Unidentified
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB19431 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR675514_1.fastq.gz | Fastqsanger.gz | |||
| DRR675514_2.fastq.gz | Fastqsanger.gz | |||
| DRR675515_1.fastq.gz | Fastqsanger.gz | |||
| DRR675515_2.fastq.gz | Fastqsanger.gz | |||
| DRR675516_1.fastq.gz | Fastqsanger.gz |
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Project description:In mammals, RNA interference (RNAi) is mostly studied as a cytoplasmic event, however, numerous reports convincingly show nuclear localization of the AGO proteins. Nevertheless, the mechanism of nuclear entry remains to be fully elucidated, and the extent of nuclear RNAi further explored. We found that reduced Lamin A levels significantly induced nuclear influx of AGO2 in SHSY5Y neuroblastoma and A375 melanoma cancer cell lines, which normally have no nuclear AGO2. The translocation of AGO2 was accompanied by aggravated cell proliferation and we further found that the loss of Lamin A leads to EGFR and Src kinase activation, which regulates the turnover and stability of cytoplasmic AGO2. Furthermore, Lamin A KO significantly reduced the activity of nuclear RNAi. This was evident by AGO fPAR-CLIP in WT and Lamin A KO cells, where we observed ca 60% less efficiency of RNAi. Mass spectrometry of AGO interactome, from the nuclear fraction, indicated that AGO2 is in complex with FAM120A, a known interactor of AGO2 that reduces the activity of RNAi by competing with AGO2 transcript binding. Therefore, loss of Lamin A starts a signaling cascade that mediates nuclear AGO2 translocation to rapidly inhibit RNAi in order to facilitate cancer proliferation
2024-10-17 | PXD042899 | Pride
Project description:In mammals, RNA interference (RNAi) is mostly studied as a cytoplasmic event, however, numerous reports convincingly showed nuclear localization of AGO proteins. Nevertheless, the mechanism of the nuclear entry remains to be fully elucidated, and the extent of nuclear RNAi explored. The nuclear import of large proteins requires active transport through the nuclear envelope (NE). Therefore, we hypothesized that the NE, and its composition, is important for nuclear AGO2 translocation. Lamin A knockout significantly induced nuclear influx of AGO2 in SHSY5Y neuroblastoma and A375 melanoma cancer cells. We unravelled that the loss of Lamin A leads to EGFR and Src kinase activation, which regulates the turnover and stability of cytoplasmic specifically AGO2. Furthermore, EGFR mediated phosphorylation at Y393 inhibits the activity of nuclear RNAi. This was evident by AGO fPAR-CLIP in WT and KO cells, where we observed a decrease in RNAi potential. Mass spectrometry of AGO interactome, from the nuclear fraction, indicated that AGO2 is in complex with FAM120A, which may further reduced the activity of RNAi by competing with AGO2 transcript binding. Therefore, loss of Lamin A starts a signalling cascade that mediates nuclear AGO2 translocation to rapidly inhibit RNAi.
2023-06-22 | GSE235156 | GEO
Project description:Tomida2003 - NFAT functions Calcium
Oscillation
This model is described in the article:
NFAT functions as a working
memory of Ca2+ signals in decoding Ca2+ oscillation.
Tomida T, Hirose K, Takizawa A,
Shibasaki F, Iino M.
EMBO J. 2003 Aug; 22(15):
3825-3832
Abstract:
Transcription by the nuclear factor of activated T cells
(NFAT) is regulated by the frequency of Ca(2+) oscillation.
However, why and how Ca(2+) oscillation regulates NFAT activity
remain elusive. NFAT is dephosphorylated by Ca(2+)-dependent
phosphatase calcineurin and translocates from the cytoplasm to
the nucleus to initiate transcription. We analyzed the kinetics
of dephosphorylation and translocation of NFAT. We show that
Ca(2+)-dependent dephosphorylation proceeds rapidly, while the
rephosphorylation and nuclear transport of NFAT proceed slowly.
Therefore, after brief Ca(2+) stimulation, dephosphorylated
NFAT has a lifetime of several minutes in the cytoplasm. Thus,
Ca(2+) oscillation induces a build-up of dephosphorylated NFAT
in the cytoplasm, allowing effective nuclear translocation,
provided that the oscillation interval is shorter than the
lifetime of dephosphorylated NFAT. We also show that Ca(2+)
oscillation is more cost-effective in inducing the
translocation of NFAT than continuous Ca(2+) signaling. Thus,
the lifetime of dephosphorylated NFAT functions as a working
memory of Ca(2+) signals and enables the control of NFAT
nuclear translocation by the frequency of Ca(2+) oscillation at
a reduced cost of Ca(2+) signaling.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000678.
