Effects of CDC5L knockdown on gene transcription levels in HeLa cell lines [RNA]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE242279 | GEO | 2026/07/20
REPOSITORIES: GEO
Similar Datasets
Project description:Stress granules (SGs) are membraneless condensates that assemble in response to cellular stress. We identified cell division cycle 5-like protein (CDC5L) as a regulator of SG dynamics, where CDC5L knockdown triggered SG formation even in the absence of exogenous stress. Reduced CDC5L levels led to upregulation of PERK at both mRNA and protein levels, suggesting transcriptional regulation. To examine the global impact of CDC5L on gene expression, particularly stress-related pathways, we performed RNA-seq in HeLa cells following siRNA-mediated CDC5L knockdown. In parallel, ChIP-PCR demonstrated that CDC5L directly binds to the PERK promoter, indicating a role as a transcriptional repressor. To further characterize CDC5L-bound genomic regions, we established a stable HeLa cell line expressing CDC5L-HA via lentiviral transduction and performed ChIP-seq to identify promoter regions directly occupied by CDC5L. Together, these transcriptomic and epigenomic datasets define CDC5L as a transcriptional regulator of stress-responsive genes.
2026-07-20 | GSE306238 | GEO
Project description:We identified the gene cell division cycle 5-like protein (CDC5L), whose knockdown induced SG formation in the absence of any cellular stress. Moreover, lower protein levels of CDC5L increased mRNA and protein levels of PERK. Through ChIP-PCR, we found that CDC5L regulated transcription by directly binding to PERK promoter.To further clarify the biological function of CDC5L as a transcriptional repressor, we expressed CDC5L-HA in the HeLa cell line, used HA antibodies for chromatin immunoprecipitation, and obtained the promoters to which CDC5L protein directly binds, and performed ChIP-seq analysis.
2026-07-20 | GSE242278 | GEO
Project description:Stress granules (SGs) are stress-induced membraneless organelles whose dynamics are tightly regulated by protein interactions and modifications. However, whether SUMOylation directly targets SG core proteins G3BP1/2 and which ligase is involved remains unclear. Capturing these key events while preserving SG integrity is challenging due to their transient and membraneless nature. To address this, we introduce a low-concentration formaldehyde crosslinking (lcFAX) method that stabilizes membraneless organelles, including G3BP1 SGs and TDP-43 nuclear bodies, enabling enhanced proteome identification. Importantly, we identify TRIM28 as a previously undefined SG-associated protein and reveal that TRIM28 SUMOylates G3BP1 at K287 and G3BP2 at K281, establishing a critical mechanism regulating SG dynamics that ultimately impacts cellular ROS and apoptosis. lcFAX-Seq also provides insights into the RNA composition of SGs. Altogether, lcFAX-MS uncovers the critical role of TRIM28-mediated SUMOylation in modulating SG dynamics, establishing lcFAX as a powerful tool for analyzing membraneless organelles and the underlying regulatory mechanisms.
2025-09-24 | GSE286197 | GEO
Project description:Stress granules (SGs) are cytoplasmic, membraneless organelles that modulate mRNA metabolism and cellular adaptation under stress, yet the mechanisms by which they regulate cancer cell survival remain unclear. Here, we identify Poly(A)-Binding Protein Cytoplasmic 1 (PABPC1), a core SG component, as stress-inducible SUMOylation target. Upon various stress conditions, SUMOylated PABPC1 promotes SG assembly and enhances cancer cell survival. Transcriptome-wide analysis reveals that SUMOylated PABPC1 selectively stabilizes mRNAs enriched in conserved U-rich elements. Mechanistically, SUMOylated PABPC1 interacts with RNA-binding protein TIA1 to form PABPC1-SUMO-TIA1 complex that recruits U-rich mRNAs into SGs, protecting them from degradation. This process facilitates the expression of U-rich genes, such as mitophagy-related genes FUNDC1, BNIP3L, thereby maintaining cellular homeostasis and promoting cell survival under adverse conditions. Our findings reveal that PABPC1 SUMOylation connects stress granule assembly with selective U-rich mRNA stabilization and mitophagy, promoting cancer cell stress adaptation.
2025-05-10 | GSE260510 | GEO
Project description:Stress granules (SGs) are cytoplasmic, membraneless organelles that modulate mRNA metabolism and cellular adaptation under stress, yet the mechanisms by which they regulate cancer cell survival remain unclear. Here, we identify Poly(A)-Binding Protein Cytoplasmic 1 (PABPC1), a core SG component, as stress-inducible SUMOylation target. Upon various stress conditions, SUMOylated PABPC1 promotes SG assembly and enhances cancer cell survival. Transcriptome-wide analysis reveals that SUMOylated PABPC1 selectively stabilizes mRNAs enriched in conserved U-rich elements. Mechanistically, SUMOylated PABPC1 interacts with RNA-binding protein TIA1 to form PABPC1-SUMO-TIA1 complex that recruits U-rich mRNAs into SGs, protecting them from degradation. This process facilitates the expression of U-rich genes, such as mitophagy-related genes FUNDC1, BNIP3L, thereby maintaining cellular homeostasis and promoting cell survival under adverse conditions. Our findings reveal that PABPC1 SUMOylation connects stress granule assembly with selective U-rich mRNA stabilization and mitophagy, promoting cancer cell stress adaptation.
