Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the Ku70 homologue HdfA deletion in Penicillium chrysogenum

ABSTRACT: Targeting an engineered DNA fragment to a specific site in chromosomes in order to disrupt, overexpress or modify the nucleotide sequence of a gene requires homologous recombination repair mechanism. This DNA repair mechanism is not predominant in fungi, resulting in extremely low targeting efficiency. To increase this efficiency, it is becoming common practice to disable the non homologous end joining (NHEJ) pathway that causes random integration, by deleting homologous gene to human KU70 and KU80 which encode proteins functioning in the NHEJ pathway. These genes have been successfully deleted in several organisms, including the yeast Kluyveromyces lactis and the fungi Neurospora Crassa and several Aspergilli species. In this study we investigated the behavior of high penicillinG-producing Penicillium chrysogenum strains, in which the KU70 or KU80 homologues, HdfA or HdfB, had been deleted. Targeting efficiency in these mutant strains was significantly increased relative to the reference strain. Both physiological and transcriptome data of chemostat cultivations of the hdfA deletion strain and the reference strain showed minimal differences. However, in a direct competition experiment to assess global strain fitness, the reference strain had a clear advantage over the deletion strain. The full characterization of these recombinant host strains is an essential step to guide the future construction of a whole genome knock-out mutant collection.

ORGANISM(S): Penicillium chrysogenum

PROVIDER: GSE12893 | GEO | 2009/03/09

SECONDARY ACCESSION(S): PRJNA110889

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Zinc finger protein ZNF384 is an adaptor of KU to DNA during classical non-homologous end-joining

Project description:DNA double-strand breaks (DSBs) are among the most deleterious types of DNA damages as they can lead to mutations and chromosomal rearrangements, which underlie cancer development and progression. Non-homologous end-joining (NHEJ) is the dominant pathway for the repair of DSBs in human cells, which involves the DNA binding proteins Ku70/Ku80. Other DNA binding proteins such as Zinc Finger (ZnF) domain-containing proteins have also been implicated in DNA repair. However, their role in NHEJ has remained elusive. Here we show that ZNF384, which is a member of the C2H2 family of ZnF proteins that binds DNA in vitro, is recruited to DSBs in vivo. ZNF384 recruitment requires the PARP/PAR-dependent expansion of damaged chromatin followed by binding of ZNF384 to the exposed DNA via its unique C2H2 motifs. Mass-spectrometry-based experiments revealed that ZNF384 interacts with the Ku70/Ku80 NHEJ complex via its N-terminus. This interaction promotes the assembly of Ku70/Ku80 at DBSs as revealed by fluorescence recovery after photobleaching and fluorescence correlation spectroscopy. By regulating Ku70/80 dynamics, ZNF384 facilitates the assembly of several downstream NHEJ factors (e.g. APLF and XRCC4) and repair by cNHEJ at DSBs. Altogether, our data suggest that ZNF384 acts as a ‘Ku-adaptor’ that binds to DSBs and Ku70/80 to facilitate their binding and the subsequent build-up of a functional cNHEJ repairosome at these lesions, high-lighting a role for ZNF384 in DSB repair and genome maintenance.

2021-11-15 | PXD020417 | Pride

Transcriptome data for HEK293T cells depleted of one subunit of DNA-PK complex: Ku70, Ku80 or DNA-PKcs.

Project description:DNA-PK is a heterotrimeric complex that consists of Ku70 (XRCC6), Ku80 (XRCC5) and DNA-PKcs (PRKDC) subunits. DNA-PK complex is a major player in DNA double strand break (DSB) repair via non-homologous end joining pathway. This process requires all of DNA-PK subunits. Ku70/Ku80 heterodimers firstly bind to DNA-ends at DSB, that increase affinity of DNA-PKcs to DNA-ends. Recruitment of DNA-PKcs subunit to DSB leads to phosphorylation events near DSB, recruitment of another NHEJ-related genes that restore DNA integrity. However, today a lot of evidence demonstrate participation of DNA-PK components in other cellular process, e.g. cytosolic DNA sensing, apoptosis regulation, cellular movement and adhesion. It is important to note that not all subunits of DNA-PK complex are necessary for these process. This demonstrate the independent functions of DNA-PK subunits. Here we for the first time using NGS-sequencing analyzed the transcriptional changes in HEK293T cells under depletion of Ku70, Ku80 or DNA-PKcs to characterize the independent functions of each subunit.

2021-07-23 | GSE180581 | GEO

Expression data in T-ALL cell lines after TOX knockdown

Project description:T-ALL is an aggressive malignancy of thymocyte. We identified a collaborative oncogenic driver, TOX (Thymocyte Selection Associated HMG box) that negatively modulates the non-homologous end joining by directly interacting to KU70/KU80.

2017-09-01 | GSE89607 | GEO

The N-Myc-Responsive LncRNA MILIP Promotes Non-Homologous DNA End Joining to Alleviate Genotoxic Stress in Human Neuroblastoma

Project description:lncRNAMILIP promotes the NHEJ pathway through facilitating Ku70-Ku80 heterodimerization and is involved in the resistance to DNA-damaging therapeutics in neuroblastoma cells.