To cite BioModels Database, please use:
Chelliah V et al. BioModels: ten-year
anniversary. Nucl. Acids Res. 2015, 43(Database
issue):D542-8.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000678 | BioModels
Project description:As an evolutionarily conserved master regulator of metabolism, mechanistic target of rapamycin complex 1 (mTORC1) regulates cell states and fates in development, cancer and aging. mTORC1 activity regulation was critical for pluripotent stem cells maintenance and cell fate transitions. Inhibition of mTORC1 induces embryonic stem cells (ESCs) entry into a paused state which reversibly arrests self-renewal leaving pluripotency intact. Hyperactivation of mTORC1 impedes both pluripotency re-establishment and exit of PSCs. As shown that mTORC1 mediates TFE3 nuclear translocation block pluripotency exit, whether similar mechanisms through transcription factor TFE3 are involved in these processes, and the detailed mechanism by which mTORC1-TFE3 regulates critical transcriptional processes for these transitions, remain unclear. In this study, we demonstrate that the nuclear translocation of TFE3, induced by hyperactivation of mTORC1, results in its binding to the nucleosome remodeling and deacetylation (NuRD) complex in both re-establishment and exit of pluripotency. This interaction inhibits the expression of various crucial genes during different fate transitions of PSCs. Our findings uncover a common and key role of TFE3-NuRD association as mediator of mTORC1 to block pluripotent cell fate transitions, with implications for various fields including physiological and pathological diseases.
2024-08-13 | GSE274330 | GEO
Project description:Membrane receptor nuclear translocation play some novel role in cancer pathology. In the current studies, we demonstrate HCAR1 distributes in cancer cell nucleus in Lung cancer; Lactate promote HCAR1 nuclear translocation. Proteomics analysis found there are a set of nuclear proteins binds with HCAR1; interaction of HCAR1 with SFPQ etc other proteins promote cell self-renewal and cell invasion in lung cancer. ChIP sequencing analysis discovered there are a set of genes were targeted by HCAR1.
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Project description:siRNA screen for modifiers of Smad4 nuclear translocation
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Project description:Autophagy mediates degradation of nuclear lamina
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Project description:Signal recognition particles (SRPs) are important components in regulating intracellular protein transport and secretion, and tumors with high expression of Signal recognition particle 9 (SRP9) have tended to have poorer overall survival, although no reports have described the relationship between its localization and prognosis in pancreatic cancer. We conducted immunohistochemical staining for SRP9 for excised specimens from pancreatic cancer surgery cases without preoperative chemotherapy or radiotherapy performed. We found that in some cases SRP9 was preferentially expressed in the nucleus of the cancerous regions, which was hardly detected in other cases, suggesting SRP9 was transported to nucleus in the former cases. Therefore, the prognosis of patients with SRP9 nuclear translocation was compared by dividing them into two groups: those with a nuclear translocation rate of >50% and ≤50%. Patients with a nuclear translocation rate of >50% had significantly better recurrence-free survival compared with nuclear translocation rate of ≤50% group (p = 0.037). Subsequent in vitro experiments also showed that its nuclear translocation rate is reduced under amino acid deficient conditions. Further, to investigate the mechanism of SRP9 nuclear translocation, we studied in vitro by introducing the genes of SRP9 splicing variants (v1 and v2) and their deletion mutants lacking C-terminal regions into MiaPaCa pancreatic cancer cells. As a result, it was confirmed that both splicing variants showed nuclear translocation regardless of C-terminal deletions. Taking advantage of the fact that SRP9 is an RNA-binding protein, we next decided to sequence RNAs that bind to nuclear translocated v1 and v2 and evaluate their function in nuclear translocation. RNA Immunoprecipitation Sequencing of nuclear translocated v1 and v2 showed that pathways involved in cancer progression and protein translation were downregulated. The further study of nuclear translocation of SRP9 may open an avenue to optimization of precise evaluation and therapeutic control of pancreatic cancer.
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Project description:To incorporate the far-red light (FR) signal into a strategy for optimizing plant growth, FAR-RED ELONGATED HYPOCOTYL1 (FHY1) mediates the nuclear translocation of the FR photoreceptor phytochrome A (phyA) and facilitates the association of phyA with the promoters of numerous associated genes crucial for the response to environmental stimuli. However, whether FHY1 plays additional roles following FR irradiation remains elusive. Here, by the global identification of FHY1 chromatin association sites through ChIP-seq analysis and by the comparison of FHY1-associated sites with phyA- associated sites, we demonstrated that nuclear FHY1 can either act independently of phyA or act in association with phyA to activate the expression of distinct target genes. We also determined that phyA can act independently of FHY1 in regulating phyA-specific target genes. Furthermore, we determined that the independent FHY1 nuclear pathway is involved in crucial developmental aspects, as in the case of inhibited seed germination under FR during salt-stress. Notably, the differential presence of cis-elements and transcription factors in common and unique FHY1 and/or phyA associated genes are indicative of the complexity of the independent and coordinated FHY1 and phyA pathways. Our study uncovers new aspects of FHY1 function beyond its currently recognized role in phyA-dependent photomorphogenesis To determine whether phyA and FHY1 associate with the same genes upon FR irradiation, four-day old etiolated 35S: GFP-FHY1 fhy1-1 transgenic seedlings were exposed to 3hr FR. The treated plants were utilized for ChIP-seq analysis with an anti-FHY1 antibody that exhibits high specificity in the detection of FR-induced FHY1-association events. FHY1 associated-DNA samples from three distinct biological replicates and an input DNA sample (as a negative control) were subjected to high-throughput Solexa (Illumina) sequencing.
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