2025-05-10 | GSE260508 | GEO
Project description:Stress granules (SGs) are stress induced RNA-protein assemblies formed from untranslating mRNPs. Mammalian SGs are non-uniform and contain “cores”, which are stable in lysates and heterogenous in protein composition. The interactions defining RNA recruitment into SGs, and whether the RNA composition varies between different cores remains unclear. Herein, we determine the SG transcriptome through purification of both PABPC1 and G3BP SG cores during both arsenite and sorbitol stress. We observe that similar RNAs are recruited to SGs independent of the protein used for core purification, suggesting individual RNA-binding proteins (RBPs) may play a limited role in defining the SG transcriptome. Analysis of the sorbitol-induced SG transcriptome reveals G3BP1/2 has little effect on RNAs recruited to SGs suggesting RNAs localize to SGs independent of individual RBPs. Taken together, we suggest that partitioning of RNAs to SGs is independent of at least some proteins, consistent with SGs forming through intermolecular RNA-RNA interactions.
2019-01-30 | GSE119977 | GEO
Project description:Membraneless organelles are formed through liquid-liquid phase separation (LLPS) without the need for lipid membranes. Various membraneless organelles, such as stress granules (SGs), nucleoli, and P-bodies, play critical roles in regulating cellular homeostasis, and proteins undergoing LLPS have been linked to numerous human diseases. However, due to their transient, heterogeneous, and membraneless nature, capturing their states with preserved integrity is challenging. In this study, we introduce a low-concentration formaldehyde crosslinking (lcFAX) method that effectively stabilizes membraneless organelles, including arsenite (AS)-induced G3BP1 SGs and TDP43 formed nuclear bodies. Using lcFAX-MS, we identified hundreds of new SG proteins. Specifically, we demonstrate that TRIM28 SUMOylates G3BP1 at K287 and G3BP2 at K281, respectively, a crucial mechanism for regulating SG dynamics. Furthermore, lcFAX-seq provides insights into the RNA composition of SGs. Altogether, lcFAX is a powerful tool for stabilizing membraneless organelles, facilitating comprehensive proteomic and transcriptomic analyses that reveal new regulatory mechanisms. Notably, lcFAX-MS highlights the critical role of TRIM28-mediated SUMOylation in modulating SG dynamics.
2024-12-27 | PXD059295 |
Project description:Stress granules (SGs) are dynamic, membrane-less organelles containing complex RNA-protein networks. The RNA components of SGs have been profiled through various approaches, characterized as long, translation-repressed, and highly epigenetically modified. However, it remains unclear whether these RNAs are uniformly distributed within SGs. In this study, we used multiple SG core proteins to genetically target the photocatalyst protein miniSOG, which allows for comprehensive CAP-seq profiling of RNA components within SGs. We discovered that RNAs associated with different SG core proteins exhibit heterogeneous distribution and distinct intrinsic features. Furthermore, we applied CAP-seq to map the RNA components in processing bodies (PBs) under both unstressed conditions and arsenite stimulation. By comparing the SG and PB transcriptomes, our data revealed that m6A modification may promote the localization of RNAs to SGs, while higher AU content may facilitate the targeting of mRNAs to PBs. This suggests potential regulatory roles in determining the subcellular localization of mRNAs within membrane-less organelles.
2024-09-29 | GSE271045 | GEO
Project description:Stress granules (SGs) are conserved reversible cytoplasmic condensates enriched with aggregation-prone proteins assembled in response to various stresses. Defects in disassembly have been associated with various neuro- and muscular degenerative diseases in humans. Plants appear to have efficient approaches to avoid the pathological conversion of SGs. However, how plants regulate SG dynamics is unclear. Here we show increase in either temperature or duration of heat stress reduces the molecular mobility of SG marker protein and suppresses SG clearance. Proteomics analysis and FRAP assays demonstrated 20S and 26S proteasomes as stable “core” components of SGs recruited early during the heat stress. Strikingly, while heat stress inhibits the activity of the overall proteasomes, it induces dramatic ubiquitylation of SG components and enhances the activities of SG-resident proteasomes, which degrade SG components even during the assembly phase. Their proteolytic activities enable the timely disassembly of SGs and secure the survival of plant cells during the recovery from heat stress.
2024-08-22 | PXD044922 | Pride
Project description:The accumulation of misfolded proteins in the endoplasmic reticulum (ER) defines a condition called ER stress that induces the unfolded protein response (UPR). The UPR in mammalian cells attenuates protein synthesis initiation, which prevents the piling up of misfolded proteins in the ER. Mammalian cells rely on Protein Kinase RNA-Like Endoplasmic Reticulum Kinase (PERK) phosphorylation of eIF2alpha to arrest protein synthesis, however, plants do not have a PERK homolog, so the question is whether plants control translation in response to ER stress. We compared changes in RNA levels in the transcriptome to the RNA levels protected by ribosomes and found a decline in translation efficiency, including many UPR genes, in response to ER stress. The decline in translation efficiency is due to the fact that many mRNAs are not loaded onto polyribosomes (polysomes) in proportion to their increase in total RNA, instead some of the transcripts accumulate in stress granules (SGs). The RNAs that populate SGs are not derived from the disassembly of polysomes because protein synthesis remains steady during stress. Thus, the surge in transcription of UPR genes in response to ER stress is accompanied by the formation of SGs, and the sequestration of mRNAs in SGs may serve to temporarily relieve the translation load during ER stress.
2020-07-08 | GSE153969 | GEO