Arabidopsis TREX components THO5A/B
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)
TISSUE(S): Plant Cell, Cell Culture
SUBMITTER: 
Astrid Bruckmann
LAB HEAD: Astrid Bruckmann
PROVIDER: PXD049030 | Pride | 2026-06-16
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 281474976750836.mgf | Mgf | |||
| 281474976750838.mgf | Mgf | |||
| 281474976750839.mgf | Mgf | |||
| 281474976750840.mgf | Mgf | |||
| 281474976750841.mgf | Mgf |
Items per page: 5 1 - 5 of 176 |
Similar Datasets
Project description:Centromeres are specialized chromosomal regions where kinetochore proteins form a protein complex that regulates the cell cycle. KNL2 is an essential protein for kinetochore assembly and plays a significant role in the loading of CENH3. Therefore, the level of KNL2 in plants and other organisms needed to be tightly regulated. Overexpressed AtKNL2 is shown to be degraded via the proteasome degradation pathway by applying an MG115 inhibitor. However, the molecular mechanisms behind the degradation pathway of KNL2 is unknown. Therefore, here we show that the APC/C-dependent degradation of KNL2 is required for maintaining the level and localization of KNL2. We confirmed that the ubiquitin-proteasome system polyubiquitinates and degrades KNL2. Further, IP-MS and Y2H library screening assays performed with KNL2 identified 32 proteins from the ubiquitination pathway. The direct interaction of KNL2 with APC2 was identified using BiFC interaction analysis. Further, the APC10 and Cdc20, core subunit of APC/C, interacts directly with KNL2 as shown by BiFC and Y2H, which is required for substrate recruitment. Moreover, Apcin inhibitor treatment suppresses the degradation of KNL2 in Arabidopsis, validating the involvement of APC/C in KNL2 degradation. Furthermore, our findings highlight the significance of the conserved D-box1 region as a degron for KNL2 in Arabidopsis, facilitating its interaction with APC/C. Further, the interaction of ubiquitin E2 conjugating enzymes (UBC19 and UBC20) with KNL2 has been demonstrated and transfer ubiquitin protein to the lysine sites 336K and 339K of KNL2. Thus, our findings advance our knowledge of cell cycle dynamics by providing insightful information about the molecular mechanisms governing KNL2 regulation.
2025-07-14 | PXD051741 | Pride
Project description:MicroRNAs (miRNAs) together with Argonaute (AGO) proteins form the core of the RNA-induced silencing complex (RISC) to regulate gene expression of their target RNAs post-transcriptionally. Argonaute proteins are subjected to intensive regulation via various post-translational modifications that can affect their stability, silencing efficacy and specificity for targeted gene regulation. We report here that in C. elegans, two conserved serine/threonine kinases - Casein Kinase 1 alpha 1 (CK1A1) and Casein Kinase 2 (CK2) - regulate a highly conserved phosphorylation cluster of 4 Serine residues (S988:S998) on the miRNA-specific AGO protein ALG-1. We show that CK1A1 phosphorylates ALG-1 at sites S992 and S995, while CK2 phosphorylates ALG-1 at sites S988 and S998. Furthermore, we demonstrate that phospho-mimicking mutants of the entire S988:S998 cluster rescue the various developmental defects observed upon depleting CK1A1 and CK2. In humans, we show that CK1A1 also acts as a priming kinase of this cluster on AGO2. Altogether, our data suggest that phosphorylation of AGO within the cluster by CK1A1 and CK2 is required for efficient miRISC-target RNA binding and silencing
2023-09-13 | PXD044139 | Pride
Project description:MicroRNAs (miRNAs) together with Argonaute (AGO) proteins form the core of the RNA-induced silencing complex (RISC) to regulate gene expression of their target RNAs post-transcriptionally. Argonaute proteins are subjected to intensive regulation via various post-translational modifications that can affect their stability, silencing efficacy and specificity for targeted gene regulation. We report here that in C. elegans, two conserved serine/threonine kinases - Casein Kinase 1 alpha 1 (CK1A1) and Casein Kinase 2 (CK2) - regulate a highly conserved phosphorylation cluster of 4 Serine residues (S988:S998) on the miRNA-specific AGO protein ALG-1. We show that CK1A1 phosphorylates ALG-1 at sites S992 and S995, while CK2 phosphorylates ALG-1 at sites S988 and S998. Furthermore, we demonstrate that phospho-mimicking mutants of the entire S988:S998 cluster rescue the various developmental defects observed upon depleting CK1A1 and CK2. In humans, we show that CK1A1 also acts as a priming kinase of this cluster on AGO2. Altogether, our data suggest that phosphorylation of AGO within the cluster by CK1A1 and CK2 is required for efficient miRISC-target RNA binding and silencing
2024-10-17 | PXD043913 | Pride
Project description:Vascular smooth muscle cells (SMCs) change between a contractile-differentiated and a proliferative-dedifferentiated phenotype in response to environmental cues. Long non-coding RNAs (lncRNAs) and N6-methyladenosine (m6A) modification regulate cell fate decision. Here we used primary human pulmonary artery SMCs (hPASMCs) and assessed the expression of lncRNAs during SMCs phenotypic modulation. A lncRNA, which we refer to as Differentiation And Growth Arrest-related lncRNA (DAGAR) was increased during differentiation and we demonstrate that it is required for this process. DAGAR was m6A-modified and regulated by the m6A reader YTHDF2 in SMCs and MRC5 cells. A marked downregulation of YTHDF1-3 proteins during both SMC differentiation and MRC5 quiescence was found, consistent with the increase of DAGAR. Remarkably, YTHDF2 immunoprecipitation followed by RNA deep sequencing (RIP-Seq) displayed an enrichment of key SMC-associated transcripts, including smooth muscle myosin heavy chain (MYH11) and members of the TGF, PDGF and VEGF pathways. Knockdown of YTHDF2 induced DAGAR and SMC marker gene expression. We conclude that the lncRNA DAGAR and YTHDF2 contribute to the regulation of SMC plasticity and differentiation programs.
