Browse
Submit Data
Databases
API
Help

Dataset Information

241 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PCNA interactome - SLX4IP acts with SLX4 and XPF-ERCC1 to promote interstrand crosslink repair

ABSTRACT: We examined the complexity of replication fork composition upon DNA damage by employing a PCNA-based proteomic screen to uncover known and new players involved in replication and replication stress response. We used camptothecin or ultraviolet radiation, that lead to fork-blocking lesions, to establish a comprehensive proteomics map of the replisome under such replication stress conditions. We identified and examined two potential candidate proteins WIZ and SALL1 for their roles in DNA replication and replication stress response.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Zhen Chen

LAB HEAD: Junjie Chen

PROVIDER: PXD011727 | Pride | 2018-12-14

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

SLX4IP acts with SLX4 and XPF-ERCC1 to promote interstrand crosslink repair.

Zhang Huimin H Chen Zhen Z Ye Yin Y Ye Zu Z Cao Dan D Xiong Yun Y Srivastava Mrinal M Feng Xu X Tang Mengfan M Wang Chao C Tainer John A JA Chen Junjie J

Nucleic acids research 20191101 19

Interstrand crosslinks (ICLs) are highly toxic DNA lesions that are repaired via a complex process requiring the coordination of several DNA repair pathways. Defects in ICL repair result in Fanconi anemia, which is characterized by bone marrow failure, developmental abnormalities, and a high incidence of malignancies. SLX4, also known as FANCP, acts as a scaffold protein and coordinates multiple endonucleases that unhook ICLs, resolve homologous recombination intermediates, and perhaps remove un ...[more]

PMID: 31495888

Similar Datasets

Replication forks proteomics reveals ATM-dependent rewiring of broken forks to promote restart

Project description:The fidelity of DNA replication is governed by a network of DNA repair mechanisms. Defects in replication fork protection can fuel genome instability in cancer, while also creating cancer-specific vulnerabilities. Here, we provide a comprehensive proteomic characterization of the replication fork response to topoisomerase 1 inhibition, a widely used mainstay chemotherapy. We reveal profound changes in the fork proteome and chromatin environment in response to seDSBs and topological stress, and classify fork repair factors according to their specificity for broken and stalled forks. These distinct fork responses also oppositely affect nucleosome occupancy and nuclear membrane interactions. ATM inhibition dramatically rewired the fork breakage response, revealing that ATM promotes HR-dependent fork restart by concomitantly promoting DNA-end resection and suppressing DSB associated protein ubiquitination and NHEJ. Together, this collection of damaged fork proteomes provides an ample resource to understand fork repair mechanisms and identify druggable targets and novel cancer vulnerabilities.

2021-01-15 | PXD018092 | Pride

SFB-tagged(S-protein tag, Flag epitope tag, and streptavidin-binding peptide tag) RNF4 wild-type and CS mutant LC-MSMS

Project description:To elucidate the role of RNF4 in DNA replication and fork reversal, we performed tandem affinity purification (TAP) using a HEK293T cell line that stably expresses SFB-tagged(S-protein tag, Flag epitope tag, and streptavidin-binding peptide tag) wild-type and CS mutant to isolate proteins that associate with RNF4.

2022-08-11 | PXD028397 | Pride

Human HEK293T cells LC-MS/MS (Gel-based proteomics)

Project description:Fanconi Anemia (FA) pathway is essential for the repair of inter-strand crosslink (ICLs). ICL induces stalled replication forks and triggers activation of FA pathway for efficient ICL repair. Given that stalled replication fork is proximal to ICLs sites, fork-associated proteins may likely coordinate with FA factors to rapidly sense ICLs for activation of FA signaling. We will use LC-MS/MS to identify such proteins that participated in the ICL repairs.

2023-05-10 | PXD028246 | Pride

Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links, part 1 of 2: CHROMASS DATA

Project description:DNA interstrand crosslinks (ICLs) block replication fork progression by inhibiting DNA strand separation. Repair of ICLs requires sequential incisions, translesion DNA synthesis, and homologous recombination, but the full set of factors involved in these transactions remains unknown. Here we established CHROmatin MASS spectrometry (CHROMASS) to study protein recruitment dynamics during perturbed DNA replication in Xenopus egg extracts. Using CHROMASS, we systematically monitored protein assembly and disassembly at ICL-containing chromatin. Among numerous prospective new DNA repair factors we identified SLF1 and SLF2, which form a complex with RAD18 and together define a new pathway that suppresses genome instability by recruiting the SMC5/6 cohesion complex to DNA lesions. Our study provides the first global analysis of an entire DNA repair pathway and reveals the mechanism of SMC5/6 relocalization to damaged DNA in vertebrate cells.

2015-05-07 | PXD000490 | Pride

DONSON encodes a novel replication fork protection factor mutated in 2 microcephalic dwarfism.

