AKIRIN2 controls the nuclear import of proteasomes in vertebrates.

Protein expression and turnover are controlled through a complex interplay of transcriptional, post-transcriptional and post-translational mechanisms to enable spatial and temporal regulation of cellular processes. To systematically elucidate such gene regulatory networks, we developed a CRISPR screening assay based on time-controlled Cas9 mutagenesis, intracellular immunostaining and fluorescence-activated cell sorting that enables the identification of regulatory factors independent of their effects on cellular fitness. We pioneered this approach by systematically probing the regulation of the transcription factor MYC, a master regulator of cell growth1-3. Our screens uncover a highly conserved protein, AKIRIN2, that is essentially required for nuclear protein degradation. We found that AKIRIN2 forms homodimers that directly bind to fully assembled 20S proteasomes to mediate their nuclear import. During mitosis, proteasomes are excluded from condensing chromatin and re-imported into newly formed daughter nuclei in a highly dynamic, AKIRIN2-dependent process. Cells undergoing mitosis in the absence of AKIRIN2 become devoid of nuclear proteasomes, rapidly causing accumulation of MYC and other nuclear proteins. Collectively, our study reveals a dedicated pathway controlling the nuclear import of proteasomes in vertebrates and establishes a scalable approach to decipher regulators in essential cellular processes.

EVI1 drives leukemogenesis through aberrant ERG activation.

Chromosomal rearrangements involving the MDS1 and EVI1 complex locus (MECOM) on chromosome 3q26 define an aggressive subtype of acute myeloid leukemia (AML) that is associated with chemotherapy resistance and dismal prognosis. Established treatment regimens commonly fail in these patients, therefore, there is an urgent need for new therapeutic concepts that will require a better understanding of the molecular and cellular functions of the ecotropic viral integration site 1 (EVI1) oncogene. To characterize gene regulatory functions of EVI1 and associated dependencies in AML, we developed experimentally tractable human and murine disease models, investigated the transcriptional consequences of EVI1 withdrawal in vitro and in vivo, and performed the first genome-wide CRISPR screens in EVI1-dependent AML. By integrating conserved transcriptional targets with genetic dependency data, we identified and characterized the ETS transcription factor ERG as a direct transcriptional target of EVI1 that is aberrantly expressed and selectively required in both human and murine EVI1-driven AML. EVI1 controls the expression of ERG and occupies a conserved intragenic enhancer region in AML cell lines and samples from patients with primary AML. Suppression of ERG induces terminal differentiation of EVI1-driven AML cells, whereas ectopic expression of ERG abrogates their dependence on EVI1, indicating that the major oncogenic functions of EVI1 are mediated through aberrant transcriptional activation of ERG. Interfering with this regulatory axis may provide entry points for the development of rational targeted therapies.

Multilayered VBC score predicts sgRNAs that efficiently generate loss-of-function alleles.

CRISPR-Cas9 screens have emerged as a transformative approach to systematically probe gene functions. The quality and success of these screens depends on the frequencies of loss-of-function alleles, particularly in negative-selection screens widely applied for probing essential genes. Using optimized screening workflows, we performed essentialome screens in cancer cell lines and embryonic stem cells and achieved dropout efficiencies that could not be explained by common frameshift frequencies. We find that these superior effect sizes are mainly determined by the impact of in-frame mutations on protein function, which can be predicted based on amino acid composition and conservation. We integrate protein features into a 'Bioscore' and fuse it with improved predictors of single-guide RNA activity and indel formation to establish a score that captures all relevant processes in CRISPR-Cas9 mutagenesis. This Vienna Bioactivity CRISPR score (www.vbc-score.org) outperforms previous prediction tools and enables the selection of sgRNAs that effectively produce loss-of-function alleles.

Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation.

Spt5 is a highly conserved RNA polymerase II (Pol II)-associated pausing and elongation factor. However, its impact on global elongation and Pol II processivity in mammalian cells has not been clarified. Here, we show that depleting Spt5 in mouse embryonic fibroblasts (MEFs) does not cause global elongation defects or decreased elongation rates. Instead, in Spt5-depleted cells, a fraction of Pol II molecules are dislodged during elongation, thus decreasing the number of Pol II complexes that complete the transcription cycle. Most strikingly, this decrease is restricted to a narrow window between 15 and 20 kb from the promoter, a distance which coincides with the stage where accelerating Pol II attains maximum elongation speed. Consequently, long genes show a greater dependency on Spt5 for optimal elongation efficiency and overall gene expression than short genes. We propose that an important role of Spt5 in mammalian elongation is to promote the processivity of those Pol II complexes that are transitioning toward maximum elongation speed 15-20 kb from the promoter.

The genomic basis of circadian and circalunar timing adaptations in a midge.

