LPS-mediated noncoding RNA IFITM4P promotes malignant progression of oral leukoplakia through nucleocytoplasmic shuttling
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA704081 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13765857_1.fastq.gz | Fastqsanger.gz | |||
| SRR13765857_2.fastq.gz | Fastqsanger.gz | |||
| SRR13765858_1.fastq.gz | Fastqsanger.gz | |||
| SRR13765858_2.fastq.gz | Fastqsanger.gz | |||
| SRR13765859_1.fastq.gz | Fastqsanger.gz |
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Project description:To identify the downstream targets of IFITM4P that regulate the proliferation of Leuk-1 cells, we performed RNA sequencing to identify differentially expressed genes.
2023-05-18 | GSE167292 | GEO
Project description:Biological oscillations are observed at many levels of cellular organization. In the social amoebae Dictyostelium discoideum, starvation-triggered multicellular development is organized by periodic cAMP waves, which provide both chemoattractant gradients and developmental signals. We report that GtaC, a GATA transcription factor, exhibits rapid nucleocytoplasmic shuttling in response to cAMP waves. This behavior requires coordinated action of a nuclear localization signal and reversible G protein-coupled receptor (GPCR)-mediated phosphorylation. While both are required for developmental gene expression, receptor occupancy promotes nuclear exit of GtaC, which leads to a transient burst of transcription at each cAMP cycle. We demonstrate that this biological circuit, like an M-bM-^@M-^\edge triggerM-bM-^@M-^], filters out high frequency signals and counts those admitted, thereby enabling cells to modulate gene expression according to the dynamic pattern of the external stimuli. Transcriptional profiling during early development of wild-type, gtaC, GFP-GtaC/gtaC, and NLSex-GFP-GtaC/gtaC strains
2014-04-15 | E-GEOD-54866 | biostudies-arrayexpress
Project description:BACKGROUND: Neointimal hyperplasia is the major cause of significant vascular complications following arterial interventions. Despite the advancements in strategies such as drug-eluting stents (DES) to minimize neointimal hyperplasia, achieving consistently effective long-term outcomes remains a challenge. Protein-protein interactions (PPIs) mediated by PDZ domains are essential for numerous biological processes. However, little is known about the role of PDZ proteins in neointima formation. This study aims to explore the role of TAX1BP3, a singular PDZ protein, in phenotypic switching of VSMCs and its implication in neointimal hyperplasia. METHODS: Subcellular localization of TAX1BP3 was assessed in isolated VSMCs or arteries obtained from mice with neointima formation. TAX1BP3 mutants were constructed to study the role of SUMOylation on TAX1BP3 nucleocytoplasmic shuttling. VSMC-specific Tax1bp3 knockout mice were generated to determine the relevant phenotypes in a carotid artery wire injury model. RNA sequencing, ATAC-sequencing, computational prediction of complex structures, and Co-immunoprecipitation (Co-IP) were performed to elucidate the underlying molecular mechanisms. AAV-mediated Tax1bp3 gene delivery and engineered AIENPs-TAX1BP3 were employed to investigate the potential translational relevance. RESULTS: TAX1BP3 exhibited dynamic nucleocytoplasmic shuttling during phenotypic switching of VSMCs. TAX1BP3 is SUMOylated at K116 and its SUMOylation is essential for maintaining the nuclear localization of TAX1BP3. Deficiency of TAX1BP3 facilitated the transition from a contractile to synthetic phenotype and aggravated neointima formation following vascular injury in mice. The integration of RNA sequencing and ATAC sequencing unveiled that TAX1BP3 primarily regulated the cell cycle progression and cell proliferation of VSMCs through YAP-TEAD transcription activity. The computational prediction of TAX1BP3/YAP1 complex structures and protein interaction related experiments revealed TAX1BP3 and TEAD1 compete for binding to YAP through its TEAD binding domain via a non-canonical PDZ manner. AAV-mediated Tax1bp3 gene delivery significantly attenuated post-injury neointima formation and the progression of atherosclerosis. AIENPs-TAX1BP3 administration effectively reduced VSMCs phenotypic switching and neointimal hyperplasia. CONCLUSIONS: These results demonstrated SUMOylation of TAX1BP3 at K116 enables its nucleocytoplasmic shuttling during phenotypic switching of VSMCs. TAX1BP3 competitively interacts with YAP-TEAD complex in a non-canonical PDZ manner and exerted its protective role in vascular neointimal hyperplasia primarily through the regulation of cell proliferation.
2025-07-01 | GSE297516 | GEO
Project description:Biological oscillations are observed at many levels of cellular organization. In the social amoebae Dictyostelium discoideum, starvation-triggered multicellular development is organized by periodic cAMP waves, which provide both chemoattractant gradients and developmental signals. We report that GtaC, a GATA transcription factor, exhibits rapid nucleocytoplasmic shuttling in response to cAMP waves. This behavior requires coordinated action of a nuclear localization signal and reversible G protein-coupled receptor (GPCR)-mediated phosphorylation. While both are required for developmental gene expression, receptor occupancy promotes nuclear exit of GtaC, which leads to a transient burst of transcription at each cAMP cycle. We demonstrate that this biological circuit, like an “edge trigger”, filters out high frequency signals and counts those admitted, thereby enabling cells to modulate gene expression according to the dynamic pattern of the external stimuli.
