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MS-based analysis of the interacting proteins of human topoisomerases (TOP3A, TOP3B)

ABSTRACT: In this study, we used MS-based proteomics to identify the binding proteins of five human topoisomerases under four different conditions with treatment of CPT, ETO, HU, and NT. The proteomics result provide a quantitavie landscape of the binding partners of nearly all human topoisomerases. Several of the identitified binding proteins for each topoisomerase were validated by further experiments.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Yun Xiong

LAB HEAD: Junjie Chen

PROVIDER: PXD056278 | Pride | 2025-11-17

REPOSITORIES: Pride

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			Action	DRS
	060720_HZ_TOP3A_3_ETO-CE.raw	Raw
	060720_HZ_TOP3A_3_ETO-KE.raw	Raw
	060720_HZ_TOP3A_3_HU-CE.raw	Raw
	060720_HZ_TOP3A_3_HU-KE.raw	Raw
	060720_HZ_TOP3A_5_ETO-CE.raw	Raw

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Publications

Proteomic Analysis of Human Topoisomerases Reveals Their Distinct and Diverse Cellular Functions.

Zhang Huimin H Xiong Yun Y Chen Zhen Z Chen Junjie J

Molecular & cellular proteomics : MCP 20251001 11

Topoisomerases are essential for resolving topological stress in DNA during key cellular processes. In human cells, six topoisomerases perform specialized yet overlapping functions to manage these challenges. To investigate their distinct and shared roles, as well as their involvement in DNA damage repair, we conducted a comprehensive analysis of the human topoisomerase-associated protein landscape. Using tandem affinity purification coupled with mass spectrometry, we mapped the protein-protein ...[more]

PMID: 41043513

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MS-based analysis of the interacting proteins of human topoisomerases (TOP1, TOP2A, TOP2B)

Project description:In this study, we used MS-based proteomics to identify the binding proteins of five human topoisomerases under four different conditions with treatment of CPT, ETO, HU, and NT. The proteomics result provide a quantitavie landscape of the binding partners of nearly all human topoisomerases. Several of the identitified binding proteins for each topoisomerase were validated by further experiments.

2025-11-17 | PXD056277 | Pride

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

Project description:Interstrand crosslinks (ICLs) are highly toxic DNA lesions, which are repaired via a complex process that requires the coordination of several DNA repair pathways. Defects in ICL repair result in Fanconi anemia (FA), which is diagnosed with bone marrow failure, development abnormalities and high incidence of malignancies. SLX4, which is also known as FANCP, acts as a scaffold protein in coordinating multi-endonucleases that function in unhooking ICLs, resolving homologous recombination intermediates, and perhaps also removing unhooked ICLs. To reveal the underlying mechanism for the involvement of SLX4IP in ICL repair, we tagged SFB to the C terminus of SLX4IP and performed tandem affinity purification and mass spectrometry analysis as outlined above. We found SLX4 and XPF-ERCC1 at the top of the list of SLX4IP-binding proteins. We also identified some other potential SLX4IP interacting proteins, such as PASK, AJUBA, LRP4 and TRIM26, but none of them has been previously indicated to participate in DNA repair. SLX4 and XPF-ERCC1 are the major SLX4IP-interacting proteins, with or without MMC treatment. SLX4 has been shown to coordinate with XPF-ERCC1 and participate in the unhooking of ICLs during the repair process. The binding of SLX4IP to both SLX4 and XPF-ERCC1 intrigued us to further investigate whether SLX4IP plays a role in regulating SLX4-XPF-ERCC1 interaction.

2019-09-13 | PXD012521 | Pride

SART3 promotes homologous recombination repair by stimulating DNA–RNA hybrids removal and DNA end resection

Project description:DNA–RNA hybrids triggered by double-strand breaks (DSBs) are crucial intermediates during DSB repair, and their timely resolution requires numbers of RNA helicases, including DEAD box 1 (DDX1). However, how these helicases are recruited to DSB-induced hybrids in time remains largely unclear. Here, we revealed that squamous cell carcinoma antigen recognized by T cells 3 (SART3) promotes DDX1 binding to DNA–RNA hybrids at DSBs for optimal homologous recombination (HR) repair. SART3 itself can associate with DNA–RNA hybrids and PAR chains, and is recruited to DSBs in both PARylation- and hybrid-dependent fashion. SART3 also associates with DDX1 and is necessary for DDX1 enrichment at DSBs. The defective SART3-DDX1 association observed in cells expressing the cancer-associated variant SART3-R836W not only abrogates the accumulation of DDX1 at DSBs, but also impairs hybrid removal and HR efficiency, leading to hypersensitivity of tumor cells to drug treatments. Interestingly, beyond impairing hybrid removal through DDX1, SART3 loss also inhibits DNA end resection, causing a more profound DSB repair defect and chemosensitivity. The stimulatory role of SART3 in end resection is mediated by its function to enhance USP15-BARD1 association and BRCA1-BARD1 retention. Together, our study reveals a previously unknown role of SART3 in DSB repair, rendering SART3 a promising target for cancer therapy.

