Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Arsenic-induced transcriptional interference generates arm-wide γH2A, with distinct telomeric and centromeric responses

ABSTRACT: Arsenic is a widespread environmental carcinogen, yet how exposure promotes tumorigenesis remains unclear. Prevailing models attribute arsenic genotoxicity to reactive oxygen species and replication-associated DNA breaks. Using calibrated γH2A mapping and genetics in budding yeast, we show that As(III) rapidly elicits a diffuse, chromosome-arm-spanning γH2A response that is replication-independent and occurs without oxidative stress. Instead, arsenic reduces RNA polymerase II chromatin occupancy and promotes loss of the Rpb1 subunit, consistent with acute transcriptional interference. We propose that transcription stress generates transient ssDNA intermediates that activate DNA damage signaling and require homologous recombination (HR) for resolution. Notably, the response is domain-specific: As(III) dampens subtelomeric γH2A while increasing telomere-proximal HR, and it promotes HR-factor recruitment together with Pol ε accumulation at centromeres. In human cells, short-term As(III) activates ATR and induces RPA foci and γH2AX. Together, these findings shift the early trigger of arsenic genotoxicity from ROS-driven breaks to transcription-linked ssDNA signaling.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE318138 | GEO | 2026/02/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Sister chromatid exchanges independent of canonical homologous recombination factors.

Project description:Sister chromatid exchanges (SCEs) are a product of joint DNA molecules resolution, and are considered to require homologous recombination (HR). Canonical HR factors BRCA1, BRCA2 and RAD51 were indeed essential for SCE induction in response to irradiation-induced DNA breaks. By contrast, replication-blocking agents, including PARP inhibitors, induced SCEs independently of BRCA1, BRCA2 or RAD51. HR-independent SCEs were associated with incomplete DNA replication, as evidenced by post-replicative single-stranded DNA (ssDNA) accumulation and enrichment of PARP inhibitor-induced SCEs at common fragile sites (CFSs). Importantly, PARP-induced DNA lesions were transmitted into mitosis, pointing towards SCEs originating from mitotic processing of underreplicated DNA. We found polymerase theta to be associated to mitotic DNA lesions, to be required for SCE formation and to prevent chromosome fragmentation upon PARP inhibition in HR-defective cells. Combined, our data show that replication-blocking agents lead to underreplicated DNA in mitosis, which is processed into SCEs independently of canonical HR factors.

2023-03-11 | PXD028670 | Pride

MCM8IP activates the MCM8-9 helicase to promote DNA synthesis and homologous recombination upon DNA damage

Project description:Homologous recombination (HR) mediates the error-free repair of DNA double-strand breaks to maintain genomic stability. Here we characterize C17orf53/MCM8IP, an OB-fold containing protein that binds ssDNA, as a DNA repair factor involved in HR. MCM8IP-deficient cells exhibit HR defects, especially in long-tract gene conversion, occurring downstream of RAD51 loading, consistent with a role for MCM8IP in HR-dependent DNA synthesis. Moreover, loss of MCM8IP confers cellular sensitivity to crosslinking agents and PARP inhibition. Importantly, we report that MCM8IP directly associates with MCM8-9, a helicase complex mutated in primary ovarian insufficiency, and RPA1. We additionally show that the interactions of MCM8IP with MCM8-9 and RPA facilitate HR and promote replication fork progression and cellular viability in response to treatment with crosslinking agents. Mechanistically, MCM8IP stimulates the helicase activity of MCM8-9. Collectively, our work identifies MCM8IP as a key regulator of DNA damage-associated DNA synthesis during DNA recombination and replication.

2020-06-15 | PXD019156 | Pride

Mechanism of Rad51 filament formation by Rad52 and Rad55-Rad57 in homologous recombination

Project description:Homologous recombination (HR) repairs double-stranded DNA breaks (DSBs). The DSBs are resected to yield single-stranded DNA (ssDNA) that are coated by Replication Protein A (RPA). Rad51 is a recombinase and catalyzes strand invasion and the search for homology. However, it binds to ssDNA with lower affinity than RPA. Thus, mediator proteins such as Rad52 (yeast) or BRCA2 (humans) are required to promote Rad51 binding to RPA-coated ssDNA, but the underlying mechanisms remain poorly understood. Saccharomyces cerevisiae Rad52 interacts with Rad51 through two distinct binding modes. We here uncover that the Rad51-binding site in the disordered C-terminus of Rad52 sorts polydisperse Rad51 into discrete monomers. We developed fluorescent-Rad51 to directly visualize filament formation in single molecule optical tweezer analysis and capture Rad52 catalyzed Rad51 loading onto RPA-coated ssDNA with a distinct preference for junctions. Addition of the Rad51-paralog Rad55-Rad57 increases the number of Rad51 bound by ~60%. Deletion of the C-terminus of Rad52 results in loss of Rad51 sorting and abrogates Rad51 binding to RPA-coated DNA. While BRCA2 and Rad52 are structurally unrelated, we show that many of the functional features are conserved. We describe a concerted Sort, Stack & Extend (SSE) mechanism for mediator-paralog catalyzed Rad51 filament formation in HR.

