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Effects of CDC5L knockdown on gene transcription levels in HeLa cell lines

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE306238 | GEO | 2026/07/20

REPOSITORIES: GEO

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Effects of CDC5L knockdown on gene transcription levels in HeLa cell lines [RNA]

Project description:Stress granules (SGs) are membraneless protein condensates that form in the cytoplasm of a cell upon exposure to cellular stressors. Here, 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. In order to identify the regulation on the overall cellular transcriptome, especially stress-related genes, after CDC5L knockdown, we used siRNA to knockdown CDC5L and performed RNA-seq in the HeLa cell line.

2026-07-20 | GSE242279 | GEO

Discovery of genes directly bound to CDC5L in HeLa cell lines [ChIP]

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

TRIM28-Mediated SUMOylation of G3BP1/2 Regulates Stress Granule Dynamics

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

PABPC1 SUMOylation enhances cell survival by promoting mitophagy through stabilizing U-rich mRNAs within stress granules (RIP-Seq)

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

PABPC1 SUMOylation enhances cell survival by promoting mitophagy through stabilizing U-rich mRNAs within stress granules (4sU-Seq)

2025-05-10 | GSE260508 | GEO

RNA partitioning into stress granules is independent of G3BP

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

lcFAX-MS-Powered Biomolecular Condensate Analysis Reveals TRIM28-Mediated G3BP1/2 SUMOylation in Regulating Stress Granule Dynamics

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 |

Reversible amyloids of pyruvate kinase couple cell metabolism and stress granule disassembly

Project description:Cells respond to stress by blocking translation, rewiring metabolism, and forming transient mRNP assemblies called stress granules (SGs). After stress release, re-establishing homeostasis requires energy-consuming processes. However, the molecular mechanisms whereby cells restore energy production to disassemble SGs and reinitiate growth after stress remain poorly understood. Here we show that, upon stress, the ATP-producing enzyme Cdc19 forms inactive amyloids, and that their rapid re-solubilization is essential to restore energy production and SG disassembly. Cdc19 re-solubilization is initiated by the glycolytic metabolite fructose-1,6-bisphosphate (FBP), which directly binds Cdc19 amyloids and facilitates conformational changes that allow Hsp104 and Ssa2 chaperone recruitment. FBP then promotes Cdc19 tetramerization and activity, which together with trehalose breakdown boosts glycolysis to further enhance SG disassembly. Together, these results provide a molecular mechanism protecting cells during stress by directly coupling metabolism and ATP production with SG dynamics via regulation of Cdc19 amyloids.

2021-08-17 | PXD026060 | Pride

Differentiation Defect Repositions Sebaceous Glands as Instigators in the Early Pathogenesis of Hidradenitis Suppurativa

Project description:<p>The role of sebaceous glands (SGs) in the early pathogenesis of hidradenitis suppurativa (HS) is undefined, with unclear causal relationship to inflammatory sequelae. The aim of this study was to determine whether SG aberrations constitute a primary pathogenic driver in early HS and elucidate the underlying mechanism. Histological study, single-cell RNA sequencing (scRNA-seq), and in vitro functional assays were employed. Clinical specimens included non-lesional skin, early lesional skin from patients diagnosed with Hurley I HS, and healthy controls. Human SZ95 sebocytes were used for mechanistic studies, including gene knockdown with lentivirus, bulk RNA sequencing, and liquid chromatography-tandem mass spectrometry based lipidomic analysis. </p><p>The size of SG was significantly reduced in HS patients. Development aberration and significant downregulation of tight junction signaling (e.g., TJP1, OCLN, CLDN1) in HS SGs were revealed by scRNA-seq, associated with compromised barrier integrity and early CD45+ immune cell infiltration. Knockdown of CLDN1 in human SZ95 sebocytes recapitulated these findings, inducing a robust pro-inflammatory response and a shift toward keratinocyte-like lineage accompanied by metabolic reprogramming, specifically overproduction of lysophosphatidylcholine (LPC). Exogenous LPC directly promoted proliferation and inflammatory cytokine secretion in HaCaT keratinocytes. Collectively, these findings reposition SGs as instigators in the early pathogenesis of HS.</p>

2025-12-28 | MTBLS13578 | MetaboLights

Membrane atg8ylation coordinates stress granule formation and mTOR inactivation in response to lysosomal damage

Project description:We report that lysosomal damage is a hitherto unknown inducer of stress granule (SG) formation and that the process termed membrane atg8ylation coordinates SG formation with mTOR inactivation during lysosomal stress. SGs were induced by lysosome-damaging agents including SARS-CoV-2ORF3a, Mycobacterium tuberculosis, and proteopathic tau. During damage, mammalian ATG8s directly interacted with the core SG proteins NUFIP2 and G3BP1. Atg8ylation was needed for their recruitment to damaged lysosomes independently of SG condensates whereupon NUFIP2 contributed to mTOR inactivation via the Ragulator-RagA/B complex. Thus, cells employ membrane atg8ylation to control and coordinate SG and mTOR responses to lysosomal damage.

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