Biology subjects

Burger, K.

Publications and source records attributed to Burger, K..

4 recordsLinked to original sources

bioRxiv2025

Stable interaction of NONO with DBHS family members upon etoposide-induced DNA damage

The Non-POU domain containing octamer binding (NONO) protein is a member of the multifunctional Drosophila behavior/human splicing (DBHS) protein family and a core component of nuclear paraspeckles. NONO forms dimers with the other two DBHS members splicing factor proline and glutamine rich (SFPQ) protein or the paraspeckle component 1 (PSCP1) to modulate RNA metabolism and gene expression both at the transcriptional and post-transcriptional level. Increasing evidence suggests that NONO participates in genome maintenance by stimulating the DNA damage response (DDR) upon induction of DNA double-strand breaks (DSBs). However, the molecular principles that engage NONO in genome stability are poorly understood. We hypothesized that the induction of DSBs alters NONO protein-protein interactions and applied label-free mass spectrometry to test for changes in the interactome of NONO in human U2OS cells upon treatment with the topoisomerase II inhibitor etoposide. Surprisingly, our mass spectrometry data reveal that etoposide treatment does not induce major changes in NONO protein-protein interactions. We confirmed this finding by orthogonal co-immunoprecipitation assays and co-localization assays. Our data suggest that the bulk of interactions between NONO and SFPQ or PSPC1 are insensitive to etoposide treatment and that DBHS family members promote genome stability as stable dimers.

biochemistry↗

bioRxiv2024

The FAIR Data Point Populator: collaborative FAIRification and population of FAIR Data Points

BackgroundUse of the FAIR principles (Findable, Accessible, Interoperable and Reusable) allows the rapidly growing number of biomedical datasets to be optimally (re)used. An important aspect of the FAIR principles is metadata. The FAIR Data Point specifications and reference implementation have been designed as an example on how to publish metadata according to the FAIR principles. Various tools to create metadata have been created, but many of these have limitations, such as interfaces that are not intuitive, metadata that does not adhere to a common metadata schema, limited scalability, and inefficient collaboration. We aim to address these limitations in the FAIR Data Point Populator. ResultsThe FAIR Data Point Populator consists of a GitHub workflow together with Excel templates that have tooltips, validation and documentation. The Excel templates are targeted towards non-technical users, and can be used collaboratively in online spreadsheet software. A more technical user then uses the GitHub workflow to read multiple entries in the Excel sheets, and transform it into machine readable metadata. This metadata is then automatically uploaded to a connected FAIR Data Point. We applied the FAIR Data Point Populator on the metadata of two datasets, and a patient registry. We were then able to run a query on the FAIR Data Point Index, in order to retrieve one of the datasets. ConclusionThe FAIR Data Point Populator addresses several limitations of other tools. It makes creating metadata easier, ensures adherence to a common metadata schema, allows bulk creation of metadata entries and increases collaboration. As a result of this, the barrier of entry for FAIRification is lower, which enables the creation of FAIR data by more people.

bioinformatics↗

bioRxiv2024

NEAT1 promotes genome stability via m6A methylation-dependent regulation of CHD4

Long non-coding (lnc)RNA emerge as regulators of genome stability. The nuclear enriched abundant transcript 1 (NEAT1) locus encodes two lncRNA isoforms that modulate gene expression, growth and proliferation in mammals. Interestingly, NEAT1 transcripts are overexpressed in many tumours and induced by DNA damage, suggesting a genome-protective function. However, the precise role of NEAT1 in the DNA damage response (DDR) is unclear. Here, we investigate the expression, modification levels, localization and structure of NEAT1 in response to DNA double-strand breaks (DSBs) induced by the topoisomerase-II inhibitor etoposide or the locus-specific endonuclease AsiSI. We find that induction of DSBs increases both the levels and N6-methyladenosine (m6A) marks on NEAT1, which promotes alterations in NEAT1 secondary structure and accumulation of hyper-methylated NEAT1 at a subset of promoter-associated DSBs to facilitate efficient DSB signalling. The depletion of NEAT1, in turn, delays the response to DSBs and triggers elevated DNA damage. The genome-protective role of NEAT1 is mediated by the RNA methyltransferase 3 (METTL3) and involves spreading of the chromodomain helicase DNA binding protein 4 (CHD4) upon release from NEAT1. Together, we describe a novel RNA-dependent DDR pathway that couples NEAT1 to the recognition and repair of DSBs.

molecular biology↗

bioRxiv2023

Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts

RNA-binding proteins (RBPs) stimulate the DNA damage response (DDR). The RBP NONO marks nuclear paraspeckles in unperturbed cells and undergoes poorly understood re-localisation to the nucleolus upon induction of DNA double-strand breaks (DSBs). Here we show that treatment with the topoisomerase-II inhibitor etoposide stimulates the production of RNA polymerase II-dependent, DNA damage-induced nucleolar antisense RNAs (diNARs) in human cells. diNARs originate from the nucleolar intergenic spacer and tether NONO to the nucleolus via its RRM1 domain. NONO occupancy at protein-coding gene promoters is reduced by etoposide, which attenuates pre-mRNA synthesis, enhances NONO binding to pre-mRNA transcripts and is accompanied by nucleolar detention of such transcripts. The depletion or mutation of NONO interferes with detention and prolongs DSB signaling. Together, we describe a nucleolar DDR pathway that shields NONO and aberrant transcripts from DSBs to promote DNA repair.

molecular biology↗