2025-07-28 | PXD065573 | Pride

RPA accumulation during class switch recombination represents 5'-3' DNA end resection during the S-G2/M phase of the cell cycle

Project description:AID promotes chromosomal translocations by inducing DNA double-strand breaks (DSBs) at immunoglobulin (Ig) genes and oncogenes in G1. RPA is a ssDNA-binding protein that associates with resected DSBs in the S phase and facilitates the assembly of factors involved in homologous repair (HR) such as Rad51. Notably, RPA deposition also marks sites of AID-mediated damage, but its role in Ig gene recombination remains unclear. Here we demonstrate that RPA associates asymmetrically with resected ssDNA in response to lesions created by AID, RAG, or other nucleases. Small amounts of RPA are deposited at AID targets in G1 in an ATM-dependent manner. In contrast, recruitment in S-G2/M is extensive, ATM-independent, and associated with Rad51 accumulation. RPA in S-G2/M increases in NHEJ-deficient lymphocytes, where there is more extensive DNA-end resection. Thus, most RPA recruitment during CSR represents salvage of un-repaired breaks by homology-based pathways during the S-G2/M phases of the cell cycle. Chip-Seq of RPA from mouse activated B cells (n = 40), mouse thymocytes (n = 6), and MEFs (n = 1). Different genotypes and/or inhibitors were used.

2013-01-02 | E-GEOD-42451 | biostudies-arrayexpress

SAMHD1 deacetylation by SIRT1 promotes DNA end resection by facilitating DNA binding at double-strand breaks

Project description:Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) has a dNTPase-independent function in promoting DNA end resection to facilitate DNA double-strand break (DSB) repair by homologous recombination (HR); however, it is not known if upstream signaling events govern this activity. Here, we show that SAMHD1 is deacetylated by the SIRT1 sirtuin deacetylase, facilitating its binding with ssDNA at DSBs, to promote DNA end resection and HR. SIRT1 complexes with and deacetylates SAMHD1 at conserved lysine 354 (K354) specifically in response to DSBs. K354 deacetylation by SIRT1 promotes DNA end resection and HR but not SAMHD1 tetramerization or dNTPase activity. Mechanistically, K354 deacetylation by SIRT1 promotes SAMHD1 recruitment to DSBs and binding to ssDNA at DSBs, which in turn facilitates CtIP ssDNA binding, leading to promotion of genome integrity. Our findings define a mechanism governing the dNTPase-independent resection function of SAMHD1 by SIRT1 deacetylation in promoting HR and genome stability.

2023-03-11 | PXD031357 | Pride

PARG inhibitor sensitivity correlates with accumulation of single strand DNA gaps in preclinical models of ovarian cancer

Project description:Poly (ADP-ribose) glycohydrolase (PARG) is a dePARylating enzyme which promotes DNA repair by removal of poly (ADP-ribose) (PAR) from PARP1-parylated proteins. Loss or inhibition of PARG results in replication stress and sensitizes cancer cells to DNA damaging agents, suggesting that PARG inhibitors may provide a therapeutic option for cancer therapy. Indeed, PARG inhibitors (PARGi) are now undergoing clinical development for patients having tumors with homologous recombination deficiency (HRD), such as ovarian and breast cancer patients with germline or somatic BRCA1/2-mutations. Biomarkers of PARGi response will be required for the optimal development of these important new drugs. PARP inhibitors kill BRCA-deficient cancer cells by increasing ssDNA gaps during replication. Here, we report that, similar to PARP inhibitors, PARGi treatment can also cause an accumulation of ssGAPs in sensitive cells. PARGi exposure increased accumulation of S-Phase specific PAR, a marker for Okazaki fragment processing (OFP) defects on lagging strands, in sensitive cells but not in resistant cells. PARGi also caused accumulation of PAR at the replication fork and increased pRPA, a marker for replication stress, at the replication fork in sensitive cells. Additionally, PARGi exhibited monotherapy activity in some HR-deficient, as well as HR-proficient, patient-derived organoids of ovarian cancer, and drug sensitivity directly correlated with the accumulation of ssDNA gaps. Taken together, PARGi treatment results in toxic accumulation of PAR at replication forks resulting in ssDNA gaps due to OFP defects during replication. Regardless of the BRCA-status, the induction of ssDNA gaps in preclinical models of ovarian cancer cells correlates with PARGi sensitivity. Patient-derived organoids will be a useful model system for testing PARGi sensitivity and functional biomarkers