Organisms use endogenous clocks to anticipate regular environmental cycles, such as days and tides. Natural variants resulting in differently timed behaviour or physiology, known as chronotypes in humans, have not been well characterized at the molecular level. We sequenced the genome of Clunio marinus, a marine midge whose reproduction is timed by circadian and circalunar clocks. Midges from different locations show strain-specific genetic timing adaptations. We examined genetic variation in five C. marinus strains from different locations and mapped quantitative trait loci for circalunar and circadian chronotypes. The region most strongly associated with circadian chronotypes generates strain-specific differences in the abundance of calcium/calmodulin-dependent kinase II.1 (CaMKII.1) splice variants. As equivalent variants were shown to alter CaMKII activity in Drosophila melanogaster, and C. marinus (Cma)-CaMKII.1 increases the transcriptional activity of the dimer of the circadian proteins Cma-CLOCK and Cma-CYCLE, we suggest that modulation of alternative splicing is a mechanism for natural adaptation in circadian timing.

Effects of a single aerobic exercise on perfused boundary region and microvascular perfusion: a field study.

The endothelium and the glycocalyx play a pivotal role in regulating microvascular function and perfusion in health and critical illness. It is unknown today, whether aerobic exercise immediately affects dimensions of the endothelial surface layer (ESL) in relation to microvascular perfusion as a physiologic adaption to increased nutritional demands. This monocentric observational study was designed to determine real-time ESL and perfusion measurements of the sublingual microcirculation using sidestream dark field imaging performed in 14 healthy subjects before and after completing a 10 km trial running distance. A novel image acquisition and analysis software automatically analysed the perfused boundary region (PBR), an inverse parameter for red blood cell (RBC) penetration of the ESL, in vessels between 5 and 25 µm diameter. Microvascular perfusion was assessed by calculating RBC filling percentage. There was no significant immediate effect of exercise on PBR and RBC filling percentage. Linear regression analysis revealed a distinct association between change of PBR and change of RBC filling percentage (regression coefficient ß: - 0.026; 95% confidence interval - 0.043 to - 0.009; p = 0.006). A single aerobic exercise did not induce a change of PBR or RBC filling percentage. The endothelium of the microvasculature facilitates efficient perfusion in vessels reacting with an increased endothelial surface layer.

SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting.

Cell type-specific transcriptome analysis is an essential tool for understanding biological processes in which diverse types of cells are involved. Although cell isolation methods such as fluorescence-activated cell sorting (FACS) in combination with transcriptome analysis have widely been used so far, their time-consuming and harsh procedures limit their applications. Here, we report a novel in vivo metabolic RNA sequencing method, SLAM-ITseq, which metabolically labels RNA with 4-thiouracil in a specific cell type in vivo followed by detection through an RNA-seq-based method that specifically distinguishes the thiolated uridine by base conversion. This method has successfully identified the cell type-specific transcriptome in three different tissues: endothelial cells in brain, epithelial cells in intestine and adipocytes in white adipose tissue. As this method does not require isolation of cells or RNA prior to the transcriptomic analysis, SLAM-ITseq provides an easy yet accurate snapshot of the transcriptional state in vivo.

Transcriptional plasticity promotes primary and acquired resistance to BET inhibition.

Following the discovery of BRD4 as a non-oncogene addiction target in acute myeloid leukaemia (AML), bromodomain and extra terminal protein (BET) inhibitors are being explored as a promising therapeutic avenue in numerous cancers. While clinical trials have reported single-agent activity in advanced haematological malignancies, mechanisms determining the response to BET inhibition remain poorly understood. To identify factors involved in primary and acquired BET resistance in leukaemia, here we perform a chromatin-focused RNAi screen in a sensitive MLL-AF9;Nras(G12D)-driven AML mouse model, and investigate dynamic transcriptional profiles in sensitive and resistant mouse and human leukaemias. Our screen shows that suppression of the PRC2 complex, contrary to effects in other contexts, promotes BET inhibitor resistance in AML. PRC2 suppression does not directly affect the regulation of Brd4-dependent transcripts, but facilitates the remodelling of regulatory pathways that restore the transcription of key targets such as Myc. Similarly, while BET inhibition triggers acute MYC repression in human leukaemias regardless of their sensitivity, resistant leukaemias are uniformly characterized by their ability to rapidly restore MYC transcription. This process involves the activation and recruitment of WNT signalling components, which compensate for the loss of BRD4 and drive resistance in various cancer models. Dynamic chromatin immunoprecipitation sequencing and self-transcribing active regulatory region sequencing of enhancer profiles reveal that BET-resistant states are characterized by remodelled regulatory landscapes, involving the activation of a focal MYC enhancer that recruits WNT machinery in response to BET inhibition. Together, our results identify and validate WNT signalling as a driver and candidate biomarker of primary and acquired BET resistance in leukaemia, and implicate the rewiring of transcriptional programs as an important mechanism promoting resistance to BET inhibitors and, potentially, other chromatin-targeted therapies.

