Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of Plk1 interacting proteins by XChIP-MS

ABSTRACT: Polo-like kinase 1 (Plk1) is an important protein kinase for checkpoint recovery and adaptation in response to DNA damage and replication stress. However, although Plk1 is present in S phase, little is known about its localization and function during unperturbed DNA replication. Using Xenopus laevis egg extracts, mimicking early embryonic replication, we developed a Plk1 chromatin immunoprecipitation approach followed by a proteomic shotgun analysis (XChIP-MS) to identify Plk1 interactions with chromatin and with specific nuclear proteins. We purified and cross-linked nuclei after pre-RC assembly before the start of DNA replication, or later during DNA replication. The DNA was fractionated by sonication and immunoprecipited using anti Plk1 or control antibodies then proteins were analyzed by nanoLC/MS/MS.

INSTRUMENT(S): TripleTOF 4600

ORGANISM(S): Xenopus Laevis (african Clawed Frog)

TISSUE(S): Egg

SUBMITTER: David Cornu

LAB HEAD: David Cornu

PROVIDER: PXD022440 | Pride | 2021-08-25

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Protein recruitment on chromatin in the presence or absence of Plk1

Project description:Polo-like kinase 1 (Plk1) is an important protein kinase for checkpoint recovery and adaptation in response to DNA damage and replication stress. However, although Plk1 is present in S phase, little is known about its localization and function during unperturbed DNA replication. Here we used a previously described Chromatin Mass spectrometry (Chromass) protocol (Project PXD000490) to compare the protein recruitment on chromatin in Xenopus egg extracts during unperturbed DNA replication in the presence or after Plk1 depletion from the extract.

2021-08-25 | PXD022572 | Pride

Phosphorylation of Rif1 by Plk1

Project description:Polo-like kinase 1 (Plk1) is an important protein kinase for checkpoint recovery and adaptation in response to DNA damage and replication stress. However, although Plk1 is present in S phase, little is known about its localization and function during unperturbed DNA replication. Here used recombinant XRif1 C-terminal domain and recombinant XPlk1 in an in vitro phosphorylation assay followed by LC/MS/MS to identify which residues are phosphorylated by Plk1 on Rif1 CTD.

2021-08-26 | PXD022410 | Pride

Quantitative ChIP-MS analysis of histone modifications present on H3K4me1- and H3K4me3-enriched mono-nucleosomes purified from crosslinked IMR-90 cells

Project description:The INO80 complex is a chromatin remodeler that regulates DNA replication, repair, and transcription. Although the INO80 complex plays a crucial role in various chromatin-associated processes, the mechanism of its recruitment to specific genomic loci is not well understood. Here we used a native ChIP-MS approach to quantitatively profile modifications present on nucleosomes co-purified with INO80 from MNAse-digested HeLa chromatin.

2023-12-12 | PXD042224 | Pride

Profiling of chromatin deposition bias in RPE-1 cells using Double-click-seq

Project description:We used double-click-seq method to profile chromatin deposition bias in RPE-1 cells. Untreated wild-type, p53 knock-out and several treatments (hydroxyurea, ATR inhibitor, curaxin) and their combinations were profiled for characterizing assymetry during DNA replication.

