Transcriptional stress in aging: integrating experimental data and modeling to quantify DNA damage accumulation

Jacinta van de Grint¹Marko Raseta¹Renata Maria Catharina Brandt¹Yvette van Loon¹Joris Demmers¹Shannon Dealy¹Jiang Chang¹Jan Hoeijmakers^1,2,3Joris Pothof^1*

• ¹Molecular Genetics, Erasmus MC, Rotterdam, Netherlands
• ²Prinses Maxima Centrum voor Kinderoncologie BV, Utrecht, Netherlands
• ³Universitat zu Koln Medizinische Fakultat, Cologne, Germany

Accumulating DNA damage plays a crucial role in aging, particularly in post-mitotic tissues by disrupting transcription and causing transcriptional stress—a state marked by reduced transcriptional productivity. Transcriptional stress disproportionately affects long genes, due to the random distribution of DNA lesions across the genome. An estimate for the total number of transcription-blocking lesions (TBLs) required to induce transcriptional stress and contribute to aging is lacking. Here, we estimated the number of TBLs accumulating with age, by integrating experimental data with a mathematical model based solely on fundamental biological principles. Using 5-ethynyluridine (EU) incorporation, we assessed transcriptional activity in dermal fibroblasts and liver tissue from Ercc1-/-, Ercc1d/-, and Xpg-/- mice —models with DNA repair deficiencies that exhibit a wide range of premature aging features between 5 and 26 weeks of age. We then compared the experimental data to our model, which captured the overall trend of transcriptional decline, supporting a correlation between accumulating DNA damage and reduced transcription during aging. Wildtype mice were found to accumulate approximately 62 TBLs per day, whereas DNA repair-deficient mice exhibited a markedly higher burden, accumulating 1600–5000 TBLs daily. These insights offer a quantitative understanding of transcriptional stress, which is crucial for elucidating the aging process.