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Links from GEO DataSets

Items: 20

1.

Protein Arginine Methyltransferase 3 Fine-Tunes the Assembly/Disassembly of Pre-ribosomes to Repress Nucleolar Stress by Interacting with RPS2B in Arabidopsis

(Submitter supplied) Ribosome biogenesis, which takes place mainly in the nucleolus, involves coordinated expression of pre-ribosomal RNAs (pre-rRNAs) and ribosomal proteins, pre-rRNA processing, and subunit assembly with the aid of numerous assembly factors. Our previous study showed that the Arabidopsis thaliana protein arginine methyltransferase AtPRMT3 regulates pre-rRNA processing; however, the underlying molecular mechanism remains unknown. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17639
4 Samples
Download data: TXT
Series
Accession:
GSE140318
ID:
200140318
2.

Functional analysis of HD2C in Arabidopsis

(Submitter supplied) Ribosome biogenesis is a fundamental process required for all cellular activities. Histone deacetylases play critical roles in many biological processes including transcriptional repression and rDNA silencing. However, their function in pre-rRNA processing remains poorly understood. Here, we discovered a previously uncharacterized role of Arabidopsis histone deacetylase HD2C in pre-rRNA processing via both canonical and non-canonical manners. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL13222
9 Samples
Download data: BW, TXT
Series
Accession:
GSE107883
ID:
200107883
3.

The nucleolar protein NOL12 is required for processing of large ribosomal subunit rRNA precursors in Arabidopsis

(Submitter supplied) NOL12 5'-3' exoribonucleases, conserved among eukaryotes, play important roles in pre-rRNA processing, ribosome assembly and export. The most well-described yeast counterpart, Rrp17, is required for maturation of 5.8 and 25S rRNAs, whereas human hNOL12 is crucial for the separation of the large (LSU) and small (SSU) ribosome subunit rRNA precursors. In this study we demonstrate that plant AtNOL12 is also involved in rRNA biogenesis, specifically in the processing of the LSU rRNA precursor, 27S pre-rRNA. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21785
6 Samples
Download data: TXT
Series
Accession:
GSE232067
ID:
200232067
4.

apum23_col3

(Submitter supplied) Gene expression analyses of three-week old soil grown wild-type (Col-3) and apum23-1 mutant. Expression profiling was conducted as an attempt to identify the genes differentially regulated in apum23-1 mutant This study was under taken to characterize a member of pumilio family, APUM23 in Arabidopsis. Pumilio, an RNA-binding protein (RBP) containing tandem repeat PUF domains, has been known to repress translational activity in early embryogenesis and polarized cells of non-plant species. more...
Organism:
Arabidopsis thaliana; Arabidopsis
Type:
Expression profiling by array
Platform:
GPL198
6 Samples
Download data: CEL
Series
Accession:
GSE23940
ID:
200023940
5.

The G-patch protein NF-κB-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis

(Submitter supplied) In eukaryotes, the synthesis of ribosomal subunits, which involves the maturation of the ribosomal (r)RNAs and assembly of ribosomal proteins, requires the co-ordinated action of a plethora of ribosome biogenesis factors. Many of these cofactors remain to be characterized in human cells. Here, we demonstrate that the human G-patch protein NF-κB-repressing factor (NKRF) forms a pre-ribosomal subcomplex with the DEAH-box helicase DHX15 and the 5’-3’ exonuclease XRN2. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL11154
4 Samples
Download data: TXT
Series
Accession:
GSE92733
ID:
200092733
6.

The nucleolar SAHY1 is involved in pre-rRNA processing and normal plant growth in Arabidopsis

(Submitter supplied) Although the nucleolus is known to be involved in the plant stress response, the underlying mechanisms remain unclear. In the present study, we genetically isolated and characterized the Arabidopsis thaliana salt hypersensitive mutant 1 (sahy1), which exhibits slow growth, short roots, and sterility. SAHY1 encodes an unknown protein that is predominantly expressed in root tips and mature pollens. Subcellular localization further demonstrated that SAHY1 is a nucleolar protein. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platform:
GPL198
12 Samples
Download data: CEL, CHP
Series
Accession:
GSE49919
ID:
200049919
7.

