E-GEOD-112441
Ontology highlight
ABSTRACT:
PROVIDER: E-GEOD-112441 | ExpressionAtlas | 2020-04-15
REPOSITORIES: ExpressionAtlas
Similar Datasets
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: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:We analyzed by RNA-seq the modulation of the transcriptome in response to light or a heat shock in wild-type and bdrs triple mutant Arabidopsis thaliana seedlings (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). We showed that the overall changes in the transcriptome were very similar in the two genotypes. However, when studying specifically gene pairs organized in tandem and with short intergenic distances, we showed that the rapid and strong regulations of upstream genes was associated with bdrs-dependent changes on the downstream gene expression that are consistent with bdrs-dependent transcriptional interferences.
2019-08-08 | GSE112442 | GEO
Project description:We used an MNase digestion of chromatin from Arabidopsis seedlings, combined or not with ChIP (native ChIP), to analyze by high-throughput sequencing the genome-wide profiles of nucleosomes (MNase-seq), and of total H3, H3K4me2, H3K4me3 and H3K36me3 (native ChIPs) in wild-type (Col-0), fpa mutant (fpa/AT2G43410, line fpa-7) and 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 found that BDR proteins occupy regions of low nucleosome density. We also observed that genes upregulated in bdrs triple mutant display high levels of RNA polymerase II on their gene bodies but low levels of H3K4me3 and H3K36me3 in wild-type seedlings. For genes with the highest levels of BDR occupancy in wild-type, increased mRNA expression in bdrs mutant is associated with reduced RNA polymerase II density profile and increased H3K4me3 and H3K36me3 levels.
2019-08-08 | GSE113076 | GEO
Project description:Analysis of the genome wide response of wild type and two mutant arabidopsis thaliana seedlings to norflurazon Keywords: Genome wide response to inhibition of chloroplast development
2008-09-23 | GSE12887 | GEO
Project description:Flis2015 - Plant clock gene circuit
(P2011.1.2 PLM_71 ver 1)
This model is described in the article:
Defining the robust
behaviour of the plant clock gene circuit with absolute RNA
timeseries and open infrastructure.
Flis A, Fernández AP, Zielinski
T, Mengin V, Sulpice R, Stratford K, Hume A, Pokhilko A, Southern
MM, Seaton DD, McWatters HG, Stitt M, Halliday KJ, Millar
AJ.
Open Biol 2015 Oct; 5(10):
Abstract:
Our understanding of the complex, transcriptional feedback
loops in the circadian clock mechanism has depended upon
quantitative, timeseries data from disparate sources. We
measure clock gene RNA profiles in Arabidopsis thaliana
seedlings, grown with or without exogenous sucrose, or in
soil-grown plants and in wild-type and mutant backgrounds. The
RNA profiles were strikingly robust across the experimental
conditions, so current mathematical models are likely to be
broadly applicable in leaf tissue. In addition to providing
reference data, unexpected behaviours included co-expression of
PRR9 and ELF4, and regulation of PRR5 by GI. Absolute RNA
quantification revealed low levels of PRR9 transcripts (peak
approx. 50 copies cell(-1)) compared with other clock genes,
and threefold higher levels of LHY RNA (more than 1500 copies
cell(-1)) than of its close relative CCA1. The data are
disseminated from BioDare, an online repository for focused
timeseries data, which is expected to benefit mechanistic
modelling. One data subset successfully constrained clock gene
expression in a complex model, using publicly available
software on parallel computers, without expert tuning or
programming. We outline the empirical and mathematical
justification for data aggregation in understanding highly
interconnected, dynamic networks such as the clock, and the
observed design constraints on the resources required to make
this approach widely accessible.
cL_m_degr, param m1, modified to ensure light rate > dark rate.
This model is hosted on
BioModels Database
and identified by:
MODEL1510190000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
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Public Domain Dedication for more information.
2015-11-09 | BIOMD0000000597 | BioModels
Project description:Analysis of the transcriptome of the reproductive meristems of Arabidopsis thaliana Col-0. We compared the transcriptome obtained from lsh1 lsh3 lsh4 triple mutant to a wild type control
2024-02-06 | GSE247357 | GEO
Project description:To see the function of CERK1 receptor-like kinase in the chitin elicitor signaling in Arabidopsis, we compared the gene expression profiles in the chitin oligosaccharide treated seedlings of wild type A. thaliana and CERK1 knock-out mutant. Keywords: Defense response
2008-10-01 | GSE9346 | GEO
Project description:Gene expression profiling in wild-type, fpa mutant and bdrs triple mutant Arabidopsis seedlings
| PRJNA446047 | ENA
Project description:The homozygous of mutants of Arabidopsis gene (AT1G60900) are early flower. This gene encodes a homolog of yeast U2AF65 which is involved in pre-mRNA splicing of target genes. To assay the introns characters of target genes of this protein in Arabidopsis thaliana, the 10-day seedlings of wild type and atu2af65b mutant were used for RNA-Seq.
2019-10-29 | E-MTAB-7521 | biostudies-arrayexpress