Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA132827 | ENA |
REPOSITORIES: ENA
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Project description:The Arabidopsis RNA-binding proteins FCA and FPA were initially identified based on their suppression of the flowering time regulator FLC. Recently, however, they have been found to influence expression of a wide range of targets in the Arabidopsis genome. Here, we use whole-genome tiling arrays to determine the extent of their targets at two stages of seedling development. A wide range of genes and transposable elements were mis-expressed in the fcafpa double mutant with a significant bias for mis-regulated genomic segments mapping to the 3’ region of genes. A large number of previously unannotated (UA) genomic segments, which mapped to intergenic regions, were also mis-expressed in the fcafpa double mutant. We characterized a subset of these UA segments in detail and established them as strand-specific and direct targets of FCA and FPA, with a complex interplay between their functions. Only a few of the UA segments also showed regulation by a histone demethylase previously linked to FCA FPA function; however, others were associated with siRNA production and DNA methylation. Our data suggest that FCA/FPA play important roles in terminating transcription at many loci, often via promotion of proximal polyadenylation, and that in their absence, ectopic transcription and/or extensive read-through transcription occurs. These transcriptional products have the potential to interfere with overlapping transcripts and flanking genes and appear to form the basis for how modulation of FCA FPA function triggers RNA-mediated chromatin silencing mechanisms at a variety of loci in the Arabidopsis genome.
2011-07-11 | GSE24364 | GEO
Project description:Extensive imprinted gene expression in Arabidopsis endosperm
| PRJNA132535 | ENA
Project description:We analyzed by RNA-seq the transcriptome of 8-day old Arabidopsis thaliana seedlings for wild-type (Col-0), single mutant for FPA (fpa/AT2G43410, line fpa-7) or a triple mutant of all three BDR proteins (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). We identified hundreds of genes differentially expressed between wild-type and bdrs triple mutant and a significant overlap in DE genes with the fpa mutant. We also analyzed the binding of BDR1 and BDR2 as well as RNA polymerase II and histone marks by ChIP-seq in wild-type, bdrs and fpa-deficient seedlings. Our data support a role of BDRs as negative elongation factors. They occupy the gene body and regulate the expression of genes involved in defense response pathways. Strikingly, by modulating 3' pausing of RNA polymerase II and possibly contributing to gene looping, they also protect a number of genes from transcriptional interferences originating from a highly expressed upstream tandem gene. Thus BDRs proteins are negative elongation factors that act as transcriptional "gatekeepers" in the Arabidopsis thaliana genome.
2019-08-08 | GSE112440 | GEO
Project description:Expression Profiling of Arabidopsis Long Intergenic Nongcoding RNA in Inflorescences, Leaves, and Roots
| PRJNA143395 | ENA
Project description:We analyzed by RNA-seq the transcriptome of 8-day old Arabidopsis thaliana seedlings for wild-type (Col-0), single mutants for BDR proteins (bdr1/AT5G25520 ; bdr2/AT5G11430 or bdr3/AT2G25640), single mutant for FPA (fpa/AT2G43410, line fpa-7) or a triple mutant of all three BDR proteins (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). We identified hundreds of genes differentially expressed between wild-type and bdrs triple mutant and a significant overlap in DE genes with the fpa mutant. We also analyzed the binding of BDR1 and BDR2 as well as RNA polymerase II and histone marks by ChIP-seq in wild-type, bdrs and fpa-deficient seedlings. Our data support a role of BDRs as negative elongation factors. They bind on the gene body and regulate the expression of genes involved in defense response pathways. Strikingly, by modulating 3' pausing of RNA polymerase II and possibly contributing to gene looping, they also protect a number of genes from transcriptional interferences originating from a highly expressed upstream tandem gene. Thus BDRs proteins are negative elongation factors that act as transcriptional "gatekeepers" in the Arabidopsis thaliana genome.
2019-08-08 | GSE112441 | GEO
Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
2018-11-14 | ST001096 | MetabolomicsWorkbench
Project description:DELLA proteins act as hubs that relay environmental information to the multiple transcriptional circuits that control growth and development through physical interaction with transcription factors from different families. We have analyzed the presence of one DELLA protein at the Arabidopsis genome by chromatin immunoprecipitation coupled to large-scale sequencing and we find that it binds at the promoters of multiple genes. Enrichment analysis shows a strong preference for cis elements recognized by specific transcription factor families. In particular, we demonstrate that DELLA proteins are recruited by type-B ARABIDOPSIS RESPONSE REGULATORS (ARR) to the promoters of cytokinin-regulated genes, where they act as transcriptional co-activators. The biological relevance of this mechanism is underpinned by the necessity of simultaneous presence of DELLAs and ARRs to restrict root meristem growth and to promote photomorphogenesis.
2015-07-23 | GSE59187 | GEO
Project description:Identification of Arabidopsis Long Intergenic Noncoding RNA regulated by RNA-dependent RNA polymerase 2 (RDR2)
| PRJNA143397 | ENA