Effect of depletion of Sas10 in pre-rRNA processing

(Submitter supplied) Ribosome small subunit (SSU) is assembled by the SSU processome which contains approximately 70 non-ribosomal protein factors. The biochemical mechanism for the SSU processome in 18S rRNA processing and maturation has been extensively studied, however, how the SSU processome components enter to the nucleolus has not been systematically investigated. Here we checked the nucleolar localization of 50 human SSU processome components and find that UTP3 and other 24 proteins enter to the nucleolus autonomously. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
4 Samples
Download data: TXT
Series
Accession:
GSE262698
ID:
200262698
8.

Effect of depletion of Sas10 on zebrafish gene expression at 5 days post fertilization

(Submitter supplied) In yeast, Upt3 overexpression caused a de-repression of the silenced genes at different loci, suggesting Utp3 might be involved in regulating gene expression. To this end, we extracted total RNA from the WT and sas10 (zebrafish homolg of yeast utp3) embryos, three biological repeats each, at 5dpf and carried out an RNA-seq analysis. Comparing the gene expression between the WT and sas10 using DESeq2 identified a total of 8574 differentially expressed genes (DEGs), including 4457 downregulated and 4117 upregulated DEGs in the sas10 mutant (criteria adopted: TPM>5 in at least one replicate, fold-change more than 1.5, p-adjust <0.05). more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
6 Samples
Download data: CSV, TXT
Series
Accession:
GSE244191
ID:
200244191
9.

The SALT HYPERSENSITIVE MUTANT 9, a nucleolar APUM23 protein, is essential for salt sensitivity in association with ABA signal pathways in Arabidopsis thaliana

(Submitter supplied) High salinity is one of the major environmental factors, which hampers plant growth, development and productivity. To better understand the regulatory mechanisms by which plants cope with salt stress, we used genetic approaches to identify salt hypersensitive mutant 9 (sahy9), a new allele of apum23, in Arabidopsis thaliana. The sahy9/apum23 mutant seedlings display postgemination developmental arrest and later become bleached under agar plates supplemented with various salt stressors. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platform:
GPL12621
4 Samples
Download data: TXT
Series
Accession:
GSE99664
ID:
200099664
10.

Protein arginine methyltransferase AtPRMT5 is involved in pre-mRNA splicing in Arabidopsis thaliana

(Submitter supplied) In this study, we analyzed the Arabidopsis homologue of PRMT5, AtPRMT5’s function in RNA processing. RNA-seq analyses revealed that AtPRMT5 is involved in a subset of pre-mRNA splicing. Several RNA processing factors involved in regulating flowering time were validated that the corresponding intron retention surely exists in atprmt5 mutants. AtSm proteins can also be methylated by AtPRMT5 in vitro and in vivo, which may be the reasons for the pre-mRNA splicing defects in atprmt5. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL10272
2 Samples
Download data: BEDGRAPH
Series
Accession:
GSE21323
ID:
200021323
11.

URB1 ensures 3' end processing of pre-rRNAs to prevent exosome-dependent degradation and is required for development [SHAPE-MaP]

(Submitter supplied) The nucleolus composes hundreds of proteins that play distinct roles in ribosomal RNA (rRNA) processing within Fibrillar Center/Dense Fibrillar Component (FC/DFC) units and ribosome assembly in Granular Component (GC). The sub-nucleolar localization of most proteins and how their unique localization facilitates rRNA processing have remained elusive. By screening 200 nucleolar candidate proteins with high-resolution, live-cell microscopy, we identified a previously undescribed sub-nucleolar compartment, named the periphery of DFC (PDFC). more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL18573
30 Samples
Download data: TXT
Series
Accession:
GSE196625
ID:
200196625
12.

URB1 ensures 3' end processing of pre-rRNAs to prevent exosome-dependent degradation and is required for development

(Submitter supplied) The nucleolus composes hundreds of proteins that play distinct roles in ribosomal RNA (rRNA) processing within Fibrillar Center/Dense Fibrillar Component (FC/DFC) units and ribosome assembly in Granular Component (GC). The sub-nucleolar localization of most proteins and how their unique localization facilitates rRNA processing have remained elusive. By screening 200 nucleolar candidate proteins with high-resolution, live-cell microscopy, we identified a previously undescribed sub-nucleolar compartment, named the periphery of DFC (PDFC). more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20795
2 Samples
Download data: BEDGRAPH
Series
Accession:
GSE194413
ID:
200194413
13.