2022-04-22 | PXD033372 | iProX

The impact of DNA-PKcs in V(D)J recombination of mouse IgK antigen locus

Project description:DNA-PKcs is a critical component of the non-homologous end joining (NHEJ) pathway, playing a role in the re-ligation of DNA double-strand breaks (DSBs) generated by RAG1/2 during V(D)J recombination in antigen loci. When NHEJ is deficient, DSBs can be repaired through alternative end joining (A-EJ). In this study, we investigated the consequences of DNA-PKcs deletion on V-J recombination at the IgK antigen locus. Our results reveal that DNA-PKcs deletion leads to inefficient V-J recombination, exhibiting phenotypes such as reduced efficiency, increased end resection, and decreased micro-insertions in the repair pattern. These findings are consistent with previously reported functions of Ku70, another key player in NHEJ. However, unlike Ku70, additional deletion of DNA-PKcs does not restore the efficiency of repair in the absence of Lig4. Instead, it reduces both end resection and microhomology-mediated repair. These observations highlight the context-dependent role of DNA-PKcs in end processing. The presence or absence of Lig4 appears to influence the function of DNA-PKcs, further emphasizing the intricate interplay between repair factors in the DNA damage response. Overall, our findings provide insights into the distinct functions of DNA-PKcs and Ku70 in V(D)J recombination and underscore the complex regulatory mechanisms underlying repair efficiency in different genetic backgrounds.

2023-09-01 | GSE232924 | GEO

Integrated omics profiling reveals FOXA1 and Ku70/Ku80 as the direct target of ivermectin for prostate carcinogenic inhibition

Project description:Here, we show that ivermectin suppress prostate cancer progression by inhibiting AR signaling pathway and attenuate cellular DNA damage repair capacity. We applied an integrated omics profiling including RNA-seq and Thermal proteome, that found pioneer factor Forkhead Box Protein A1 (FOXA1) and Non-homologous End Joining (NHEJ) repair executer Ku70/Ku80 was the direct target of Ivermectin in prostate cancer. Ivermectin binds to these two proteins and block their biological function, which results in blockade of AR signaling transcription and deficiency of DNA double-strand breaks (DSBs) repair system, and thereby leads to G0/G1 arrest and trigger synthetic lethality Our findings demonstrate both the effect and target of Ivermectin in prostate cancer comprehensively and systemically, indicating that use of Ivermectin may constitute a new therapeutic approach for prostate cancer.

2022-04-01 | GSE169356 | GEO

DNA-PK Promotes DNA End Resection at DNA Double Strand Breaks in G0 cells [ChIP-Seq]

Project description:DNA double-strand break (DSB) repair by homologous recombination is confined to the S and G2 phases of the cell cycle partly due to 53BP1 antagonizing DNA end resection in G1 phase and non-cycling quiescent (G0) cells where DSBs must be repaired by non-homologous end joining (NHEJ). Unexpectedly, we uncovered extensive MRE11- and CtIP-dependent DNA end resection at DSBs in G0 mammalian cells. A whole genome CRISPR/Cas9 screen revealed the DNA-dependent kinase (DNA-PK) complex as a key factor in promoting DNA end resection in G0 cells. In agreement, depletion of FBXL12, which promotes ubiquitylation and removal of the KU70/KU80 subunits of DNA-PK from DSBs, promotes even more extensive resection in G0 cells. In contrast, a requirement for DNA-PK in promoting DNA end resection in cycling cells at the G1 or G2 phase cells was not observed. Our findings establish that DNA-PK uniquely promotes DNA end resection in G0, but not in G1 or G2 phase cells, and has important implications for DNA DSB repair in quiescent cells.

2022-05-16 | GSE186086 | GEO

DNA-PK Promotes DNA End Resection at DNA Double Strand Breaks in G0 cells [END-seq]

2022-05-16 | GSE186085 | GEO

Ku80/Ku70 complex associated RNA in HEK293T cells

Project description:We report the Ku80/Ku70 complex associated RNA in HEK293T cells using RNA-seq following PAR-Clip.

2024-04-09 | GSE219220 | GEO

Ku70 and Ligase IV deficiencies reveal distinct alternative end-joining outcomes in G1-arrested progenitor B cells

Project description:Classical nonhomologous end-joining (C-NHEJ) repairs DNA double-stranded breaks (DSBs) throughout interphase but is thought to predominate in G1-phase when homologous recombination is unavailable. Complexes containing the Ku70/80 ("Ku") and XRCC4/Ligase IV (Lig4) core C-NHEJ factors are required, respectively, for sensing and joining DSBs. While such factors are exclusively required for joining RAG1/2-initiated DSBs during V(D)J recombination in G1-phase lymphocyte progenitors, cycling cells deficient for core C-NHEJ factors join chromosomal DSBs by alternative end-joining (A-EJ) pathways. Restriction of V(D)J recombination to C-NHEJ has been attributed to RAG-mediated exclusion of A-EJ; however, it remains unclear whether A-EJ is similarly excluded from more general DSBs in G1. Here, we report that Ku actively and robustly suppresses A-EJ of RAG1/2 and two classes of engineered endonuclease-mediated DSBs in G1-arrested progenitor B cell lines. Thus, while targeted DSBs remain as free broken ends in Lig4-deficient G1-arrested progenitor B cells, deletion of Ku70 in Lig4-deficient cells restores DSB rejoining and translocation to levels observed in Ku70-deficient counterparts. Correspondingly, while V(D)J recombination is abrogated in Ligase4-deficient lines, V(D)J-like joining occurs in Ku70-deficient and Ku70/Lig4 double-deficient lines through a translocation-based A-EJ mechanism. We conclude that in G1, Lig4-deficient progenitor B cells are functionally end-joining deficient due to a near complete Ku-dependent block in A-EJ. Thus, the differential impacts of Ku deficiency versus XRCC4/Ligase IV deficiency on V(D)J recombination, severity of neuronal apoptosis, and embryonic development, including Ku-deficiency rescuing Lig4-deficient embryonic lethality, may be explained by Ku-mediated inhibition of A-EJ in the G1 cell cycle phase.

2021-05-08 | GSE162453 | GEO

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