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Cells dedicate significant energy to build proteins often organized in multiprotein assemblies with tightly regulated stoichiometries. As genes encoding subunits assembling in a multisubunit complex are dispersed in the genome of eukaryotes, it is unclear how these protein complexes assemble. Here, we show that mammalian nuclear transcription complexes (TFIID, TREX-2 and SAGA) composed of a large number of subunits, but lacking precise architectural details are built co-translationally. We demonstrate that dimerization domains and their positions in the interacting subunits determine the co-translational assembly pathway (simultaneous or sequential). The lack of co-translational interaction can lead to degradation of the partner protein. Thus, protein synthesis and complex assembly are linked in building mammalian multisubunit complexes, suggesting that co-translational assembly is a general principle in mammalian cells to avoid non-specific interactions and protein aggregation. These findings will also advance structural biology by defining endogenous co-translational building blocks in the architecture of multisubunit complexes. Genes encoding protein complex subunits are often dispersed in the genome of eukaryotes, raising the question how these protein complexes assemble. Here, the authors provide evidence that mammalian nuclear transcription complexes are formed co-translationally to ensure specific and functional interactions.

Background Mobile health (mHealth)— the use of medical applications in healthcare settings —include tools that can support self-management after surgery and thereby contribute to early postoperative recovery. Providing patients with timely and interactive information through mHealth is hypothesized to positively influence recovery after reverse shoulder arthroplasty (RSA). The aim of this study is to determine the effectiveness of both interactive and personalized information and a rehabilitation protocol with a mobile application compared to generic non-personalized digital information on postoperative recovery in patients undergoing primary RSA. Methods A multicentre randomised controlled trial will be conducted in two Dutch hospitals. In total 170 patients undergoing elective, primary RSA will be included. Participants will be randomly allocated to one of the two groups on a 1:1 ratio. The intervention group will receive interactive postoperative information on a daily basis. The control group will receive generic, non-personalized digital information. The primary outcome is defined as functional recovery measured using the Oxford Shoulder Score (OSS) at 6 weeks. Secondary outcomes are: pain, physical functioning, quality of life, length of stay, complications, treatment satisfaction and app usage. The between group difference will be analysed using linear mixed-effects regression. Discussion This randomised controlled trial will compare the postoperative recovery rate in patients undergoing RSA between patients receiving an interactive mHealth application with generic digital information. The results from this study can contribute to improving postoperative care for patients undergoing RSA. Trial registration This trial is registered in ClinicalTrials.gov (NCT06520085) on the 22nd of July 2024.

Zygotic genome activation (ZGA) is crucial for maternal to zygotic transition at the 2-8-cell stage in order to overcome silencing of genes and enable transcription from the zygotic genome. In humans, ZGA is induced by DUX4, a pioneer factor that drives expression of downstream germline-specific genes and retroelements. Here we show that herpesviruses from all subfamilies, papillomaviruses and Merkel cell polyomavirus actively induce DUX4 expression to promote viral transcription and replication. Analysis of single-cell sequencing data sets from patients shows that viral DUX4 activation is of relevance in vivo. Herpes-simplex virus 1 (HSV-1) immediate early proteins directly induce expression of DUX4 and its target genes, which mimics zygotic genome activation. Upon HSV-1 infection, DUX4 directly binds to the viral genome and promotes viral transcription. DUX4 is functionally required for infection, since genetic depletion by CRISPR/Cas9 as well as degradation of DUX4 by nanobody constructs abrogates HSV-1 replication. Our results show that DNA viruses including herpesviruses mimic an embryonic-like transcriptional program that prevents epigenetic silencing of the viral genome and facilitates herpesviral gene expression. Neugebauer et al. show activation of the usually silenced embryonic factor DUX4 by herpesviruses in vitro and in patients, and demonstrate that depletion of DUX4 by nanobody degraders abrogates viral replication.

Metastasis arises from disseminated tumour cells (DTCs) that are characterized by intrinsic phenotypic plasticity and the capability of seeding to secondary organs. DTCs can remain latent for years before giving rise to symptomatic overt metastasis. In this context, DTCs fluctuate between a quiescent and proliferative state in response to systemic and microenvironmental signals including immune-mediated surveillance. Despite its relevance, how intrinsic mechanisms sustain DTCs plasticity has not been addressed. By interrogating the epigenetic state of metastatic cells, we find that tumour progression is coupled with the activation of oncogenic enhancers that are organized in variable interconnected chromatin domains. This spatial chromatin context leads to the activation of a robust transcriptional response upon repeated exposure to retinoic acid (RA). We show that this adaptive mechanism sustains the quiescence of DTCs through the activation of the master regulator SOX9. Finally, we determine that RA-stimulated transcriptional memory increases the fitness of metastatic cells by supporting the escape of quiescent DTCs from NK-mediated immune surveillance. Overall, these findings highlight the contribution of oncogenic enhancers in establishing transcriptional memories as an adaptive mechanism to reinforce cancer dormancy and immune escape, thus amenable for therapeutic intervention. Metastasis arises from disseminated tumour cells (DTCs) while the underlying mechanism of DTCs plasticity remains underexplored. Here, the authors show that spatially organized oncogenic enhancers on chromatin sustain the establishment of retinoic acid (RA)-stimulated transcriptional memory through activation of SOX9, supporting the escape of quiescent DTCs from NK-mediated immune surveillance.