2021-10-04 | E-MTAB-8624 | biostudies-arrayexpress

SeqA Chip-chip analysis of E. coli MG1655 and derivatives

Project description:Chromosomes are composed of enormously long DNA molecules which must be distributed correctly as the cells grow and divide. In Escherichia coli the new DNA behind the replication forks is specifically bound by the SeqA protein. SeqA binds to GATC sequences which are methylated on the A of the old strand but not on the new strand. Binding lasts for a period of time until Dam methyltransferase methylates the new strand. It is therefore believed that a region of hemi-methylated DNA covered by SeqA follows the replication fork. We show that this is indeed the case by using global ChIP on Chip analysis and a newly developed method for methylation analysis. A comparison of rapid and slow growth conditions showed that in cells with multiple replication forks per chromosome, the old forks bind little SeqA. Analysis of strains with strong SeqA binding sites at different chromosomal loci supported this finding. The results indicate that a re-organization of the chromosome occurs at a timepoint when new forks have travelled about 20% and old forks about 75% of the way to the terminus. This timepoint coincides with the end of origin sequestration. It is so far not known what brings about the end of origin sequestration. Here we suggest that a reorganization event occurs resulting in both origin desequestration and loss of old replication forks from the SeqA structures. SeqA ChIP-Chip analysis of unsynchronized E. coli MG1655 and in cells synchronized regarding initiation of DNA replication; SeqA ChIP-Chip of Dam overproducing strain and SeqA4 mutant; SeqA ChIP-Chip of strains with chromosomal insertions of strong SeqA binding site. Methylation analysis of synchronized E. coli MG1655dnaC2 cells 0 and 15 min after initiation.

2012-02-22 | E-GEOD-28280 | biostudies-arrayexpress

Identification of direct targets of Arabidopsis JAGGED in floral buds

Project description:JAGGED (JAG) is a regulatory gene that controls shoot organ growth in Arabidopsis. To reveal the molecular links between JAG and the cellular activities required for tissue growth, we used chromatin immunoprecipitation-high-throughput sequencing (ChIP-Seq). To reveal the genome-wide JAG binding sites, we used anti-GFP antibodies to pull down JAG-bound DNA from jag-2 inflorescences complemented with a genomic JAG-GFP fusion (JAG:JAG-GFP) [14]. ChIP-Seq was performed and analyzed in triplicate, with wild-type inflorescences used as epitope-negative controls.

2014-03-05 | E-GEOD-51537 | biostudies-arrayexpress

ChIP-chip by array of Arabidopsis endosperm nuclei expressing a PHE1::PHE1-GFP reporter using H3K27me3 and IgG antibodies

Project description:ChIP was performed using chromatin from sorted endosperm nuclei expressing a PHE1::PHE1-GFP reporter. The following antibodies were used: anti H3K27me3 (Millipore, cat. 07-449) and IgG (Sigma I50006).

2010-12-14 | E-TABM-1008 | biostudies-arrayexpress

Chromatin immunoprecipitation of Arabidopsis 4 day-old light-treated seedlings using anti H3, CT, pan, anti H3K9me2 and IgG antibodies

Project description:ChIP was performed using 100 mg of 4 day-old light-treated seedlings. The following antibodies were used: anti H3, CT, pan (Millipore 07-690), anti H3K9me2 (Diagenode pAb-060-050) and IgG (Sigma I50006).

2009-12-08 | E-MEXP-2480 | biostudies-arrayexpress

Identification of Yap-interacting proteins in Xenopus egg extracts by co-immunoprecipitation coupled to LC/MS/MS

Project description:Yap (Yes-associated protein 1) is a downstream effector of the Hippo signaling pathway and known as a transcriptional co-activator. We previously identified Yap1 as a novel factor implicated in the control of the temporal DNA replication program in Xenopus retinal stem cells. However, whether Yap is directly involved in DNA replication dynamics and whether it could regulate DNA replication during early embryonic divisions in the absence of transcription remained to be investigated. We now found that in Yap depleted Xenopus laevis egg extracts the activation of replication origins was increased. In order to understand by which mechanism Yap could regulate the initiation of DNA replication in the absence of transcription we searched for new interacting factors. We immunoprecipitated Yap from Xenopus laevis egg extracts using anti-Yap, compared to control antibodies, and analyzed co-immunoprecipitating proteins by nanoLC/MS/MS.

2022-08-09 | PXD029345 | Pride

CGH mesurement of DNA replication in wild-type and cdc6-mn replication deficient strains.

Project description:Comparative genome hybridization (CGH) was used to measure relative DNA replication after 8 hours in meiosis for wild-type and cdc6-mn cells. We measured DNA replication after 8 hours in meiosis for wild-type and cdc6-mn cells on microarrays using CGH.

2013-09-20 | E-GEOD-46840 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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