Biology subjects

van der Woude, M.

Publications and source records attributed to van der Woude, M..

5 recordsLinked to original sources

bioRxiv2025

Nanoclustering of a plant transcription factor enables strong yet specific DNA binding

Transcription factors (TFs) are traditionally depicted as monomeric, or oligomeric, units that recognize and bind specific DNA sequences to regulate transcription. Emerging evidence suggests that many TFs can undergo liquid phase separation, resulting in condensates that bind DNA through a different mechanism. For the Auxin Response Factors (ARFs), canonical plant TFs, evidence for both scenarios exists. But which of these scenarios is operational in the plant nucleus is unclear. Here, we demonstrate using MpARF2 of Marchantia polymorpha that a third scenario is operational: MpARF2 forms nanoscopic clusters under physiological conditions. Nanoclusters combine DNA-binding features that cannot be accessed by the other two scenarios: high-affinity, switch-like, and sequence-specific. Our results suggest nanoclustering as a mechanism that equips TFs with the DNA-binding properties necessary for transcriptional regulation. TeaserTranscription factor nanoclusters balance the DNA-binding trade-off between weakly binding oligomers and nonspecific condensates.

plant biology↗

bioRxiv2025

RNA polymerase II processing facilitates DNA repair and prevents DNA damage-induced neuronal and developmental failure

Hereditary transcription-coupled nucleotide excision repair (TC-NER) defects cause severe developmental and neurodegenerative features, as observed in Cockayne syndrome (CS), or mild cutaneous UV sensitivity, as observed in UV-sensitive syndrome. The mechanisms underlying the strikingly different clinical features of these syndromes are not fully understood. Using C. elegans, we demonstrate that TC-NER deficiency leads to DNA damage-induced motoneuronal and developmental failure, primarily caused by the lack of lesion removal due to persistent lesion-stalling of RNA polymerase II. If, in the absence of TC-NER, lesion-stalled RNA polymerase II is processed and removed, global genome NER acts as backup pathway to repair transcription-blocking lesions and prevents DNA damage-induced developmental failure. Our results furthermore show that processing of lesion-stalled RNA Polymerase II facilitates TC-NER and involves the activity of multiple E3 ubiquitin ligases. These findings reveal that persistently stalled RNA polymerase II, rather than TC-NER deficiency, is the major driver of severe disease features associated with TC-NER defects.

molecular biology↗

bioRxiv2023

Recovery of protein synthesis to measure transcription-coupled DNA repair in living cells and tissues

Transcription-coupled nucleotide excision repair (TC-NER) is an important DNA repair mechanism that protects against the negative effects of transcription-blocking DNA lesions. Hereditary TC-NER deficiency causes pleiotropic and often severe neurodegenerative and progeroid symptoms. Multiple assays have been developed for the clinic and for research to measure TC-NER activity, which is hampered by the relatively low abundance of repair events taking place in transcribed DNA. Recovery of RNA Synthesis is widely used as indirect TC-NER assay based on the notion that lesion-blocked transcription only resumes after successful TC-NER. Here, we show that measuring novel synthesis of a protein that has been degraded prior to DNA damage induction is an equally effective but more versatile manner to indirectly monitor TC-NER. This Recovery of Protein Synthesis (RPS) assay is readily adaptable for use with different degradable proteins and readouts, including fluorescence imaging and immunoblot. Moreover, with the RPS assay TC-NER activity can be measured in real-time, in various living cells types and even in differentiated tissues of living organisms. As example, we show that TC-NER capacity declines in aging muscle tissue of C. elegans. Therefore, the RPS assay constitutes an important novel clinical and research tool to investigate transcription-coupled DNA repair.

genetics↗

bioRxiv2021

C. elegans TFIIH subunit GTF-2H5/TTDA is a non-essential transcription factor indispensable for DNA repair

The 10-subunit TFIIH complex is vital to both transcription initiation and nucleotide excision repair. Hereditary mutations in its smallest subunit, TTDA/GTF2H5, cause a photosensitive form of the rare developmental brittle hair disorder trichothiodystrophy (TTD). Some TTD features are thought to be caused by subtle transcription or gene expression defects. Strikingly, TTDA/GTF2H5 knockout mice are not viable, which makes it difficult to investigate how TTDA/GTF2H5 promotes transcription in vivo. Here, we show that deficiency of the C. elegans TTDA ortholog GTF-2H5 is, however, compatible with viability and growth, in contrast to depletion of other TFIIH subunits. We also show that GTF-2H5 promotes the stability of TFIIH in multiple tissues and is indispensable for nucleotide excision repair, in which it facilitates recruitment of the TFIIH complex to DNA damage. Strikingly, when transcription is challenged, gtf-2H5 embryos die due to the intrinsic TFIIH fragility in the absence of GTF-2H5. These results support the idea that TTDA/GTF2H5 mutations cause transcription impairment underlying trichothiodystrophy and establish C. elegans as potential model for studying the pathogenesis of this disease.

genetics↗

bioRxiv2021

Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability

Correct transcription is crucial for life. However, DNA damage severely impedes elongating RNA Polymerase II (Pol II), causing transcription inhibition and transcription-replication conflicts. Cells are equipped with intricate mechanisms to counteract the severe consequence of these transcription-blocking lesions (TBLs). However, the exact mechanism and factors involved remain largely unknown. Here, using a genome-wide CRISPR/cas9 screen, we identified elongation factor ELOF1 as an important new factor in the transcription stress response upon DNA damage. We show that ELOF1 has an evolutionary conserved role in Transcription-Coupled Nucleotide Excision Repair (TC-NER), where it promotes recruitment of the TC-NER factors UVSSA and TFIIH to efficiently repair TBLs and resume transcription. Additionally, ELOF1 modulates transcription to protect cells from transcription-mediated replication stress, thereby preserving genome stability. Thus, ELOF1 protects the transcription machinery from DNA damage by two distinct mechanisms.

cell biology↗