Ontology highlight
ABSTRACT:
PROVIDER: PRJNA477550 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7413590.fastq.gz | Fastqsanger.gz | |||
| SRR7413591_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR7413592_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR7413593_1.fastq.gz | Fastqsanger.gz | |||
| SRR7413593_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 14 |
Similar Datasets
Project description:Pentatricopeptide repeat-containing polyadenylation factor defines mitochondrial mRNA identity and stability in trypanosomes
| PRJNA376028 | ENA
Project description:Control of the dimensions of organ primordia is crucial for proper organogenesis in the development of multicellular organisms. Lateral root formation is a major type of plant organogenesis important for postembryonic development of the root system. Lateral root formation begins with a few rounds of asymmetric, anticlinal cell division (formative cell division) in the pericycle, which determines the basal dimensions of root primordia. Here we show, based on molecular genetic analysis of temperature-dependent fasciation (TDF) mutants of Arabidopsis thaliana, that mitochondria play an unexpected role in the restriction of formative cell division and thus in the control of the basal dimensions of lateral root primordia. Three TDF mutants, root redifferentiation defective 1 (rrd1), rrd2, and root initiation defective 4 (rid4), exhibit lateral root fasciation from excess formative cell division under high-temperature conditions. We identify RRD1 as encoding a poly(A)-specific ribonuclease (PARN)-like protein and RRD2 and RID4 as encoding pentatricopeptide repeat (PPR) proteins. Subcellular localization and predicted functions of these proteins implicate them in poly(A)-dependent RNA degradation in mitochondria. This characterization is supported by the finding that mitochondrial RNAs with poly(A) tails, most of which are mRNAs of respiratory chain components, accumulate at an unusually high level in these TDF mutants. Explants of three mutants (rrd1, rrd2, rid4) and wild type were cultured on B5 medium supplemented with 0.5 mg/L IBA for the induction of lateral root formation. After 12 hours of culture at 28C, explants were collected and used for microarray analysis. Analysis was performed in three biological replicates.
2012-02-10 | E-GEOD-34595 | biostudies-arrayexpress
Project description:Control of the dimensions of organ primordia is crucial for proper organogenesis in the development of multicellular organisms. Lateral root formation is a major type of plant organogenesis important for postembryonic development of the root system. Lateral root formation begins with a few rounds of asymmetric, anticlinal cell division (formative cell division) in the pericycle, which determines the basal dimensions of root primordia. Here we show, based on molecular genetic analysis of temperature-dependent fasciation (TDF) mutants of Arabidopsis thaliana, that mitochondria play an unexpected role in the restriction of formative cell division and thus in the control of the basal dimensions of lateral root primordia. Three TDF mutants, root redifferentiation defective 1 (rrd1), rrd2, and root initiation defective 4 (rid4), exhibit lateral root fasciation from excess formative cell division under high-temperature conditions. We identify RRD1 as encoding a poly(A)-specific ribonuclease (PARN)-like protein and RRD2 and RID4 as encoding pentatricopeptide repeat (PPR) proteins. Subcellular localization and predicted functions of these proteins implicate them in poly(A)-dependent RNA degradation in mitochondria. This characterization is supported by the finding that mitochondrial RNAs with poly(A) tails, most of which are mRNAs of respiratory chain components, accumulate at an unusually high level in these TDF mutants.
2012-02-10 | GSE34595 | GEO
Project description:Study of the role of the FLV/DOT4 protein in post-transcriptional regulation of chloroplast gene expression. DOT4 is a pentatricopeptide repeat protein targeted to the chloroplast which regulates the editing of the rpoC1 transcript The editing level of rpoC1 varies from one tissue to the other and because the main macroscopic phenotype of the flv/dot4 mutant are white leaf margins. We compared the leaf border to the leaf center of wild-type Col0 plants but also the leaf borders of col0 and flv/dot4 knock out mutants by sequencing total RNA depleted from rRNA to get a global view of gene expression (including post-transcrional modifications) of the 3 plant genomes: nucleus, chloroplast and mitochondria. mRNA seq on wild-type Col and FLV mutants knock out.