Project description:To ensure efficient genome duplication, cells have evolved a multitude of factors that promote unperturbed DNA replication, and protect, repair and restart damaged forks. Here we identify DONSON as a novel fork protection factor, and report biallelic DONSON mutations in individuals with microcephalic dwarfism. We demonstrate that DONSON is a component of the replisome that stabilises forks during normal genome replication. Loss of DONSON leads to severe replication-associated DNA damage arising from nucleolytic cleavage of stalled replication forks. Furthermore, ATR-dependent ,signalling in response to replication stress is impaired in DONSON-deficient cells, resulting in decreased checkpoint activity, and potentiating chromosomal instability. Hypomorphic mutations substantially reduce DONSON protein levels and impair fork stability in patient cells, consistent with defective DNA replication underlying the disease phenotype In summary, we identify mutations in DONSON as a common cause of microcephalic dwarfism, and establish DONSON as a critical replication fork protein required for mammalian DNA replication and genome stability

2017-02-10 | PXD005690 | Pride

Identification of novel 53BP1 associated proteins

Project description:We used homologous recombination based CRISPR Knock-in strategy to insert a SFB tag at C terminal of 53BP1 in 293T cells. We performed tandem affinity purification of endogenous 53BP1 in both soluble and chromatin fraction to uncover known and new 53BP1 binding proteins which might play roles in DNA damage response. We identified and examined FOXK1 for its role in DNA damage response through the interaction with 53BP1 mainly in soluble fraction.

2021-09-09 | PXD020090 | Pride

Unchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1

Project description:DNA ligase I (LigI), the predominant enzyme that joins Okazaki fragments, interacts with PCNA and Pol d. LigI also interacts with UHRF1, linking Okazaki fragment joining with DNA maintenance methylation. Okazaki fragments can also be joined by a relatively poorly characterized DNA ligase IIIa (LigIIIa)-dependent backup pathway. Here we examined the effect of LigI-deficiency on proteins at the replication fork. Notably, LigI-deficiency did not alter the kinetics of association of the PCNA clamp, the leading strand polymerase Pol e, DNA maintenance methylation proteins and core histones with newly synthesized DNA. While the absence of major changes in replication and methylation proteins is consistent with the similar proliferation rate and DNA methylation levels of the LIG1 null cells compared with the parental cells, the increased levels of LigIIIa/XRCC1 and Pol d at the replication fork and in bulk chromatin indicate that there are subtle replication defects in the absence of LigI. Interestingly, the non-replicative histone H1 variant, H1.0, is present in the chromatin of LigI-deficient mouse and human cells. This alteration was not corrected by expression of wild type LigI, suggesting that it is a stable epigenetic change that may contribute to the immunodeficiencies linked with inherited LigI-deficiency syndrome.

2023-04-04 | PXD039547 | Pride

Analysis of histone PTMs in nascent chromatin in new and old histones upon DNA damage (CAL353, CAL358) using the NCC-SILAC approach

Project description:Dynamic recycling and de novo deposition of histones are fundamental for chromatin restoration. Histone post-translational modifications (PTMs) are assumed to have a causal role in establishing distinct chromatin structures. However, it remains unknown how specific histone PTMs are regulated at broken replication fork. To get better insight into histone PTMs during DNA damage response, we combined NCC (Nascent chromatin capture) with SILAC-MS for identification of histone PTMs at replication forks upon CPT (camptothecin).

2021-01-18 | PXD018220 | Pride

Regulation of Rad52-dependent replication fork recovery through serine ADP-ribosylation of PolD3

Project description:Although Poly(ADP-ribose)-polymerases (PARPs) are key regulators of genome stability, how site-specific ADP-ribosylation regulates DNA repair is unclear. Here, we describe a novel role for PARP1 and PARP2 in regulating Rad52-dependent replication fork repair to maintain cell viability when HR is dysfunctional, suppress replication-associated DNA damage, and maintain genome stability. Mechanistically, Mre11 is required for induction of PARP activity in response to replication stress that in turn promotes break-induced replication (BIR) through assembly of Rad52 at stalled/damaged replication forks. Further, by mapping ADP-ribosylation sites induced upon replication stress, we identify that PolD3 is a target for PARP1/PARP2 and importantly, that its site-specific ADP-ribosylation is required for BIR activity, replication fork recovery and genome stability. Overall, these data identify a critical role for Mre11-dependent PARP activation and site-specific ADP-ribosylation in regulating BIR to maintain genome integrity during DNA synthesis.

2023-10-24 | PXD035661 | Pride

TEFM regulates both transcription elongation and RNA processing in mitochondria

Project description:Regulation of replication and expression of mitochondrial DNA (mtDNA) is essential for cellular energy conversion via oxidative phosphorylation. The mitochondrial transcription elongation factor (TEFM) has been proposed to regulate the switch between transcription termination for replication primer formation and processive, near-genome length transcription for mtDNA gene expression. Here, we report that Tefm is essential for mouse embryogenesis and that levels of promoter-distal mitochondrial transcripts are drastically reduced in conditional Tefm-knockout hearts. In contrast, the promoter-proximal transcripts are much increased in Tefm knockouts, but they mostly terminate before the region where the switch from transcription to replication occurs, and consequently de novo mtDNA replication is profoundly reduced. Unexpectedly, deep sequencing of RNA from Tefm knockouts revealed accumulation of unprocessed transcripts in addition to defective transcription elongation. Furthermore, a proximity labelling (BioID) assay showed that TEFM interacts with multiple RNA processing factors. Our data demonstrate that TEFM acts as a general transcription elongation factor, necessary for both gene transcription and replication primer formation, and loss of TEFM affects RNA processing in mammalian mitochondria.

2019-04-25 | PXD013398 | Pride

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