2014-04-15 | GSE54866 | GEO
Project description:TAX1BP3 is a SUMOylated Nucleocytoplasmic Shuttling Protein and Protects Against Vascular Neointimal Hyperplasia
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Project description:mRNA level is controlled by factors that mediate both mRNA synthesis and decay, including the 5’ to 3’ exonuclease Xrn1 - a major mRNA synthesis and decay factor. Here we show that nucleocytoplasmic shuttling of several mRNA decay factors plays a key role in determining both mRNA synthesis and decay. Shuttling is regulated by RNA-controlled binding of the karyopherin Kap120 to two nuclear localization sequences (NLSs) in Xrn1, location of one of which is conserved from yeast to human. The decaying RNA binds and masks NLS1, establishing a link between mRNA decay and Xrn1 shuttling. Preventing Xrn1 import, either by deleting KAP120 or mutating the two Xrn1 NLSs, compromise transcription and, unexpectedly, also the cytoplasmic decay, uncovering a cytoplasmic decay pathway that initiates in the nucleus. Most mRNAs are degraded by both the “classical” and the novel pathways, the ratio between them represents a full spectrum. Importantly, Xrn1 shuttling is required for proper adaptation to environmental changes, in particular to ever changing environmental fluctuations.
2022-09-19 | PXD036414 | Pride
Project description:BACKGROUND: The phenotypic switching of vascular smooth muscle cells (VSMCs) plays a crucial role in vascular homeostasis. Protein-protein interactions (PPIs) mediated by PDZ domains is essential for cardiac functions. However, little is known about the role of PDZ proteins in regulating the phenotypic switching of VSMCs. In this study, we aim to explore the role of TAX1BP3, a singular PDZ protein, in maintaining the contractile phenotype of VSMCs. METHODS: Subcellular localization of TAX1BP3 was assessed in isolated VSMCs and arteries from mice or donors with in-stent restenosis and atherosclerosis. VSMC-specific Tax1bp3 knockout mice were generated to determine the relevant phenotypes in a carotid artery wire injury model. RNA sequencing, ATAC-sequencing, computational prediction of complex structures, and coCo-immunoprecipitation (Co-IP) were performed to elucidate the underlying molecular mechanisms. AAV-mediated Tax1bp3 gene delivery and recombinant TAX1BP3 were employed to investigate the potential translational relevance. RESULTS: TAX1BP3 exhibited dynamic nucleocytoplasmic shuttling during phenotypic switching of VSMCs. Deficiency of TAX1BP3 facilitated the transition from a contractile to a synthetic phenotype and aggravated neointima formation following vascular injury in mice. The integration of RNA sequencing and ATAC sequencing unveiled that TAX1BP3 primarily regulated the cell cycle progression and cell proliferation of VAMCs through YAP-TEAD transcription activity. The computational prediction of TAX1BP3/YAP1 complex structures and protein interaction related experiments revealed TAX1BP3 and TEAD1 compete for binding to YAP through its TEAD binding domain via a non-canonical PDZ manner. AAV-mediated Tax1bp3 gene delivery markedly attenuated post-injury neointima formation and the progression of atherosclerosis. Recombinant TAX1BP3 administration effectively reduced VSMCs proliferation and intimal hyperplasia following vascular injury in vitro and in vivo. CONCLUSIONS: Our results identified TAX1BP3 , a novel nucleocytoplasmic protein, a singular PDZ protein, that competitively interacts with YAP/-TEAD complex in a non-canonical PDZ manner and exerted its protective role in phenotypic switching and vascular intimal hyperplasia primarily through the regulation of cell proliferation.
2025-09-16 | GSE255240 | GEO
Project description:BACKGROUND: The phenotypic switching of vascular smooth muscle cells (VSMCs) plays a crucial role in vascular homeostasis. Protein-protein interactions (PPIs) mediated by PDZ domains is essential for cardiac functions. However, little is known about the role of PDZ proteins in regulating the phenotypic switching of VSMCs. In this study, we aim to explore the role of TAX1BP3, a singular PDZ protein, in maintaining the contractile phenotype of VSMCs. METHODS: Subcellular localization of TAX1BP3 was assessed in isolated VSMCs and arteries from mice or donors with in-stent restenosis and atherosclerosis. VSMC-specific Tax1bp3 knockout mice were generated to determine the relevant phenotypes in a carotid artery wire injury model. RNA sequencing, ATAC-sequencing, computational prediction of complex structures, and coCo-immunoprecipitation (Co-IP) were performed to elucidate the underlying molecular mechanisms. AAV-mediated Tax1bp3 gene delivery and recombinant TAX1BP3 were employed to investigate the potential translational relevance. RESULTS: TAX1BP3 exhibited dynamic nucleocytoplasmic shuttling during phenotypic switching of VSMCs. Deficiency of TAX1BP3 facilitated the transition from a contractile to a synthetic phenotype and aggravated neointima formation following vascular injury in mice. The integration of RNA sequencing and ATAC sequencing unveiled that TAX1BP3 primarily regulated the cell cycle progression and cell proliferation of VAMCs through YAP-TEAD transcription activity. The computational prediction of TAX1BP3/YAP1 complex structures and protein interaction related experiments revealed TAX1BP3 and TEAD1 compete for binding to YAP through its TEAD binding domain via a non-canonical PDZ manner. AAV-mediated Tax1bp3 gene delivery markedly attenuated post-injury neointima formation and the progression of atherosclerosis. Recombinant TAX1BP3 administration effectively reduced VSMCs proliferation and intimal hyperplasia following vascular injury in vitro and in vivo. CONCLUSIONS: Our results identified TAX1BP3 , a novel nucleocytoplasmic protein, a singular PDZ protein, that competitively interacts with YAP/-TEAD complex in a non-canonical PDZ manner and exerted its protective role in phenotypic switching and vascular intimal hyperplasia primarily through the regulation of cell proliferation.
