Damage in the DNA inhibits transcription of genes by RNA polymerase II, which copies the genetic information of DNA into RNA. This impediment of RNA polymerase II results in severe cellular dysfunction and accelerated aging. Through a consortium combining unique complementary knowledge and expertise, we can study for the first time the causes and consequences of DNA damage from the perspective of a single molecule to that of a whole organism. Using this approach, we will study what exactly happens to RNA polymerase when encountering DNA damage, and directly link this to the consequences at the cellular and organism level.

Cultured embryonic stem cells (ESCs) can self-renew (the ability to go through numerous cycles of cell division while maintaining their undifferentiated, pluripotent states) and differentiate into one or more, cell type(s) under defined conditions, accompanied by exit from pluripotency. Transcriptional and epigenetic regulation of stem cells has been extensively investigated, including interconversion of differently caught pluripotency states in vitro. However, translational regulation is also important for stem cell fate. Although less studied, it is a fundamental mechanism for harnessing the full scope of stem cell biology, which provides essential concepts for its use in diagnostic and drug screening, and towards stem cell based therapeutic applications. My research with the microtubule-associated protein CLASP2 clearly links dynamic microtubules to protein trafficking, cellular signaling and, unexpectedly, to translational regulation. I have identified a novel function of CLASP in RNA-regulation through its interaction with the microtubule- and RNA-binding protein JAKMIP1. A growing number of signal effector proteins and partners thereof are found to interact with RNA, leading to my interest in JAKMIP1 function. Depletion of JAKMIP1 affects several pluripotency genes and impairs self-renewal and differentiation of ESCs. My work aims to address the mechanism by which JAKMIP1 controls translation in ESCs and the functional relevance of such regulation in maintaining stem cell identity. For this, I will engineer the JAKMIP1 locus in ESCs using CRISPR/Cas9 technology. These cells will then be used for novel high-throughput analyses, including Ribo-SEQ, and iCLIP, and also advanced fluorescence microscopy to study protein behavior and interactions in living cells.

DNA is intricately packed within the cell nucleus in a structure called chromatin. This packaging contains all the instructions needed for cells to perform their functions. Understanding how chromatin regulates DNA accessibility is a key focus in biomedical research. In various diseases, such as cancer, chromatin structure is often altered, which may contribute to disease development. At the Dutch Chromatin Meeting, experts gather to exchange data and ideas, aiming to advance scientific knowledge in this important field.

Psychiatric patients are ambivalent about the value biomarker research. On the one hand, they hope it can give them "definite" proof that their condition is real. On the other hand, they are afraid of stigmatization. Patients stress that biomarker technology should not replace ‘subjective’ experiences in their conversations with psychiatrists. With regard to physicians, in this case urologists, often they disagreed with developers of biomarkers on 1) the perceived advantages of biomarkers; 2) the scientific and clinical evidence; 3) the advantages of other technologies such as MRI in urology; and 4) the value of other diagnostic tests

Hereditary defects in the essential and multifunctional transcription and DNA repair factor TFIIH are associated with several distinct, clinically heterogeneous diseases characterized by cancer predisposition, (progressive) neurological defects, developmental failure and segmental progeria, whose pathogenesis is not fully understood. The function and activity of TFIIH has been thoroughly investigated, but it is still not entirely clear how mutations in the same complex can lead to diverse symptoms and human diseases and why the impact of hereditary mutations differs depending on the tissue type. Systematic comparison of TFIIH mutations in cells is difficult because TFIIH is essential and patient cells are not isogenic and often compound-heterozygote. To better understand mutant TFIIH activity in cells, in this project we propose to generate and functionally compare multiple patient-derived mutations in the same TFIIH gene, in isogenic human cells and in C. elegans as in vivo model. To this end, we will label, by knock-in, endogenous TFIIH with the multi-purpose GFP-tag while simultaneously introducing patient-derived mutations in its XPD helicase subunit, using CRISPR-Cas9. Next, using state-of-the-art DNA repair assays, live cell confocal imaging, proteomics and genomics approaches, we will thoroughly investigate the activity of each mutant TFIIH in nucleotide excision repair and transcription, in relation to its phenotypic impact, in both human cells in culture and in vivo, in C. elegans, to study mutant TFIIH mechanism and impact in differentiated cell types such as neurons. As functional TFIIH is essential for life and because its dysfunction causes developmental failure, cancer and aging, it is of major importance to understand its precise activity to be able to promote human health.