Structural insights into human TFIIIC promoter recognition

Transcription factor (TF) IIIC recruits RNA polymerase (Pol) III to most of its target genes. Recognition of intragenic A- and B-box motifs in transfer RNA (tRNA) genes by TFIIIC modules τA and τB is the first critical step for tRNA synthesis but is mechanistically poorly understood. Here, we report cryo-electron microscopy structures of the six-subunit human TFIIIC complex unbound and bound to a tRNA gene. The τB module recognizes the B-box via DNA shape and sequence readout through the assembly of multiple winged-helix domains. TFIIIC220 forms an integral part of both τA and τB connecting the two subcomplexes via a ~550-amino acid residue flexible linker. Our data provide a structural mechanism by which high-affinity B-box recognition anchors TFIIIC to promoter DNA and permits scanning for low-affinity A-boxes and TFIIIB for Pol III activation.

Conformational transitions of the Spindly adaptor underlie its interaction with Dynein and Dynactin

Cytoplasmic Dynein 1, or Dynein, is a microtubule minus end-directed motor. Dynein motility requires Dynactin and a family of activating adaptors that stabilize the Dynein-Dynactin complex and promote regulated interactions with cargo in space and time. How activating adaptors limit Dynein activation to specialized subcellular locales is unclear. Here, we reveal that Spindly, a mitotic Dynein adaptor at the kinetochore corona, exists natively in a closed conformation that occludes binding of Dynein-Dynactin to its CC1 box and Spindly motif. A structure-based analysis identified various mutations promoting an open conformation of Spindly that binds Dynein-Dynactin. A region of Spindly downstream from the Spindly motif and not required for cargo binding faces the CC1 box and stabilizes the intramolecular closed conformation. This region is also required for robust kinetochore localization of Spindly, suggesting that kinetochores promote Spindly activation to recruit Dynein. Thus, our work illustrates how specific Dynein activation at a defined cellular locale may require multiple factors.

Mental health and well-being of students at TU Dresden

Background

University life can be a particularly challenging phase in the development of young adults. Current research shows that mental disorders occur more frequently in students compared to workers of the same age. The coronavirus pandemic has exacerbated the problem. The TUDo! Study, done in cooperation with the FU Berlin, aimed to assess the health status of students at TU Dresden, with a focus on mental health.

Methods

In 2020/2021 students at TU Dresden (excluding students in the medical school) completed an online-based questionnaire. Validated questionnaires, e.g. the PHQ 4 (depressive disorder and generalized anxiety disorder) and the ERI student (student gratification crisis) were used. We evaluated descriptively and analytically, according to the questionnaire-specific specifications.

Results

A total of 2,683 students (12.3%) at the TU Dresden took part in the survey. The majority of study participants were female (n = 1,507; 56.7%) and had an average age of 22.9 years (SD = 4.3). 32.8% (n = 856/2,611) of the participating students reported a depressive syndrome and 32.5% (n = 848/2,612) a generalized anxiety disorder. Almost half of participating students (40,0%; n = 515/1,310) indicated an imbalance between effort (E) and reward (R) (ER ratio>1). 51.23% (n = 693/1,50) of respondents reported a decline of mental well-being because of the coronavirus pandemic.

Discussion

Unlike similar studies, this study shows that TU Dresden students were particularly affected with regards to perceived psychological stress and complaints. The existing differences seem to be partly due to the coronavirus pandemic. These results indicate that universities should regularly check their studying conditions and provide appropriate preventive measures.

Key messages

• Students are at higher risk than workers of the same age for mental health problems.

• Students reported a decline in mental well-being due to the coronavirus pandemic.

Architecture of the yeast Pol III pre-termination complex and pausing mechanism on poly(dT) termination signals

RNA polymerase (Pol) III is specialized to transcribe short, abundant RNAs, for which it terminates transcription on polythymine (dT) stretches on the non-template (NT) strand. When Pol III reaches the termination signal, it pauses and forms the pre-termination complex (PTC). Here, we report cryoelectron microscopy (cryo-EM) structures of the yeast Pol III PTC and complementary functional states at resolutions of 2.7-3.9 Å. Pol III recognizes the poly(dT) termination signal with subunit C128 that forms a hydrogen-bond network with the NT strand and, thereby, induces pausing. Mutating key interacting residues interferes with transcription termination in vitro, impairs yeast growth, and causes global termination defects in vivo, confirming our structural results. Additional cryo-EM analysis reveals that C53-C37, a Pol III subcomplex and key termination factor, participates indirectly in Pol III termination. We propose a mechanistic model of Pol III transcription termination and rationalize why Pol III, unlike Pol I and Pol II, terminates on poly(dT) signals.

An integrated model for termination of RNA polymerase III transcription

RNA polymerase III (RNAPIII) synthesizes essential and abundant noncoding RNAs such as transfer RNAs. Controlling RNAPIII span of activity by accurate and efficient termination is a challenging necessity to ensure robust gene expression and to prevent conflicts with other DNA-associated machineries. The mechanism of RNAPIII termination is believed to be simpler than that of other eukaryotic RNA polymerases, solely relying on the recognition of a T-tract in the nontemplate strand. Here, we combine high-resolution genome-wide analyses and in vitro transcription termination assays to revisit the mechanism of RNAPIII transcription termination in budding yeast. We show that T-tracts are necessary but not always sufficient for termination and that secondary structures of the nascent RNAs are important auxiliary cis-acting elements. Moreover, we show that the helicase Sen1 plays a key role in a fail-safe termination pathway. Our results provide a comprehensive model illustrating how multiple mechanisms cooperate to ensure efficient RNAPIII transcription termination.