2025-09-16 | GSE255241 | GEO
Project description:BACKGROUND: The phenotypic switching of vascular smooth muscle cells (VSMCs) plays a crucial role in vascular homeostasis. Protein-protein interactions (PPIs) mediated by PDZ domains is essential for cardiac functions. However, little is known about the role of PDZ proteins in regulating the phenotypic switching of VSMCs. In this study, we aim to explore the role of TAX1BP3, a singular PDZ protein, in maintaining the contractile phenotype of VSMCs. METHODS: Subcellular localization of TAX1BP3 was assessed in isolated VSMCs and arteries from mice or donors with in-stent restenosis and atherosclerosis. VSMC-specific Tax1bp3 knockout mice were generated to determine the relevant phenotypes in a carotid artery wire injury model. RNA sequencing, ATAC-sequencing, computational prediction of complex structures, and coCo-immunoprecipitation (Co-IP) were performed to elucidate the underlying molecular mechanisms. AAV-mediated Tax1bp3 gene delivery and recombinant TAX1BP3 were employed to investigate the potential translational relevance. RESULTS: TAX1BP3 exhibited dynamic nucleocytoplasmic shuttling during phenotypic switching of VSMCs. Deficiency of TAX1BP3 facilitated the transition from a contractile to a synthetic phenotype and aggravated neointima formation following vascular injury in mice. The integration of RNA sequencing and ATAC sequencing unveiled that TAX1BP3 primarily regulated the cell cycle progression and cell proliferation of VAMCs through YAP-TEAD transcription activity. The computational prediction of TAX1BP3/YAP1 complex structures and protein interaction related experiments revealed TAX1BP3 and TEAD1 compete for binding to YAP through its TEAD binding domain via a non-canonical PDZ manner. AAV-mediated Tax1bp3 gene delivery markedly attenuated post-injury neointima formation and the progression of atherosclerosis. Recombinant TAX1BP3 administration effectively reduced VSMCs proliferation and intimal hyperplasia following vascular injury in vitro and in vivo. CONCLUSIONS: Our results identified TAX1BP3 , a novel nucleocytoplasmic protein, a singular PDZ protein, that competitively interacts with YAP/-TEAD complex in a non-canonical PDZ manner and exerted its protective role in phenotypic switching and vascular intimal hyperplasia primarily through the regulation of cell proliferation.
2025-09-16 | GSE255239 | GEO
Project description:Objective This study aimed to investigate the expression and clinical significance of N6-methyladenosine (m6A) modification of circular RNA (circRNA) in oral leukoplakia (OLK) and oral squamous carcinoma cell (OSCC) tissues. Methods Using methylation RNA immunoprecipitation high-throughput sequencing technology (MeRIP-seq) and RNA high-throughput sequencing technology (RNA-seq), the first circRNA transcriptome analysis for detecting m6A methylationome profiles in OLK and OSCC tissues was obtained, followed by bioinformatics analysis. The qRT-PCR technique and protein immunoblotting technique were used to detect the expression of m6A methylesterase in OLK versus OSCC tissues. Results In this study, 275 differential m6A methylation peaks were identified in OLK and OSCC, among which 193 peaks were up-regulated and 82 were down-regulated. Additionally, 198 differential m6A methylation modified circRNAs were observed, with 127 up-regulated and 71 down-regulated (FC ≥ 2, P < 0.05). Most of the identified circRNAs that underwent m6A methylation alterations were derived from overlapping regions. It was found that the differential expression of circRNAs was not correlated with the joint analysis of significantly different m6A-circRNAs between the two groups. Furthermore, downregulation of mETTL14 and FTO protein levels was observed in OSCC tissues, although there were no discernible alterations in RNA levels. Conclusion Our study suggests that m6A methylation modification of circRNA may play a role in the development of oral leukoplakia, and that METTL14 and FTO may be important methylation enzymes that influence the development of oral leukoplakia. These findings may open up new research directions for in-depth investigations to clarify the molecular mechanisms of OLK carcinogenesis.
2023-09-20 | GSE243097 | GEO