in 4 genotypes with 3 biological replicates each.

2015-04-13 | E-GEOD-57936 | biostudies-arrayexpress

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

In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs

Project description:Background: Cytoplasmic degradation of endogenous RNAs is an integral part of RNA quality control (RQC) and often relies on the removal of the 5' cap structure and their subsequent 5M-bM-^@M-^Y to 3M-bM-^@M-^Y degradation. In parallel, many eukaryotes degrade exogenous and selected endogenous RNAs through post-transcriptional gene silencing (PTGS). In plants, PTGS depends on small interfering (si)RNAs produced after the conversion of single-stranded RNAs to double-stranded RNAs by the cellular RNA DEPENDENT RNA POLYMERASE 6 (RDR6). PTGS and RQC compete for transgene-derived RNAs, but it is unknown whether this competition also occurs for endogenous transcripts. Results: We show that that upon decapping impairment hundreds of endogenous mRNAs give rise to a new class of siRNAs, a subset of which depends on RDR6 for their production. Conclusions: Our results suggest that the decapping of aberrant endogenous RNA in P-bodies limits their entry into the PTGS pathway and prevents the subsequent deleterious consequences arising from this entry. We anticipate that the siRNAs identified in decapping mutants represent a subset of a larger ensemble of endogenous siRNAs that we coin rqc-siRNAs because they accumulate when RQC processes are impaired. Small RNA-seq experiments performed in duplicates for each condition.

2015-01-21 | E-GEOD-65056 | biostudies-arrayexpress

rnapaths--3_02/2012-RNAPATHS-3

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

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