2016-02-12 | E-GEOD-71149 | biostudies-arrayexpress
Project description:Aiming at defining the protein content and composition of a single mitochondrion of Arabidopsis thaliana, shotgun analyses were performed on purified mitochondria from cultured heterotrophic Arabidopsis cells. Based on microscopic observations on the size of mitochondria, as well as biochemical properties, such as protein concentration, average molecular mass of proteins, and the average length of the signal peptide, intensity-based absolute quantification (iBAQ) values were applied to calculate the copy number of each identified protein species within a single mitochondrion. Copy numbers of the individual proteins span five orders of magnitude, ranging from >40,000 for Voltage-Dependent Anion Channel 1 (VDAC1) to sub-stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat (PPR) proteins that modify mitochondrial transcripts. Aiming at defining the protein content and composition of a single mitochondrion of Arabidopsis thaliana, shotgun analyses were performed on purified mitochondria from cultured heterotrophic Arabidopsis cells. Based on microscopic observations on the size of mitochondria, as well as biochemical properties, such as protein concentration, average molecular mass of proteins, and the average length of the signal peptide, intensity-based absolute quantification (iBAQ) values were applied to calculate the copy number of each identified protein species within a single mitochondrion. Copy numbers of the individual proteins span five orders of magnitude, ranging from >40,000 for Voltage-Dependent Anion Channel 1 (VDAC1) to sub-stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat (PPR) proteins that modify mitochondrial transcripts. Aiming at defining the protein content and composition of a single mitochondrion of Arabidopsis thaliana, shotgun analyses were performed on purified mitochondria from cultured heterotrophic Arabidopsis cells. Based on microscopic observations on the size of mitochondria, as well as biochemical properties, such as protein concentration, average molecular mass of proteins, and the average length of the signal peptide, intensity-based absolute quantification (iBAQ) values were applied to calculate the copy number of each identified protein species within a single mitochondrion. Copy numbers of the individual proteins span five orders of magnitude, ranging from >40,000 for Voltage-Dependent Anion Channel 1 (VDAC1) to sub-stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat (PPR) proteins that modify mitochondrial transcripts.
2019-09-11 | PXD014292 | Pride
Project description:Study of the role of the FLV/DOT4 protein in post-transcriptional regulation of chloroplast gene expression. DOT4 is a pentatricopeptide repeat protein targeted to the chloroplast which regulates the editing of the rpoC1 transcript
2016-02-12 | GSE71149 | GEO
Project description:Trypanosomes are unicellular eukaryotes that rely heavily on post-transcriptional mechanisms to control gene expression. DRBD3 is an RNA-binding protein known to play important roles in mRNA processing, stability, transport and translation. It was found to associate with grumpy, a long non-coding RNA (lncRNA) recently characterized in Trypanosoma brucei. Here, we explore the role of DRBD3 in lncRNA metabolism and show that its depletion leads to the upregulation of a specific subset of approximately one hundred lncRNAs in both bloodstream and procyclic forms, likely through the activation of cryptic splice sites. The effect of DRBD3 depletion on lncRNA expression appears to be mostly indirect, and results from reduced levels of the poly(A) polymerase PAP1 following DRBD3 silencing. In addition to its impact on lncRNAs, DRBD3 loss also affects the processing of protein-coding genes, leading to alternative trans-splicing and protein truncation. Furthermore, we demonstrate that DRBD3 regulates the splicing of the newly identified intron in the transcript encoding the RNA-binding protein RBP20, and is important for maintaining the balance between trans- and cis-splicing. Our results position DRBD3 as a high-level regulatory factor that shapes the expression landscape of both coding and non-coding genes in trypanosomes
2025-11-06 | GSE272310 | GEO
Project description:1. evaluation of diagnostic importance of insulin like growth factor binding protein3 in patient with recently diagnosed as Colorectal cancer
2. correlation between the diagnostic efficacy of insulin like growth factor binding protein 3 with routine marker carcinoembryonic antigen.
| 59449 | ecrin-mdr-crc