Ontology highlight
ABSTRACT:
PROVIDER: PRJNA673927 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12968633_1.fastq.gz | Fastqsanger.gz | |||
| SRR12968633_2.fastq.gz | Fastqsanger.gz | |||
| SRR12968634_1.fastq.gz | Fastqsanger.gz | |||
| SRR12968634_2.fastq.gz | Fastqsanger.gz | |||
| SRR12968635_1.fastq.gz | Fastqsanger.gz |
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Project description:In the 1950s the drug thalidomide administered as a sedative to pregnant women led ot the birth of thousands of children with multiple defects. Despite its teratogenicity, thalidomide and ist IMiD derivatives recently emerged as effective treatments for multiple myeloma and 5q-dysplasia. IMiDs target the CUL4-RBX1-DDB1-CRBN (CRL4(CRBN)) ubiquitin ligase. Through an unbiased screen we identify the homeobox trranscription factor MEIS2 as an endogenous substrate of CRL4(CRBN). By definition, a specific target of CRL4(CRBN) is expected to have a very low intensity on negative control arrays (E1_E2), (E1_CRBN), (E1_E2_Cdt2), (E1_E2_Cdt2_revlimid), (E1_E2_Cdt2_CSN) or with CRL4(CRBN) in presence of inhibitor (E1_E2_CRBN_revlimid) and high intensity on arrays with CRL4(CRBN) (E1_E2_CRBN) or CRL4(CRBN) in presence of CSN (E1_E2_CRBN_CSN) Accordingly 16 protein microarrays were subjected to in vitro ubiquitylation using the following enzyme combinations: 3x Uba1+UbcH5a; 2x Uba1+UbcH5a+CRL4(DDB2); 3x Uba1+UbcH5a+CRL4(CRBN); 2x Uba1+UbcH5a+CRL4(CRBN)+lenalidomide; 2x Uba1+UbcH5a+CRL4(CRBN)+CSN; 2x Uba1+UbcH5a+CRL4(Cdt2); 1x Uba1+UbcH5a+CRL4(Cdt2)+CSN; 1x Uba1+UbcH5a+CRL4(Cdt2)+lenalidomide
2014-05-13 | E-GEOD-57554 | biostudies-arrayexpress
Project description:Most developmental processes associated with fruit patterning take place at the floral meristem (FM). Age-regulated microRNA156 (miR156) and gibberellins (GA) integrate to control flowering time, but it is unclear how GA and miR156 interplay during fruit patterning. Here, we used genetic, molecular, and imaging tools to demonstrate that GA and age synergistically control tomato reproductive development. We found that low levels of miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL/SBP) transcripts or high GA responses/levels led to enlarged FMs, defects in FM determinacy, and fruits with increased locule number. Conversely, low GA responses reduced locule number and indeterminacy, and the expression of a miR156-resistant form of SlSBP15 (rSBP15) reduces FM size by decreasing cell size and cell number. Importantly, we discovered that GA levels/responses may be partially responsible for the fruit defects observed in 156OE and rSBP15 plants. GA and miR156-targeted SlSBPs regulate classical genes associated with floral determinacy, such as CRABS CLAWa (SlCRCa), and GA and SlSBPs act synergistically with tomato CLAVATA3 (SlCLV3) to control early flower and fruit development. Our findings indicate that gibberellins and age-dependent miR156-targeted SlSBPs co-operate to regulate FM activity and locule formation, thereby offering a novel mechanism of controlling fruit patterning.
2023-07-25 | GSE223674 | GEO
Project description:Samples from fruit juice vesicle tissue from three lemon genotypes (Frost Lisbon, Faris "sour" and Faris "sweet") differing in fruit acidity were compared at two developmental timepoints (immature, mature). Faris lemon appears to be a graft chimera with the L2 layer derived from normal acid lemon and layer L1 from Millsweet limetta or a closely related genotype. Fruit of Faris sour and Faris sweet grew on different branches of the same tree, with sour fruit developing on branches with L1 and L2 from acid lemon. genotype: Faris sweet lemon - developmental stage: PO:0007009 FF.01 fruit size 30%,(3-replications); genotype: Faris sweet lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening,(3-replications); genotype: Faris acid lemon - developmental stage: PO:0007009 FF.01 fruit size 30%,(3-replications); genotype: Faris acid lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening,(3-replications); genotype: Frost Lisbon lemon - developmental stage: PO:0007009 FF.01 fruit size 30%,(3-replications); genotype: Frost Lisbon lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening,(3-replications) PLEXdb (http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Mikeal L. Roose. The equivalent experiment is CT1 at PLEXdb.