Effects of a Brief Web-Based "Social Norms"-Intervention on Alcohol, Tobacco and Cannabis Use Among German University Students: Results of a Cluster-Controlled Trial Conducted at Eight Universities

Background and Aim: "Social norms" (SN)-interventions are aimed at changing existing misperceptions regarding peer substance use by providing feedback on actual norms, thereby affecting personal substance use. It is unknown whether SN-intervention effects previously demonstrated in US students can be replicated in German students. The aim of the INSIST-study was to examine the effects of a web-based SN-intervention on substance use. Design: Cluster-controlled trial. Setting: Eight Universities in Germany. Participants and Measurements: Students were recruited at four intervention vs. four delayed intervention control Universities. 4,463 students completed baseline, 1,255 students (59% female) completed both baseline and 5-months follow-up web-based surveys on personal and perceived peer substance use. Intervention participants received feedback contrasting personal and perceived peer use with previously assessed use and perceptions of same-sex, same-university peers. Intervention effects were assessed via multivariable mixed logistic regression models. Findings: Relative to controls, reception of SN-feedback was associated with higher odds for decreased alcohol use (OR: 1.91, 95% CI 1.42-2.56). This effect was most pronounced in students overestimating peer use at baseline and under or accurately estimating it at follow-up (OR: 6.28, 95% CI 2.00-19.8). The OR was 1.33 (95% CI 0.67-2.65) for decreased cannabis use in students at intervention Universities and was statistically significant at 1.70 (95% CI 1.13-2.55) when contrasting unchanged and decreased with increased use. Regarding tobacco use and episodes of drunkenness, no intervention effects were found. Conclusions: This study was the first cluster-controlled trial suggesting beneficial effects of web-based SN-intervention on alcohol and cannabis use in a large sample of German University students. Clinical Trial Registration: The trial registration number of the INSIST-study is DRKS00007635 at the "German Clinical Trials Register."

Activation of the Endonuclease that Defines mRNA 3' Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex

Cleavage and polyadenylation factor (CPF/CPSF) is a multi-protein complex essential for formation of eukaryotic mRNA 3' ends. CPF cleaves pre-mRNAs at a specific site and adds a poly(A) tail. The cleavage reaction defines the 3' end of the mature mRNA, and thus the activity of the endonuclease is highly regulated. Here, we show that reconstitution of specific pre-mRNA cleavage with recombinant yeast proteins requires incorporation of the Ysh1 endonuclease into an eight-subunit "CPF_core" complex. Cleavage also requires the accessory cleavage factors IA and IB, which bind substrate pre-mRNAs and CPF, likely facilitating assembly of an active complex. Using X-ray crystallography, electron microscopy, and mass spectrometry, we determine the structure of Ysh1 bound to Mpe1 and the arrangement of subunits within CPF_core. Together, our data suggest that the active mRNA 3' end processing machinery is a dynamic assembly that is licensed to cleave only when all protein factors come together at the polyadenylation site.

Structure and decoy-mediated inhibition of the SOX18/Prox1-DNA interaction

The transcription factor (TF) SOX18 drives lymphatic vessel development in both embryogenesis and tumour-induced neo-lymphangiogenesis. Genetic disruption of Sox18 in a mouse model protects from tumour metastasis and established the SOX18 protein as a molecular target. Here, we report the crystal structure of the SOX18 DNA binding high-mobility group (HMG) box bound to a DNA element regulating Prox1 transcription. The crystals diffracted to 1.75Å presenting the highest resolution structure of a SOX/DNA complex presently available revealing water structure, structural adjustments at the DNA contact interface and non-canonical conformations of the DNA backbone. To explore alternatives to challenging small molecule approaches for targeting the DNA-binding activity of SOX18, we designed a set of five decoys based on modified Prox1-DNA. Four decoys potently inhibited DNA binding of SOX18 in vitro and did not interact with non-SOX TFs. Serum stability, nuclease resistance and thermal denaturation assays demonstrated that a decoy circularized with a hexaethylene glycol linker and terminal phosphorothioate modifications is most stable. This SOX decoy also interfered with the expression of a luciferase reporter under control of a SOX18-dependent VCAM1 promoter in COS7 cells. Collectively, we propose SOX decoys as potential strategy for inhibiting SOX18 activity to disrupt tumour-induced neo-lymphangiogenesis.

The GYF domain protein CD2BP2 is critical for embryogenesis and podocyte function

Scaffolding proteins play pivotal roles in the assembly of macromolecular machines such as the spliceosome. The adaptor protein CD2BP2, originally identified as a binding partner of the adhesion molecule CD2, is a pre-spliceosomal assembly factor that utilizes its glycine-tyrosine-phenylalanine (GYF) domain to co-localize with spliceosomal proteins. So far, its function in vertebrates is unknown. Using conditional gene targeting in mice, we show that CD2BP2 is crucial for embryogenesis, leading to growth retardation, defects in vascularization, and premature death at embryonic day 10.5 when absent. Ablation of the protein in bone marrow-derived macrophages indicates that CD2BP2 is involved in the alternative splicing of mRNA transcripts from diverse origins. At the molecular level, we identified the phosphatase PP1 to be recruited to the spliceosome via the N-terminus of CD2BP2. Given the strong expression of CD2BP2 in podocytes of the kidney, we use selective depletion of CD2BP2, in combination with next-generation sequencing, to monitor changes in exon usage of genes critical for podocyte functions, including VEGF and actin regulators. CD2BP2-depleted podocytes display foot process effacement, and cause proteinuria and ultimately lethal kidney failure in mice. Collectively, our study defines CD2BP2 as a non-redundant splicing factor essential for embryonic development and podocyte integrity.