Hanspeter Naegeli

The three-dimensional (3D) genome architecture is highly elastic, adapting to nuclear processes such as transcription and the DNA damage response (Dekker & Mirny 2016; Carré-Simon & Fabre 2021). Nucleotide excision repair (NER) acts within this chromatin context to detect and repair mutagenic lesions induced by ultraviolet (UV) irradiation (Sancar 2016). UV irradiation has been shown to induce restructuring of the 3D genome across multiple scales, including chromatin compartments, domains, and loops. However, the extent to which NER activity contributes to this remodelling is unresolved, as the only prior study tracking such UV-induced changes was limited to repair-proficient cells (Kaya & Adebali 2025). Here, by combining genome-wide chromatin profiling of repair-deficient human cells with loop extrusion simulations, we show that lesion-stalled RNA polymerase II (RNAPII) and repair-associated barriers constrain loop extrusion. These events counter the loop-lengthening effects of UV-induced transcriptional shutdown, leading to shorter chromatin loops and reinforced chromatin domains that facilitate efficient lesion recognition and repair. The contribution by NER machinery underscores 3D genome reorganisation as an active mechanism both initiated and harnessed by DNA repair, rather than a passive consequence of DNA damage. The contribution by RNAPII extends its role beyond activating transcription-coupled repair to promoting a genome-wide repair-permissive state. Together, these findings advance our understanding of how nuclear processes coordinate on a shared chromatin substrate to preserve genome integrity.

The mammalian genome is hierarchically structured to maintain accessibility and flexibility for essential nuclear processes such as transcription and DNA repair. A recent study using high-throughput 3D genome mapping reveals that nucleotide excision repair triggers large-scale chromatin rearrangements, reinforcing topologically associating domains and chromatin compartments. Notably, similar principles of chromatin stabilization are observed during double-strand break repair, consistent with the notion that chromatin restructuring may be an active and conserved DNA repair strategy rather than a passive consequence of damage. The observed stabilization is postulated to optimize repair efficiency by reducing the search space for damage, enhancing DNA accessibility at damage sites, increasing local concentrations of repair factors, and preventing aberrant chromosomal rearrangements. By synthesizing emerging evidence on nucleotide excision repair–driven chromatin dynamics and its parallels with double-strand break repair, this review examines how genome architecture actively shapes the DNA damage response and highlights broader implications for genetic diseases and therapeutic strategies.

To recognize DNA adducts, nucleotide excision repair (NER) deploys the XPC sensor, which detects damage-induced helical distortions, followed by engagement of TFIIH for lesion verification. Accessory players ensure that this factor handover takes place in chromatin where DNA is tightly wrapped around histones. Here, we describe how the histone methyltransferase ASH1L, once activated by MRG15, helps XPC and TFIIH to navigate through chromatin and induce global-genome NER hotspots. Upon UV irradiation, ASH1L adds H3K4me3 all over the genome (except in active gene promoters), thus priming chromatin for XPC relocations from native to damaged DNA. The ASH1L-MRG15 complex further recruits the histone chaperone FACT to DNA lesions. In the absence of ASH1L, MRG15 or FACT, XPC is misplaced and persists on damaged DNA without being able to deliver the lesions to TFIIH. We conclude that ASH1L-MRG15 makes damage verifiable by the NER machinery through the sequential deposition of H3K4me3 and FACT.

The thematic synthesis “Optimized use of antibiotics and behavior changes” summarises the NRP 72 research that developed and tested interventions aimed at reducing and optimising antibiotic usage. It formulates detailed conclusions and recommendations in this area, which have been drafted in collaboration with researchers and numerous stakeholders.

Much confusion has been generated in the safety assessment of food-grade TiO2 (E171) by the comingling of studies conducted on submicron-sized particles with those examining the toxicity of more minuscule counterparts. As E171 displays a nano-sized tail in its particle distribution (up to 36 % of particles with a diameter < 100 nm), it was thought that potential hazards of this food additive can be extrapolated from studies on thoroughly nanoscale formulations. This simplistic procedure may, however, overestimate the effects of the nano-sized tail of E171 because TiO2 particles readily aggregate or agglomerate in aqueous suspensions and biological matrices. The resulting larger clusters display a reduced oral bioavailability in comparison to the same material in nano-sized dimensions. Also, even if taken up in trace amounts, the smaller particles likely remain appended to larger particles or clusters and these aggregates or conglomerates may nullify to a great extent their “nano” characteristics. The purpose of this review is, therefore, to reevaluate the literature on the toxicity of TiO2 particles focusing on studies that are directly relevant for the assessment of E171. The purpose is not to avert a ban on the use of E171 in food, which might well be justified in light of the uncertainties associated with this additive employed solely for its colorant properties. Instead, it will be important to avoid in the future this same bias towards a fictional “nano” hazard, especially when evaluating more innovative engineered particles that confer true benefits for example by enhancing nutritional properties, quality, freshness, traceability or sustainability of food.

The European Commission mandated EFSA to complement its original scientific opinion on soybean MON 87769 × MON 89788 (EFSA‐GMO‐NL‐2010‐85) considering additional information on the human nutritional ...

This paper evaluates the potential hazards of food and feed derived from RNAi plants including: adverse changes of plant metabolism; mechanisms and...

EFSA requested its Scientific Committee to prepare a guidance document on appraising and integrating evidence from epidemiological studies for use in EFSA's scientific assessments. The guidance document provides an introduction to epidemiological studies and illustrates the typical biases of the different epidemiological study designs. It describes key epidemiological concepts relevant for evidence appraisal. Regarding study reliability, measures of association, exposure assessment, statistical inferences, systematic error and effect modification are explained. Regarding study relevance, the guidance describes the concept of external validity. The principles of appraising epidemiological studies are illustrated, and an overview of Risk of Bias (RoB) tools is given. A decision tree is developed to assist in the selection of the appropriate Risk of Bias tool, depending on study question, population and design. The customisation of the study appraisal process is explained, detailing the use of RoB tools and assessing the risk of bias in the body of evidence. Several examples of appraising experimental and observational studies using a Risk of Bias tool are annexed to the document to illustrate the application of the approach. This document constitutes a draft that will be applied in EFSA's assessments during a 1‐year pilot phase and be revised and complemented as necessary. Before finalisation of the document, a public consultation will be launched.

The excision of mutagenic DNA adducts by the nucleotide excision repair (NER) pathway is essential for genome stability, which is key to avoiding genetic diseases, premature aging, cancer and neurologic disorders. Due to the need to process an extraordinarily high damage density embedded in the nucleosome landscape of chromatin, NER activity provides a unique functional caliper to understand how histone modifiers modulate DNA damage responses. At least three distinct lysine methyltransferases (KMTs) targeting histones have been shown to facilitate the detection of ultraviolet (UV) light-induced DNA lesions in the difficult to access DNA wrapped around histones in nucleosomes. By methylating core histones, these KMTs generate docking sites for DNA damage recognition factors before the chromatin structure is ultimately relaxed and the offending lesions are effectively excised. In view of their function in priming nucleosomes for DNA repair, mutations of genes coding for these KMTs are expected to cause the accumulation of DNA damage promoting cancer and other chronic diseases. Research on the question of how KMTs modulate DNA repair might pave the way to the development of pharmacologic agents for novel therapeutic strategies.