Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comprehensive characterization of Minichromosome Maintenance Complex (MCM) protein interactions using affinity and proximity purifications coupled to mass spectrometry.

ABSTRACT: This project is the complete interactome of the Minichromosome Maintenance (MCM) complex by using AP-MS and BioID approaches for all the different MCM proteins. Overall, our analysis identified unique and shared interaction partners and proteins enriched for distinct biological processes including DNA replication, DNA repair and cell cycle regulation. Furthermore, we mapped the changes in protein interactions of the MCM complex in response to DNA damage, identifying a new role for this complex in DNA repair. In summary, we demonstrate the complementarity of these approaches for the characterization of protein interactions within the MCM complex.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Dr Francois-Michel Boisvert

PROVIDER: MSV000080198 | MassIVE |

SECONDARY ACCESSION(S): PXD004089

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Publications

Comprehensive Characterization of Minichromosome Maintenance Complex (MCM) Protein Interactions Using Affinity and Proximity Purifications Coupled to Mass Spectrometry.

Dubois Marie-Line ML Bastin Charlotte C Lévesque Dominique D Boisvert François-Michel FM

Journal of proteome research 20160816 9

The extensive identification of protein-protein interactions under different conditions is an important challenge to understand the cellular functions of proteins. Here we use and compare different approaches including affinity purification and purification by proximity coupled to mass spectrometry to identify protein complexes. We explore the complete interactome of the minichromosome maintenance (MCM) complex by using both approaches for all of the different MCM proteins. Overall, our analysis ...[more]

PMID: 27494197

Similar Datasets

Comprehensive characterization of Minichromosome Maintenance Complex (MCM) protein interactions using affinity and proximity purifications coupled to mass spectrometry.

Project description:This project is the complete interactome of the Minichromosome Maintenance (MCM) complex by using AP-MS and BioID approaches for all the different MCM proteins. Overall, our analysis identified unique and shared interaction partners and proteins enriched for distinct biological processes including DNA replication, DNA repair and cell cycle regulation. Furthermore, we mapped the changes in protein interactions of the MCM complex in response to DNA damage, identifying a new role for this complex in DNA repair. In summary, we demonstrate the complementarity of these approaches for the characterization of protein interactions within the MCM complex.

2016-08-09 | PXD004089 | Pride

NSMF promotes the replication stress-induced DNA damage response for genome maintenance

Project description:Proper activation of DNA repair pathways in response to DNA replication stress is critical for maintaining genomic integrity. Due to the complex nature of the replication fork (RF), problems at the RF require multiple proteins, which remain unidentified, for resolution. In this study, we identified the NMDA receptor synaptonuclear signaling and neuronal migration factor (NSMF) as a key replication stress response factor that is important for ataxia telangiectasia and Rad3-related protein (ATR) activation. NSMF localizes rapidly to stalled RFs and acts as a scaffold to modulate replication protein A (RPA) complex formation with cell division cycle 5-like (CDC5L) and ATR/ATR-interacting protein (ATRIP). Depletion of NSMF compromised phosphorylation and ubiquitination of RPA2 and the ATR signaling cascade, resulting in genomic instability at RFs under DNA replication stress. Consistently, NSMF knockout (KO) mice exhibited increased genomic instability and hypersensitivity to genotoxic stress. NSMF deficiency in human and mouse cells also caused increased chromosomal instability. Collectively, these findings demonstrate that NSMF regulates the ATR pathway and the replication stress response network for genome maintenance and cell survival.

2021-09-09 | PXD021942 | Pride

Eaf7 identifies a native protein trimer linked to RNA polymerase-coupled nucleosome recycling

Project description:The NuA4 histone acetyltransferase (HAT) complex is required for gene specific regulation, cell cycle progression, and DNA repair. Dissection of the 13-subunit complex reveals that the Eaf7 subunit bridges Eaf5 with Eaf3, a H3K36me3-binding chromodomain protein, and this Eaf5/7/3 trimer is anchored to NuA4 through Eaf5. This subcomplex represents a functional module as deletions of these genes create similar phenotypes and a large portion of the trimer exists in a native form outside the NuA4 complex. Gene-specific and genome-wide location analyses indicate that the Eaf5/7/3 trimer correlates with transcription activity and is enriched over the coding region. In agreement with a role in transcription elongation, the Eaf5/7/3 trimer interacts with phosphorylated RNA polymerase II and helps its progression. In addition, loss of Eaf5/7/3 partially suppresses intragenic cryptic transcription arising in set2 mutant cells, suggesting a role in nucleosome destabilization. Such a function is supported by genetic interactions with the FACT histone chaperone. On the other hand, loss of the trimer leads to an increase of replication-independent histone exchange over the coding region of transcribed genes. Taken together, these results lead to a model where Eaf5/7/3 associates with elongating polymerase and is involved in the disassembly of nucleosomes in front of the polymerase, but also in their recycling in its wake.

2014-09-25 | E-MTAB-1780 | biostudies-arrayexpress

Extending the dynamic range of label-free mass spectrometric quantification of affinity purifications.