2011-12-07 | E-GEOD-12804 | biostudies-arrayexpress
Project description:Ubiquitin-mediated proteolysis play a significant role in various biological processes including transcription, DNA repair and cell cycle progression. The identification of Set8 and Set8b (a splice isoform) histone H4K20 methyl transferase as a substrate for the cullin-based ubiquitin ligase (CRL4-Cdt2) demonstrate that this pathway plays a significant role in promoting cell cycle progression, specifically promoting G2 progression. This study investigate the effect of failure to degrade Set8 in S-phase of the cell cycle via CRL4-Cdt2 on gene expression. We used microarrays to detail the effect of the expression of stable form of Set8b H4K20 mono-methyl transferase (Set8b_deltaPIP2) on gene expression Human osteosarcoma-derived human cells were transduced with retroviruses encoding either wt-Set8b or a mutant of Setb8 which is resistant to degradation via CRL4-Cdt2 ubiquitin ligase complex (Set8b_deltaPIP2) or with an a control pMSCV empty virus. 5 days after transduction, cells were harvested and the RNA was extracted by Trizol (Invitrogen) and hybridized to the affymetrix chips array.
2010-09-18 | E-GEOD-24170 | biostudies-arrayexpress
Project description:CRL4-DCAF15 control of cohesin dynamics sustains cell proliferation [HiC]
| PRJNA1008732 | ENA
Project description:Despite the emerging evidence of ferroptosis implicated in diverse pathological scenarios, molecular adaptors linking its oxidative inducers and chromatin as carrier of stable epigenetic memory for its propagation remain elusive. Here, we report the identification of two WD40 proteins DCAF8 and WDR76 as substrate adaptor and molecular inhibitor respectively of the Cullin-4 RING ubiquitin ligase (CRL4) system for stability control of the chromatin remodeler LSH. Degradation analysis and CRL4-DCAF8 complex reconstitution demonstrate that CRL4DCAF8 is a bona fide E3 ligase for LSH. In contrast, WDR76 antagonizes DCAF8-targeted LSH proteolysis through competitive inhibition of the holo-CRL4DCAF8-LSH complex assembly. Importantly, this opposing regulatory strategy is utilized in lipid hydroperoxide induced ferroptosis, and we identify key redox homeostasis genes significantly regulated by the DCAF8/WDR76/LSH axis through transcriptomic epistasis analysis. Such responsiveness could be attributed to increased ratio of DCAF8 over WDR76 for antagonistic LSH association accompanying ROS overproduction invoked decrease of TET-catalyzed DNA oxidation. Evaluation of epigenetic dynamics at DCAF8/WDR76/LSH-regulated gene promoters reveals linker histone H1- and LSH-associated transcriptional repression is coordinately removed in ferroptosis. Together with phenotypes driven by WDR76 and DCAF8 manipulations, these data identify DCAF8- and WDR76-governed LSH degradation as a crucial node in ferroptosis, tumorigenesis and senescence.
2021-06-09 | GSE135361 | GEO
Project description:Cell cycle progression in mammals is modulated by two ubiquitin ligase complexes, CRL4 and SCF, which facilitate degradation of chromatin substrates involved in the regulation of DNA replication. One member of the CRL4 complex, RepID (DCAF14/PHIP), is a WD40-containing protein that selectively binds and activates a group of replication origins. We found that RepID recruits the CRL4 complex to chromatin prior to DNA synthesis, thus playing a crucial architectural role in the proper licensing of chromosomes for replication. In the absence of RepID, cells rely on the alternative ubiquitin ligase, SKP2-containing SCF, to progress through the cell cycle. RepID depletion markedly increases cellular sensitivity to SKP2 inhibitors, which triggered massive genome re-replication. Both RepID and SKP2 interact with distinct, non-overlapping groups of replication origins, suggesting that selective interactions of replication origins with specific CRL components execute the DNA replication program and maintain genomic stability by preventing re-initiation of DNA replication.
2018-06-27 | GSE114703 | GEO
Project description:CRL4-DCAF15 control of cohesin dynamics sustains cell proliferation [RNA-seq_dTAG]
| PRJNA1105321 | ENA