Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome and analysis of Wdr70 deletion by next-generation sequencing

ABSTRACT: CRL4 is a family of SCF-like ubiquitin ligase constituted by Cul4-Ddb1-RING finger scaffold and DCAF substrate adaptors. We revealed Wdr70 as a novel DCAF protein that assembles with Cul4-Ddb1 and functions as chromatin remodeling factor in Schizosaccharomyces pombe.Besides its function in DNA repair, CRL4Wdr70 is speculated to regulate gene expression in a subset of yeast transcriptome. Here we use the next-generation sequencing to show that deletion of Wdr70 gene disturbs the gene expression profile of G2-synchronised yeast cells. Examination of genome-wide gene expression in 2 different yeast strains using Illumina Hiseq2500.

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Cong Liu

PROVIDER: E-GEOD-79830 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome and analysis of Wdr70 deletion by next-generation sequencing

Project description:CRL4 is a family of SCF-like ubiquitin ligase constituted by Cul4-Ddb1-RING finger scaffold and DCAF substrate adaptors. We revealed Wdr70 as a novel DCAF protein that assembles with Cul4-Ddb1 and functions as chromatin remodeling factor in Schizosaccharomyces pombe.Besides its function in DNA repair, CRL4Wdr70 is speculated to regulate gene expression in a subset of yeast transcriptome. Here we use the next-generation sequencing to show that deletion of Wdr70 gene disturbs the gene expression profile of G2-synchronised yeast cells.

2016-04-04 | GSE79830 | GEO

DDB1 Binds Histone Reader BRWD3 to Activate the Transcriptional Cascade in Adipogenesis and Promote Onset of Obesity (ChIP-seq II)

Project description:DDB1 is typically recognized as a component of the Cullin4 (CUL4)-RING E3 ubiquitin ligase complex. Here, we show that DDB1 functions independently of CUL4 to promote adipogenesis and diet-induced obesity. In contrast to depletion of CUL4A or CUL4B that stimulates adipogenesis, lack of DDB1 dramatically suppresses the process. Re-introduction of a DDB1 mutant that lacks the binding ability to CUL4A or CUL4B fully restores adipogenesis in DDB1-deficient preadipocytes. Furthermore, while inducibly knocking out Cul4a or Cul4b in mice aggravates diet-induced obesity, Ddb1+/- mice are lean on high-fat diet. Mechanistically, by binding the bromodomain-containing histone reader BRWD3, DDB1 is recruited to acetylated histones in the proximal promoters of immediate-early response genes, where it facilitates the release of paused RNA polymerase II (Pol II) and activates the transcription of these genes. Our findings have thus uncovered a mechanism of activating the transcriptional cascade in adipogenesis by DDB1-mediated release of paused Pol II.

2023-09-17 | GSE168136 | GEO

DDB1 Binds Histone Reader BRWD3 to Activate the Transcriptional Cascade in Adipogenesis and Promote Onset of Obesity (RNA-Seq)

2023-09-17 | GSE158172 | GEO

DDB1 Binds Histone Reader BRWD3 to Activate the Transcriptional Cascade in Adipogenesis and Promote Onset of Obesity (ChIP-Seq)

2023-09-17 | GSE158171 | GEO

Pulse-SILAC and interactomics reveal distinct DDB1-CUL4 associated factors (DCAFs), cellular functions, and protein substrates

Project description:Cullin-RING finger ligases (CRLs) represent the largest family of ubiquitin ligases. They are responsible for the ubiquitination of ~20% of cellular proteins degraded through the proteasome, by catalyzing the transfer of E2-loaded ubiquitin to a substrate. Seven Cullins are described in vertebrates. Among them, CUL4 associates with DDB1 to form the CUL4-DDB1 ubiquitin ligase complex, which is involved in protein ubiquitination and in the regulation of many cellular processes. Substrate recognition adaptors named DDB1/CUL4 associated factors (DCAF) mediate the specificity of CUL4-DDB1 and have a short structural motif of approximately forty amino acids terminating in a tryptophan (W)-aspartic acid (D) dipeptide, called the WD40 domain. Using different approaches (bioinformatics/structural analyses), independent studies suggested that at least sixty WD40-containing proteins could act as adaptors for the DDB1/CUL4 complex. To better define this association and classification, the interaction of each DCAFs with DDB1 was determined, and new partners and potential substrates were identified. Using BioID and AP-MS approaches, we demonstrated that seven WD40 proteins can be considered DCAFs with a high confidence level. Identifying protein interactions does not always lead to identifying protein substrates for E3-ubiquitin ligases, so we measured changes in protein stability or degradation by pulse-SILAC to identify changes in protein degradation following the expression of each DCAF. In conclusion, these results provide new insights into the roles of DCAFs in regulating the activity of the DDB1-CUL4 complex, in protein targeting, and characterized the cellular processes involved