2024-10-31 | GSE270384 | GEO

RPA accumulation during class switch recombination represents 5'-3' DNA end resection during the S-G2/M phase of the cell cycle

2013-01-02 | GSE42451 | GEO

Rtt105 promotes DNA replication by functioning as an RPA chaperone

Project description:Single-stranded DNA (ssDNA) binding protein Replication Protein A (RPA) is essential for protecting ssDNA at replication forks. However, how RPA is loaded to replication forks remains unexplored. Here, we show that Regulator of Ty1 transposition protein 105 (Rtt105) binds RPA and is required for the association of RPA with replication forks. Cells lacking Rtt105 exhibit dramatic genome instability and severe defects in DNA replication. Intriguingly, both the RPA nuclear import and its ability to bind DNA replication forks were greatly compromised in rtt105 mutant cells, however, targeting RPA to the nucleus cannot rescue the defect of RPA binding to replication forks. Importantly, Rtt105 promotes the binding of RPA to ssDNA but does not associate with the final RPA-ssDNA complex in vitro. Moreover, single-molecule studies revealed that Rtt105 affects the binding mode of RPA to ssDNA. These results support a model in which Rtt105 functions as an RPA chaperone that escorts RPA to nucleus and assemble RPA onto ssDNA at replication forks.

2018-07-27 | GSE101536 | GEO

The Bloom Syndrome Complex Senses RPA-Coated Single-Stranded DNA to Restart Stalled Replication Forks

Project description:The Bloom syndrome helicase BLM interacts with topoisomerase IIIa (TOP3A), RMI1 and RMI2 to form the BTR complex, which dissolves double Holliday junctions to produce non-crossover products during homologous recombination (HR). BLM also promotes DNA-end resection and stalled replication fork restart. However, it is still unclear how the activities of the BTR complex are regulated in cells. Here, we identify multiple highly conserved short linear peptide motifs within the BTR complex that interact cooperatively with RPA. Furthermore, we demonstrate that RPA-binding is essential for stable recruitment of BLM to DNA damage sites and for stalled fork restart, but not for its roles in HR. Disruption of RPA-binding thus constitutes a novel separation-of-function mutation of the BTR complex, and suggest a model in which BTR contains the intrinsic ability to measure levels of RPA-ssDNA at replication forks, which controls its recruitment and activation in response to replication stress.

2021-01-05 | PXD018322 | Pride

ExoChew-Seq: An in vitro method for investigating singlestranded DNA-protein interactions

Project description:During various cellular DNA transactions such as DNA replication and repair, genomic doublestranded DNA (dsDNA) is transiently unwound to generate single-stranded DNA (ssDNA). Several proteins interact with ssDNA, site- and/or structure-specifically, to regulate key cellular processes. Investigating these processes requires genome-wide identification of these ssDNA sequences. However, because of the transient nature of ssDNA in vivo techniques cannot reveal all such sequences requiring an in vitro alternative. Traditionally, ssDNA libraries are prepared by boiling or alkali-treatment of dsDNA libraries, but these techniques have their limitations as ssDNA can rapidly reanneal to generate dsDNA. We present here ExoChew, a novel enzymatic technique, which generates persistent ssDNA libraries from dsDNA libraries. In ExoChew, T7 exonuclease (T7 exo) or E. coli exonuclease III (Exo III), which binds and cleaves dsDNA in a specific direction, generates ssDNA libraries from dsDNA libraries. To validate the technique and demonstrate its applications, we conducted a genome-wide search for hnRNP K binding sites in an ExoChew-generated ssDNA library from mouse genomic DNA. The hnRNP K-bound ssDNA fragments were sequenced (ExoChew-seq) and a consensus hnRNP K binding motif was identified. Two other potential uses of ExoChew are the generation and genome-wide identification of ssDNA secondary structures and protein-ssDNA interactions.

2025-09-19 | GSE308562 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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