2025-05-06 | PXD029550 | Pride
Project description:Numerous long non-coding RNAs (lncRNAs) were shown to have functional impact on cellular processes, such as human epidermal homeostasis, but for only a few the mode of action has been elucidated. Here, we report that lncRNA LINC00941 controls keratinocyte differentiation on a global level through association with the MTA2/NuRD complex, one of the major chromatin remodelers in cells. LINC00941 was found to interact with NuRD-associated MTA2, suppressing the expression of the transcription factor EGR3, a regulator of epidermal differentiation. Both LINC00941 and the MTA2/NuRD complex are enriched in non-differentiated keratinocytes and repress the expression of differentiation genes through epigenetic silencing of EGR3, consequentially preventing premature differentiation of human progenitor cells.
2024-04-08 | PXD043838 | Pride
Project description:Circular RNAs (circRNAs) are frequently generated during splicing. Their physiological roles, however, remain largely elusive. Some specific circRNAs function as microRNA (miRNA) or RNA binding protein (RBP) sponges or encode for proteins and are actively translated. Due to the lack of accessible ends, circRNAs are resistant to exonucleolytic cleavage and thus are more stable than linear RNAs. Nevertheless, circRNAs are most likely turned over by cellular degradation pathways. Here, we used a biochemical purification strategy to find nucleases that could degrade circRNAs. We identified the exosome-associated nuclease DIS3, which contains an endonucleolytic PIN domain and an exonuclease domain. We show that DIS3 can degrade circRNAs independently of the exosome in vitro. Although moderately, RNA-seq reveals that selected circRNAs are stabilized when DIS3 is reduced in vivo. Based on our data, we propose a model, in which cytoplasmic DIS3 contributes to the turnover of circRNAs in human cells.
2025-05-05 | PXD050442 | Pride
Project description:The factors that underlie the increasing incidence of diabetes with age are poorly understood. We examined whether telomere length, known to decrease with age, plays a role in the age-dependent increased incidence of diabetes. We show that in mice with short telomeres, insulin secretion is impaired and leads to glucose intolerance despite the presence of an intact M-NM-2-cell mass. Islets from mice with short telomeres displayed evidence of M-NM-2-cell dysfunction, and in response to glucose, had defective mitochondrial membrane depolarization as well as Ca2+ handling which limited insulin release. Short telomeres induced the hallmarks of senescence including premature accumulation of p16INK4a, and altered gene expression of key pathways essential for signaling and insulin secretion. Short telomeres also had an additive damaging effect to endoplasmic reticulum stress which occurs in the late stages of type 2 diabetes. This manifested as more severe hyperglycemia in insulin mutant Akita mice which had a more profound loss of M-NM-2-cell mass and increased M-NM-2-cell apoptosis. Our data identify impaired signaling in the setting of senescence as a novel mechanism of telomere-mediated disease, and implicate telomere length as a determinant of risk and pathogenesis in diabetes. The experiment is designed to analyze gene expression profiles of islets from mice with short telomeres compared to those of wildtype mice.