2023-10-11 | PXD042903 | Pride

Identification of protein substrates of the Cullin-RING E3 ubiquitin ligase CRL4 through its substrate recognition factors DCAFs

Project description:Cullin-RING finger Ligases (CRLs) represent the largest family of E3 ubiquitin ligases and are responsible for ubiquitination of ~20% of cellular proteins degraded through the proteasome, catalyzing the transfer of E2-loaded ubiquitin to a substrate. Eight Cullins were described in vertebrates and among them, CUL4 associates with DDB1 acting as an adaptor to form the CUL4-DDB1 ubiquitin ligase complex, involved in protein ubiquitination and regulation of many cellular processes. The specificity of CUL4-DDB1 is mediated by substrate recognition adaptors named DDB1/CUL4 associated factors (DCAFs), which are characterized by the presence of a short structural motif of approximately 40 amino acids terminating in a tryptophan (W)-aspartic acid (D) dipeptide, the WD40 domain. Using different approaches (bioinformatics/structural analyses), independent studies suggested at least 60 different WD40 containing proteins that could act as adaptors for the DDB1/CUL4 complex. In this study, we aimed to validate the DCAFs based on their interaction with DDB1 and to define new partners and potential substrates of each DCAF using affinity purification followed by mass spectrometry. Using BioID and AP-MS approaches, we confirmed seven WDR40 protein that can be considered as DCAF with a high confidence level. Because identification of protein substrates of E3-ubiquitin ligases is not always guaranteed by identifying protein interactions, changes in protein stability and protein degradation was measured by pulse-SILAC to identify the protein substrates targeted for proteasomal degradation by each DCAFs. In conclusion, this work provides new insights into the roles of DCAFs as substrate adaptors for the DDB1-CUL4 complex, identifies the proteins targeting and the cellular processes that are involved.

2023-10-24 | PXD037482 | Pride

CRL4(CRBN) ubiquitin ligase profiling

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).

2014-05-13 | GSE57554 | GEO

Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses

Project description:crosslinking mass spectrometry results for sulfo-SDA crosslinking of human CUL4-NEDD8/ROC1/DDB1/DCAF1-CtD in complex with SAMHD1 and Vpr protein from simian immunodeficiency virus infecting Cercopithecus cephus (SIVmus Vpr)

2021-07-20 | PXD020453 | Pride

Chemical cross-linking of the Spindly-RZZ complex followed by mass spectrometry

Project description:Kinetochores are macromolecular assemblies that connect chromosomes to spindle microtubules during mitosis. The metazoan-specific ≈800 kilodalton ROD-Zwilch-ZW10 (RZZ) complex builds a fibrous corona that assembles on mitotic kinetochores prior to microtubule attachment to promote chromosome alignment and robust spindle assembly checkpoint signaling. Here, we combine biochemical reconstitutions, single particle electron cryo microscopy, cross-linking mass spectrometry, and structural modeling to build a complete model of human RZZ

2022-02-28 | PXD005287 | Pride

The E3 ubiquitin ligase DDB1 controls homeostasis of hematopoietic stem and progenitor cells

Project description:Hematopoietic stem cells (HSC) are regulated to keep the balance between self-renewal and differentiation. However, little is known about post-translational regulations in HSCs. In this study, we characterize the role of DDB1, a component of the Cul4A-DDB1 E3 ubiquitin ligase complex, in HSCs and progenitors by using conditional DDB1 knockout models. We show that the maintenance and differentiation of both adult and fetal HSCs and progenitor cells is dependent on DDB1 function. Deletion of DDB1 alters cell cycle progression and induces apoptosis. Furthermore, deletion of DDB1 in developing thymocytes had no effects on T cell differentiation, whereas DDB1-deficient peripheral T cells were not able to enter cell cycle when stimulated in vitro. In addition, DDB1 is essential for T cell leukemia initiation. Our results reveal that DDB1 is required for adult and fetal hematopoiesis as it controls progenitor and stem cell homeostasis. Transcriptional consequences of inactivating DDB1 in fetal LSK cells. Four samples were analyzed: wild-type (WT) control and DDB1-deficient (DDB1) Lin-ckit+Sca1+ (LSK) cells sorted from fetal livers E16.5 of DDB1 flox/flox, VavCre+ and control mice.

2015-07-10 | E-GEOD-70658 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data