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AP-MS of GFP-MCM2 in the cellular response to etoposide induced DNA damage.

ABSTRACT: SILAC quantitative proteomics using immunoprecipitation of GFP-tagged fusion proteins to identify proteins interacting with the MCM complex, and quantify changes in interactions in response to DNA damage. U2OS cells expressing GFP-MCM2 were used to purify the MCM complex following treatment or not with etoposide, a topoisomerase II inhibitor causing DNA damage.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell

DISEASE(S): Osteosarcoma

SUBMITTER: Francois-Michel Boisvert

LAB HEAD: Francois-Michel Boisvert

PROVIDER: PXD001949 | Pride | 2017-12-06

REPOSITORIES: Pride

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Publications

Quantitative Proteomics Reveals Dynamic Interactions of the Minichromosome Maintenance Complex (MCM) in the Cellular Response to Etoposide Induced DNA Damage.

Drissi Romain R Dubois Marie-Line ML Douziech Mélanie M Boisvert François-Michel FM

Molecular & cellular proteomics : MCP 20150511 7

The minichromosome maintenance complex (MCM) proteins are required for processive DNA replication and are a target of S-phase checkpoints. The eukaryotic MCM complex consists of six proteins (MCM2-7) that form a heterohexameric ring with DNA helicase activity, which is loaded on chromatin to form the pre-replication complex. Upon entry in S phase, the helicase is activated and opens the DNA duplex to recruit DNA polymerases at the replication fork. The MCM complex thus plays a crucial role durin ...[more]

PMID: 25963833

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Destabilization of the MiniChromosome Maintenance (MCM) complex modulates the cellular response to DNA double strand breaks induced by Etoposide.

Project description:DNA replication during S phase involves thousands of replication forks that must be coordinated to ensure that every DNA section is only replicated once. The minichromosome maintenance proteins, MCM2 to MCM7, form a heteromeric DNA helicase required for both initiation of DNA replication and elongation of DNA replication. Although only two DNA helicase activities are required to establish a bidirectional replication fork from each origin of replication, a large excess of MCM complexes is loaded and distributed along the chromatin. The function of the additional MCM complexes is not well understood, as most of them are displaced from the DNA during S-phase, apparently without playing an active role in DNA replication. DNA damage response (DDR) kinases activated by stalled forks prevent the replication machinery from being activated, indicating a tight relationship between DDR and DNA replication. To investigate the role of MCM proteins in the cellular response to DNA damage, we used shRNA targeting MCM2 or MCM3 to determine the impact of the reduction of the MCM complex. The alteration of MCM proteins induced a change in the activation of important factors of the DDR in response to Etoposide treatment. The phosphorylation of γ-H2AX, CHK1 and CHK2 is affected following DNA damage induced by treatment with Etoposide without affecting cell viability. Using assays measuring homologous recombination (HR) and non-homologous end-joining (NHEJ), we have identified a decrease of HR, but not NHEJ, associated with a decrease of the MCM complex demonstrating a role for the MCM complex in homologous recombination.

2019-11-12 | PXD009539 | Pride

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

Genome-wide expression analysis of human hTert immortalized fibroblasts after downregulation of MCM2

Project description:Minichromosome maintenance (MCM) proteins facilitate replication by licensing origins and unwinding the DNA double strand. Interestingly, the number of MCM hexamers greatly exceeds the number of firing origins suggesting additional roles of MCMs. Here we show a hitherto unanticipated function of MCM2 in cilia formation in human cells and zebrafish that is uncoupled from replication. Zebrafish depleted of MCM2 develop ciliopathy-phenotypes including microcephaly and aberrant heart looping due to malformed cilia. In non-cycling human fibroblasts, loss of MCM2 promotes transcription of a subset of genes, which cause cilia shortening and centriole overduplication. Chromatin immunoprecipitation experiments show that MCM2 binds to transcription start sites of cilia inhibiting genes. We propose that such binding may block RNA polymerase II-mediated transcription. Depletion of a second MCM (MCM7), which functions in complex with MCM2 during its canonical functions, reveals an overlapping cilia-deficiency phenotype likely unconnected to replication, although MCM7 appears to regulate a distinct subset of genes and pathways. Our data suggests that MCM2 and 7 exert a role in ciliogenesis in post-mitotic tissues.

2018-10-20 | GSE120766 | GEO

Mcm2-7 is an Active Player in the DNA Replication Checkpoint Signaling Cascade via Proposed Modulation of its DNA Gate

Project description:Genome wide characterization of Mcm2-7 localization and origin activity for mrc1 and mcm mutant alleles.

2015-04-20 | GSE38032 | GEO

Effect of mini-chromosome maintenance protein 2 deficiency on the locations of DNA replication origins

Project description:Mini-chromosome maintenance (MCM) proteins are loaded to chromatin during G1-phase and define potential locations of DNA replication initiation. MCM protein deficiency results in genome instability and high rates of cancer in mouse models. Here we develop a method of nascent strand capture and release and show that MCM2 deficiency reduces DNA replication initiation in gene rich regions of the genome. DNA structural properties are shown to correlate with sequence motifs associated with replication origins and with locations that are preferentially affected by MCM2 deficiency. Reduced nascent strand density correlates with sites of recurrent focal CNVs in tumors arising in MCM2-deficient mice, consistent with a direct relationship between sites of reduced DNA replication initiation and genetic damage. Between 10 and 90% of human tumors, depending on type, carry heterozygous loss or mutation of one or more Mcm2-7 genes which is expected to compromise DNA replication origin licensing and result in elevated rates of genome damage at a subset of gene rich locations. Mcm2 deficient vs. wild type