The transcriptional machinery is essential for gene expression and regulation; dysregulation of transcription can result in a range of pathologies, including neurodegeneration, cancer, developmental disorders and cardiovascular disease. A key component of RNA polymerase II-mediated transcription is the basal transcription factor IID, which is formed of the TATA box-binding protein (TBP) and 14 TBP-associated factors (TAFs), the largest of which is the TAF1 protein, encoded on the X chromosome (Xq13.1). TAF1 is dysregulated in X-linked dystonia–parkinsonism and congenital mutations in the gene are causative for neurodevelopmental phenotypes; TAF1 dysfunction is also associated with cardiac anomalies and cancer. However, how TAF1 contributes to pathology is unclear. Here, we highlight the key aspects of the TAF1 gene and protein function that may link transcriptional regulation with disorders of development, growth and adult-onset disorders of motor impairment. We highlight the need to experimentally investigate the full range of TAF1 messenger RNA variants and protein isoforms in human and mouse to aid our understanding of TAF1 biology. Furthermore, the X-linked nature of TAF1 -related diseases adds complexity to understanding phenotypes. Overall, we shed light on the aspects of TAF1 biology that may contribute to disease and areas that could be addressed for future research and targeted therapeutics.

H2A.Z-nucleosomes are present in both euchromatin and heterochromatin and it has proven difficult to interpret their disparate roles in the context of their stability features. Using an in situ assay of nucleosome stability and DT40 cells expressing engineered forms of the histone variant we show that native H2A.Z, but not C-terminally truncated H2A.Z (H2A.Z∆C), is released from nucleosomes of peripheral heterochromatin at unusually high salt concentrations. H2A.Z and H3K9me3 landscapes are reorganized in H2A.Z∆C-nuclei and overall sensitivity of chromatin to nucleases is increased. These tail-dependent differences are recapitulated upon treatment of HeLa nuclei with the H2A.Z-tail-peptide (C9), with MNase sensitivity being increased genome-wide. Fluorescence correlation spectroscopy revealed C9 binding to reconstituted nucleosomes. When introduced into live cells, C9 elicited chromatin reorganization, overall nucleosome destabilization and changes in gene expression. Thus, H2A.Z-nucleosomes influence global chromatin architecture in a tail-dependent manner, what can be modulated by introducing the tail-peptide into live cells. Here the authors reveal triple heterogeneity of H2A.Z containing nucleosomes, attributed to interactions involving the C-terminal tail of the histone variant, and demonstrate modulation of global chromatin architecture using a synthetic tail peptide.

Purpose Research to date suggests that physical activity is associated with improved sleep, but studies have predominantly relied on self-report measures and have not accounted for school day/free day variability. To address these gaps in the literature, the aim of the present study was to (a) quantify physical activity in adolescents using long-term daily actigraphy measurement and (b) to examine the association between actigraphically assessed steps and sleep behavior in a sample of healthy adolescents. To be able to capture intra- and inter-individual differences in the daily physical activity of adolescents, we examined within as well as between subjects effects and its association with sleep. Methods Fifty adolescents between 10 and 14 years of age were included in the present study. In total 5989 days of actigraphy measurement (average of 119 ± 40 days per participant; range = 39–195 days) were analyzed. We use multilevel modeling to disentangle the within and between subject effects of physical activity on sleep. In this way, we examine within an individual, the association between steps during the day and subsequent sleep on a day-to-day basis. On the other hand, our between subjects’ analysis allows us to ascertain whether individuals with more overall physical activity have better sleep. Results Within a subject more steps on school and free days were associated with later bed times on school and free days as well as later rise times on school days only. On the other hand, comparing between subjects’ effects, more steps were associated with lower sleep efficiency on free and school days. No other significant associations were found for the other sleep variables. Conclusion Our results obtained through objective and long-term measurement of both sleep and number of steps suggest weak or non-significant associations between these measures for most sleep variables. We emphasize the importance of the methodology and the separation of within subject from between subject features when examining the relationship between physical activity and sleep.

Cancer sequencing studies have revealed that urothelial carcinomas harbour recurrent mutations in multiple genes that control epigenetics. A major challenge for basic and clinical researchers is to convert this genetic information into biological and pathological insights, as well as to tailor novel therapeutic modalities for individual patients with bladder cancer.

The process of eukaryotic transcription initiation involves the assembly of basal transcription factor complexes on the gene promoter. The recruitment of TFIID is an early and important step in this process. Gene promoters contain distinct DNA sequence elements and are marked by the presence of post-translationally modified nucleosomes. The contributions of these individual features for TFIID recruitment remain to be elucidated. Here, we use immobilized reconstituted promoter nucleosomes, conventional biochemistry and quantitative mass spectrometry to investigate the influence of distinct histone modifications and functional DNA-elements on the binding of TFIID. Our data reveal synergistic effects of H3K4me3, H3K14ac and a TATA box sequence on TFIID binding in vitro. Stoichiometry analyses of affinity purified human TFIID identified the presence of a stable dimeric core. Several peripheral TAFs, including those interacting with distinct promoter features, are substoichiometric yet present in substantial amounts. Finally, we find that the TAF3 subunit of TFIID binds to poised promoters in an H3K4me3-dependent manner. Moreover, the PHD-finger of TAF3 is important for rapid induction of target genes. Thus, fine-tuning of TFIID engagement on promoters is driven by synergistic contacts with both DNA-elements and histone modifications, eventually resulting in a high affinity interaction and activation of transcription.