2025-01-30 | PXD053595 | Pride

Identification of dASF/SF2 potential mRNA targets

Project description:Deciphering the role of alternative splicing in developmental processes relies on the identification of key genes whose expression is controlled by splicing regulators throughout growth of a whole organism. Targeting expression of five SR proteins in the developing eye of Drosophila allowed us to show that these splicing factors induce various phenotypic alterations concerning eye organogenesis and viability. Although both dASF/SF2 and B52 caused defects in ommatidia structure, only B52 impairs normal photoreceptor axons projection and neurogenesis in visual ganglia. Consistently, microarray analyses revealed that many of the B52 targets are involved in brain organogenesis and we show that their splicing profile is altered both in B52 loss and gain of function. Conversely, a large proportion of dASF/SF2 targets are involved in eye development. This differential effect argues that SR proteins confer accuracy to developmental gene-expression programs, thus ensuring tissue identity and supporting cell-lineage decisions. Keywords: genetic modification Experiment aimed at identifying dASF/SF2 potential mRNA targets in the Drosophila developing eye Control: GMR X GFP-NLS trangenic larvae The 2 IP- GFP cy3 vs ASF cy5 rep.1 and IP- GFP cy5 vs ASF cy3 rep.1 samples correspond to dye-swap experiments. Two replicates (rep1 and rep2) are included.

2007-09-17 | E-GEOD-5857 | biostudies-arrayexpress

Identification of B52 potential mRNA targets

Project description:Deciphering the role of alternative splicing in developmental processes relies on the identification of key genes whose expression is controlled by splicing regulators throughout growth of a whole organism. Targeting expression of five SR proteins in the developing eye of Drosophila allowed us to show that these splicing factors induce various phenotypic alterations concerning eye organogenesis and viability. Although both dASF/SF2 and B52 caused defects in ommatidia structure, only B52 impairs normal photoreceptor axons projection and neurogenesis in visual ganglia. Consistently, microarray analyses revealed that many of the B52 targets are involved in brain organogenesis and we show that their splicing profile is altered both in B52 loss and gain of function. Conversely, a large proportion of dASF/SF2 targets are involved in eye development. This differential effect argues that SR proteins confer accuracy to developmental gene-expression programs, thus ensuring tissue identity and supporting cell-lineage decisions. Keywords: genetic modification Experiment aimed at identifying B52 potential mRNA targets in the Drosophila developing eye Control: GMR X GFP-NLS trangenic larvae The 2 IP- GFP cy3 vs B52 cy5 rep.1 and IP- GFP cy5 vs B52 cy3 rep.1 samples correspond to dye-swap experiments. Two replicates (rep1 and rep2) are included.

2007-09-17 | E-GEOD-5858 | biostudies-arrayexpress

TFIP11 competes with the Bloom syndrome helicase for binding to stalled replication forks to preserve genome stability

Project description:Replication fork reversal is a key protective mechanism against replication stress in higher eukaryotic cells and occurs via a series of coordinated enzymatic reactions. The Bloom syndrome gene product, BLM, is a member of the highly conserved RecQ helicase family and has been implicated in this process, but its precise regulation and role remain poorly understood. Here, we show that, upon replication stress, the GCFC domain-containing protein TFIP11 competes with the BLM helicase for association with stalled replication forks, thereby facilitates RAD51-mediated stalled fork reversal. Consequently, loss of TFIP11 results in aberrant accumulation of BLM at stalled forks, which in turn compromises RAD51 recruitment, impairs replication stress-induced fork reversal and slowing, hypersensitizes cells to replication stress-inducing agents, and enhances chromosomal instability. These findings reveal a previously unidentified regulatory mechanism that modulates the activities of BLM and RAD51 at stalled forks and thus genome integrity.

2024-05-24 | PXD042222 | Pride

HOXB13 WT and G84E mass spectrometry

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2023-03-11 | PXD030810 | Pride

Truncated PARP1 promotes RNA Polymerase III during apoptosis

Project description:The N-terminal three zinc finger motifs of PARP1 are evolutionarily conserved in multicellular organism。However, during apoptosis, human PARP1 is mainly cleaved by caspase 3 at D214. As a result, the truncated PARP1 loses two N-terminal zinc finger motifs and only contains the third zinc finger motif, the BRCT domain, the WGR domain and the C-terminal catalytic domain. Interestingly, when we explored the domain architecture of PARP1 in other organisms, we found that similar to human tPARP1, PARP1 orthologs in several lower organisms do not have the N-terminal two zinc fingers or even they lack the third zinc finger motif. It indicates that even without the first two zinc finger motifs, tPARP1 may still catalyze ADP-ribosylation and play an important role in certain biological processes. To reveal the biological function of tPARP1, we performed tandem affinity purification and searched for the possible substrates.

2022-02-15 | PXD018691 | Pride

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Arabidopsis SME interactome reveals spliceosome components

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