Project description: Not available

| S-EPMC3277747 | biostudies-literature

Genome maintenance functions of Trypanosoma brucei DNA Polymerase N include telomere association and a role in antigenic variation

Project description:Maintenance of genome integrity is critical to guarantee transfer of an intact genome from parent to offspring during cell division. DNA polymerases (Pols) provide roles in both replication of the genome and the repair of a wide range of lesions. Amongst replicative DNA Pols, translesion DNA Pols play a particular role: replication to bypass DNA damage, often at the cost of mutation. All cells express a range of translesion Pols, but little work has examined their function in parasites, including whether the enzymes might contribute to hostparasite interactions. Here, we describe a dual function of translesion PolN in African trypanosomes. Previously we demonstrated that PolN is associated with telomeric sequences and now we show that RNAi-mediated depletion of PolN results in slowed growth, altered DNA content, changes in cell morphology, and increased sensitivity to DNA damaging agents. Depletion of PolN leads to chromosome segregation defects and accumulation of DNA damage. We also show that PolN displays discrete localisation at the nuclear periphery in the absence of exogenous DNA damage. In addition, we demonstrate that PolN depletion leads to deregulation of telomeric variant surface glycoprotein genes, linking the function of this translesion DNA polymerase to host immune evasion by antigenic variation.

2021-09-08 | PXD015648 | Pride

Optimisation of Downscaled Tandem Affinity Purifications to Identify Core Protein Complexes.

Project description: Not available

| S-EPMC3785125 | biostudies-other

PBAF loss leads to DNA damage induced inflammatory signalling through defective G2/M checkpoint maintenance

Project description:PBRM1 is a subunit of the PBAF (SWI/SNF) chromatin remodelling complex that is mutated in approximately 40% of clear cell renal cell carcinomas (ccRCC). PBRM1 loss has been implicated in the response to immune checkpoint inhibitor (ICI) therapy in ccRCC. However, it is unclear how PBRM1 influences this. DNA damage-induced inflammatory signalling is an important factor determining ICI therapy response. This response is kept in check by the G2/M checkpoint, which prevents progression through mitosis with unrepaired damage. Here, we show that PBRM1 is required for p53-dependent maintenance of the G2/M checkpoint. In its absence, p53-dependent transcriptional upregulation of p21 is delayed, leading to defective repression of DREAM complex targets and premature entry into mitosis. Consequently, DNA damage induced inflammatory signalling pathways are activated by cytosolic DNA. Notably, p53 is infrequently mutated in ccRCC, so PBRM1 mutational status is critical to G2/M checkpoint maintenance following DNA damage in this cancer. These findings have implications for ICI therapy responses in ccRCC.

2022-10-13 | PXD028336 | Pride

Neurospora MUS-30 is an LSH/DDM1 homolog required for normal genome maintenance

Project description:LSH/DDM1 enzymes are required for DNA methylation in higher eukaryotes and have poorly defined roles in genome maintenance in yeast, plants, and animals. The filamentous fungus Neurospora crassa is a tractable system that encodes a single LSH/DDM1 homolog (NCU06306). We report that the Neurospora LSH/DDM1 enzyme is encoded by mutagen sensitive-30 (mus-30), a locus identified in a genetic screen over 25 years ago. We show that MUS-30-deficient cells have normal DNA methylation, but are hypersensitive to the DNA damaging agent MMS (methyl methanesulfonate). MUS-30 is a nuclear protein, consistent with its predicted role as a chromatin remodeling enzyme, and levels of MUS-30 are increased following DNA damage. MUS-30 co-purifies with Neurospora WDR76, a homolog of yeast Changed Mutation Rate-1 and mammalian WD40 repeat domain 76. Deletion of wdr76 rescued MMS-hypersensitivity of Dmus-30 strains, demonstrating that the MUS-30-WDR76 interaction is functionally important. DNA damage-sensitivity of Dmus-30 is also partially suppressed by deletion of methyl adenine glycosylase-1, a component of the base excision repair machinery (BER); however, the rate of BER is not affected in Dmus-30 strains. It was reported that mammalian LSH is required for efficient double strand break (DSB) repair. We found that MUS-30-deficient cells were not defective for DSB repair, and we observed a negative genetic interaction between Dmus-30 and Dmei-3, the Neurospora RAD51 homolog required for homologous recombination. These data are consistent with a role for MUS-30 that is independent of DSB repair. Our findings demonstrate that LSH/DDM1 enzymes are key regulators of genome stability in eukaryotes. crf5-1 isolates (two replicates each from the F1 and F2 generation) were grown in Vogel's minimal medium for 48 hours. As a control, two replicates of the wildtype strain were grown under identical conditions.

2015-12-21 | E-GEOD-70518 | biostudies-arrayexpress

Photodamage repair pathways contribute to the accurate maintenance of DNA methylome landscape upon UV exposure

Project description:Photodamage repair pathways contribute to the accurate maintenance of DNA methylome landscape upon UV exposure

| PRJNA548919 | ENA

Pervasive transcription-coupled DNA repair in E. coli

Project description:Pervasive transcription-coupled DNA repair in E. coli

| PRJNA721479 | ENA