Arabidopsis HOT3/eIF5B1 constrains rRNA RNAi by facilitating 18S rRNA maturation during translation initiation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL26208 GPL23157 GPL17639
71 Samples
Download data: TXT
Series
Accession:
GSE223172
ID:
200223172
14.

Arabidopsis HOT3/eIF5B1 constrains rRNA RNAi by facilitating 18S rRNA maturation during translation initiation (miRNA-Seq)

(Submitter supplied) Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S rRNA 3’ end maturation during late-40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the effects of eIF5B have not been studied at the genome-wide level in any organism, and 18S rRNA 3’ end maturation is poorly understood in plants. more...
Organism:
Arabidopsis thaliana
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17639
8 Samples
Download data: TXT
Series
Accession:
GSE223171
ID:
200223171
15.

Arabidopsis HOT3/eIF5B1 constrains rRNA RNAi by facilitating 18S rRNA maturation during translation initiation (RNA-Seq)

(Submitter supplied) Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S rRNA 3’ end maturation during late-40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the effects of eIF5B have not been studied at the genome-wide level in any organism, and 18S rRNA 3’ end maturation is poorly understood in plants. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26208
7 Samples
Download data: TXT
Series
Accession:
GSE223169
ID:
200223169
16.

Arabidopsis HOT3/eIF5B1 constrains rRNA RNAi by facilitating 18S rRNA maturation during translation initiation (Ribo-Seq)

(Submitter supplied) Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S rRNA 3’ end maturation during late-40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the effects of eIF5B have not been studied at the genome-wide level in any organism, and 18S rRNA 3’ end maturation is poorly understood in plants. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL23157
8 Samples
Download data: TXT
Series
Accession:
GSE223168
ID:
200223168
17.

Arabidopsis HOT3/eIF5B1 constrains rRNA RNAi by facilitating 18S rRNA maturation during translation initiation (18S END-Seq)

(Submitter supplied) Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S rRNA 3’ end maturation during late-40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the effects of eIF5B have not been studied at the genome-wide level in any organism, and 18S rRNA 3’ end maturation is poorly understood in plants. more...
Organism:
Arabidopsis thaliana
Type:
Other
Platform:
GPL17639
48 Samples
Download data: TXT
Series
Accession:
GSE223167
ID:
200223167
18.

rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL17021
42 Samples
Download data: BW, TXT
Series
Accession:
GSE166041
ID:
200166041
19.

rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [Hi-C]

(Submitter supplied) Nucleolus is the organelle for ribosome biogenesis and sensing various types of stress. Its role in regulating stem cell fate is unclear. Here, we present multiple lines of evidence that nucleolar stress induced by interfering rRNA biogenesis can drive two-cell stage embryo-like (2C-like) transcriptional program and induce an expanded 2C-like cell population in mouse embryonic stem (mES) cells. Mechanistically, the liquid-liquid phase separation (LLPS) mediated by rRNA and nucleolar proteins maintains the formation of peri-nucleolar heterochromatin (PNH). more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL17021
2 Samples
Download data: TXT
Series
Accession:
GSE166032
ID:
200166032
20.

rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [scRNA-seq]

(Submitter supplied) Nucleolus is the organelle for ribosome biogenesis and sensing various types of stress. Its role in regulating stem cell fate is unclear. Here, we present multiple lines of evidence that nucleolar stress induced by interfering rRNA biogenesis can drive two-cell stage embryo-like (2C-like) transcriptional program and induce an expanded 2C-like cell population in mouse embryonic stem (mES) cells. Mechanistically, the liquid-liquid phase separation (LLPS) mediated by rRNA and nucleolar proteins maintains the formation of peri-nucleolar heterochromatin (PNH). more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
8 Samples
Download data: CSV
Series
Accession:
GSE166027
ID:
200166027
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