2013-10-01 | E-GEOD-25040 | biostudies-arrayexpress
Project description:Histone phosphorylation plays key roles in stress-induced transcriptional reprogramming in metazoans but its function(s) in land plants has remained relatively unexplored. Here we report that an Arabidopsis mutant defective in At3g03940 and At5g18190, encoding closely related Ser/Thr protein kinases, shows pleiotropic phenotypes including dwarfism and hypersensitivity to osmotic/salt stress. The double mutant has reduced global levels of phosphorylated histone H3 threonine 3 (H3T3ph), which are not enhanced, unlike the response in the wild type, by drought-like treatments. Genome-wide analyses revealed increased H3T3ph, slight enhancement in trimethylated histone H3 lysine 4 (H3K4me3), and a modest decrease in histone H3 occupancy in pericentromeric/knob regions of wild type plants under osmotic stress. However, despite these changes in heterochromatin, transposons and repeats remained largely transcriptionally repressed. In contrast, this reorganization of heterochromatin was mostly absent in the double mutant, which even under normal conditions exhibited lower H3T3ph levels in pericentromeric regions, and a few transposons and repeat sequences showed modest transcriptional activation. Interestingly, within actively transcribed protein-coding genes, H3T3ph density was minimal in 5’ genic regions, coincidental with a peak of H3K4me3 accumulation. This pattern was not affected in the double mutant, implying the existence of additional H3T3 protein kinases in Arabidopsis. Our results suggest that At3g03940 and At5g18190 are involved in the phosphorylation of H3T3 in pericentromeric/knob regions and that this repressive epigenetic mark may be important for maintaining proper heterochromatic organization and, possibly, chromosome function(s). Columbia-0 and double mutant at3g03940/at518190 knockdown plants were grown in 12 hr light for 3 weeks in pots with soil covered with miracloth to prevent soil contamination of leaf tissues. Control was kept in normal watered state, for other samples (peg) drought stress was induced by treatment with 30% Polyethylene glycol (PEG 6,000) for 5 hours. Pulldowns on H3, H3K4, and H3T3 were performed on all samples with 3-4 replicates.
2015-07-22 | E-GEOD-68370 | biostudies-arrayexpress
Project description:Epigenetic regulation is a dynamic and reversible process that controls gene expression. Abnormal function results in downregulation or upregulation of pathways leading to diseases, such as cancer. The enzymes that establish and maintain epigenetic marks, such as histone methyltransferases (HMTs), are therapeutic targets as their and, importantly, the epigenetic modifications are reversible. Noteworthy, HMTs, as the other epigenetic enzymes and readers, form together multiprotein complexes that in concert regulate histone marks. To probe the epigenetic protein complexes in a biological system, we developed a reliable chemical biology high-content imaging strategy to screen compound libraries on multiple histone marks inside cells simultaneously. The advantage is double: (1) it identifies directly a drug that is active in cells on a specific histone mark and (2) it reveals the crosstalk between the epigenetic marks. By this approach, we identified that compound 4, a published CARM1 (PRMT4) inhibitor, inhibits both histone mark H3R2me2a (regulated by CARM1) and H3K79me2 (regulated by DOT1L) pointing out a synergistic interaction between the two HMTs. The results obtained by the screening assay were validated by mass spectrometry and other techniques confirming the crosstalk between the two marks and HMTs. Prompted by the interaction between CARM1 and DOT1L we combined compound 4 and DOT1L inhibitor EPZ-5676 resulting in a stronger cell proliferation inhibition and apoptosis, indicating that our approach provides also a novel strategy to identify effective synergistic drug combinations for cancer therapy.
2022-05-19 | PXD022873 | Pride
Project description:Some triple-negative breast cancer (TNBC) patients evaluated as Miller-Payne 4 with ypN0 after neoadjuvant chemotherapy (NACT) who have better prognosis should avoid escalation of therapy. We aim to identify these patients through evaluating pretherapeutic spatial distributions of immunophenotypes. Our retrospective study in patients with TNBC assessed as Miller-Payne grade 4/5 with ypN0 showed that Miller-Payne 4 with ypN0 group had poorer 5-year disease-free survival (DFS, 63.8% vs 83.0%, p=0.003) and the 5-year overall survival (OS, 71.0% vs 85.5%, p=0.007) than Miller-Payne 5 with ypN0 group. High TILs were significantly associated with better DFS and OS in patients with Miller-Payne 4 and ypN0 (both p=0.016). Spatially, detected by multiplexed ion beam imaging by time of flight combined with proteomics, tumors assessed as Miller-Payne 4 and ypN0 with good prognosis exhibited an inflamed phenotype, with dominant CD8+ T cells on tumor center, few scattered CD68+ myeloid-derived cells far away from T cells, and deposit of increased activated molecules of lymphocyte. While those with poor prognosis presented excluded phenotype, with few CD8+ T cells restricted to invasive margin and a high density of CD14+CD68+CD11c+ myeloid cells. A good classifier model based on 29 spatial immunophenotypes was established by the random forest algorithm (AUC=0.975), for identifying patients with Miller-Payne 4 and ypN0 who had favorable prognosis. We also observed similar signatures in patients with Miller-Payne 5 and ypN0. Taken together, spatial immunophenotypes may assess the prognosis in TNBC patients with Miller-Payne 4 and ypN0 after NACT.
2023-07-08 | PXD029186 | Pride