2015-01-14 | E-GEOD-64933 | biostudies-arrayexpress

Mechanisms of MCM2-7 loading and initial DNA melting at near base-pair resolution

Project description:The loading and activation of the replicative helicase MCM2-7 are key events during the G1-S phase transition.In budding yeast, the origin recognition complex (ORC) binds to the conserved DNA elements A and B1 of the autonomously replicating sequence (ARS).This is followed by the consecutive loading of two MCM2-7 hetero-hexamers into a MCM2-7 double-hexamer(DH).In S-phase the MCM2-7DH is activated, resulting in two Cdc45-MCM-GINS(CMG) helicases that bidirectionally unwind DNA ahead of the replication fork.Here,we show that MCM2-7 helicase loading across the B1 element displaces ORC fromo rigins.This allows ORC binding and helicase loading at lower affinity binding sites and origins throughout the genome.Furthermore, we mapped the sites of initial DNA unwinding genome-wide and show that these sites appear near the N-terminal domains of the MCM2-7 double-hexamer in proximity of the B1 element.Finally, employing a chemical-biology approach, we establish that during helicase activation the Mcm2/5 interface acts as the DNA exit gate for single-stranded-DNA extrusion.Our work identifies that helicase loading follows a distributive mechanism, allowing for equal MCM2-7 loading across the genome and surprisingly finds that DNA unwinding initiates from the helicase N-terminal interface in proximity to the ARS B1 element.

2024-06-21 | GSE240472 | GEO

The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer

Project description:The controlled assembly of replication forks is critical for genome stability. The Dbf4-dependent Cdc7 kinase (DDK) initiates replisome assembly by phosphorylating the MCM2-7 replicative helicase at the N-terminal tails of Mcm2, Mcm4 and Mcm6. At present, it remains poorly understood how DDK docks onto the helicase and how the kinase targets distal Mcm subunits for phosphorylation. By cryo-electron microscopy and biochemical analysis we discovered that an interaction between the HBRCT domain of Dbf4 with Mcm2 serves as an anchoring point, which supports binding of DDK across the MCM2-7 double-hexamer interface and phosphorylation of Mcm4 on the opposite hexamer. Moreover, a rotation of DDK along its anchoring point allows phosphorylation of Mcm2 and Mcm6 on opposite hexamers. In summary, our work provides fundamental insights in the DDK structure, control and the selective activation of the MCM2-7 helicase during DNA replication, which can be exploited for development of novel DDK inhibitors.

2022-05-31 | PXD031315 | Pride

Post-licensing specification of eukaryotic replication origins by facilitated Mcm2-7 sliding along DNA

Project description:Eukaryotic genomes are replicated from many origin sites that are licensed by the loading of inactive double hexamers of the replicative DNA helicase, Mcm2-7. How eukaryotic origin positions are specified remains elusive. Here we show that, contrary to the bacterial paradigm, eukaryotic origins are not irrevocably defined by selection of the loading site for the replicative helicase, but can shift in position after helicase loading. Using purified proteins, we show that DNA translocases, including RNA polymerase, can push budding yeast Mcm2-7 double hexamers along DNA. Displaced Mcm2-7 double hexamers support DNA replication initiation distal to the loading site in vitro. In yeast cells that are defective for transcription termination, collisions with RNA polymerase induce a shift in origin positions that correlates with the direction of transcription. These results reveal a eukaryotic origin specification mechanism that departs from the classical replicon model, helping eukaryotic cells to negotiate transcription-replication conflict. 4 samples: one replicate for WT at 37C, two replicates for rat1-1 at 37C, and one replicate for rat1-1 at 24C. All are single-end sequenced via Ion Torrent PGM methodology. rat1 = Nuclear 5' to 3' single-stranded RNA exonuclease; involved in RNA metabolism (http://www.yeastgenome.org/locus/S000005574/overview). 4 ChIP seq samples and their duplicates are submitted. rat1-1 ORC ChIP at 24C and 37C; rat1-1 MCM ChIP at 24C and 37C.

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Mechanisms of MCM2-7 loading and initial DNA melting at near base-pair resolution [MCM4 & ORC2 ChIP-exo]

Project description:The loading and activation of the replicative helicase MCM2-7 are key events during the G1-S phase transition. In budding yeast, the origin recognition complex (ORC) binds to the conserved DNA elements A and B1 of the autonomously replicating sequence (ARS). This is followed by the consecutive loading of two MCM2-7 hetero-hexamers into a MCM2-7 double-hexamer (DH). In S-phase the MCM2-7 DH is activated, resulting in two Cdc45-MCM-GINS (CMG) helicases that bidirectionally unwind DNA ahead of the replication fork. Here, we show that MCM2-7 helicase loading across the B1 element displaces ORC from origins. This allows ORC binding and helicase loading at lower affinity binding sites and origins throughout the genome. Furthermore, we mapped the sites of initial DNA unwinding genome-wide and show that these sites appear near the N-terminal domains of the MCM2-7 double-hexamer in proximity of the B1 element. Finally, employing a chemical-biology approach, we establish that during helicase activation the Mcm2/5 interface acts as the DNA exit gate for single-stranded-DNA extrusion. Our work identifies that helicase loading follows a distributive mechanism, allowing for equal MCM2-7 loading across the genome and surprisingly finds that DNA unwinding initiates from the helicase N-terminal interface in proximity to the ARS B1 element.

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Effect of mini-chromosome maintenance protein 2 deficiency on the locations of DNA replication origins

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