Thiol-linked alkylation of RNA to assess expression dynamics.

Gene expression profiling by high-throughput sequencing reveals qualitative and quantitative changes in RNA species at steady state but obscures the intracellular dynamics of RNA transcription, processing and decay. We developed thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM seq), an orthogonal-chemistry-based RNA sequencing technology that detects 4-thiouridine (s4U) incorporation in RNA species at single-nucleotide resolution. In combination with well-established metabolic RNA labeling protocols and coupled to standard, low-input, high-throughput RNA sequencing methods, SLAM seq enabled rapid access to RNA-polymerase-II-dependent gene expression dynamics in the context of total RNA. We validated the method in mouse embryonic stem cells by showing that the RNA-polymerase-II-dependent transcriptional output scaled with Oct4/Sox2/Nanog-defined enhancer activity, and we provide quantitative and mechanistic evidence for transcript-specific RNA turnover mediated by post-transcriptional gene regulatory pathways initiated by microRNAs and N6-methyladenosine. SLAM seq facilitates the dissection of fundamental mechanisms that control gene expression in an accessible, cost-effective and scalable manner.

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets.

BACKGROUND: Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are emerging as powerful tools to study dynamic cellular processes. The recovery, quantification and interpretation of such events in high-throughput sequencing datasets demands specialized bioinformatics approaches. RESULTS: Here, we present Digital Unmasking of Nucleotide conversions in K-mers (DUNK), a data analysis pipeline enabling the quantification of nucleotide conversions in high-throughput sequencing datasets. We demonstrate using experimentally generated and simulated datasets that DUNK allows constant mapping rates irrespective of nucleotide-conversion rates, promotes the recovery of multimapping reads and employs Single Nucleotide Polymorphism (SNP) masking to uncouple true SNPs from nucleotide conversions to facilitate a robust and sensitive quantification of nucleotide-conversions. As a first application, we implement this strategy as SLAM-DUNK for the analysis of SLAMseq profiles, in which 4-thiouridine-labeled transcripts are detected based on T > C conversions. SLAM-DUNK provides both raw counts of nucleotide-conversion containing reads as well as a base-content and read coverage normalized approach for estimating the fractions of labeled transcripts as readout. CONCLUSION: Beyond providing a readily accessible tool for analyzing SLAMseq and related time-resolved RNA sequencing methods (TimeLapse-seq, TUC-seq), DUNK establishes a broadly applicable strategy for quantifying nucleotide conversions.

Transition metal cations on the move: simultaneous operando X-ray absorption spectroscopy and X-ray diffraction investigations during Li uptake and release of a NiFe2O4/CNT composite.

We report on results of a comprehensive investigation on reaction mechanisms occurring during Li uptake and release of the composite NiFe2O4/CNT. Operando X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS) data collected simultaneously using one in situ cell allowed thorough elucidation of structural and electronic alterations happening during Li uptake. From the beginning of Li uptake, the Bragg intensity of the spinel reflections decreases which can be explained by reduction of Fe3+ ions and simultaneous movement of the Fe2+ cations from tetrahedral 8a to empty octahedral 16c sites. The reduction of Fe3+ is clearly evidenced by XAS. The occupation of tetrahedral sites by Li+ can be excluded based on results of density functional theory calculations. Increasing the Li content leads to formation of a new crystalline phase resembling a monoxide with a NaCl-like structure. The appearance of the new phase is accompanied by a steady decrease of the sizes of coherently scattering domains of the spinel and a growth of the domains of the monoxide phase. After uptake of about 2.5 Li per NiFe2O4, all Fe3+ cations are reduced to Fe2+ and the tetrahedral 8a sites are empty (XAS spectra). Careful Rietveld refinements of X-ray powder patterns demonstrate that the tetrahedral 8a site is successively depleted with increasing Li content. Interestingly, the occupancy of the octahedral 16d site is also slightly reduced. Increasing the Li content beyond 2.5 Li/NiFe2O4 leads to successive reduction of the cations to very small metal particles embedded in a Li2O matrix (as evidenced by 7Li MAS NMR investigations). During Li release metallic Ni and Fe are reoxidized to Ni2+ resp. Fe3+. The cycling stability of NiFe2O4/CNT is significantly improved compared to pure NiFe2O4 or a mechanical mixture of NiFe2O4 and CNTs.

Structural origins of the cohesive energy in metal-terpyridine oligomer thin-films.

FeII-terpyridine based oligomers have attracted considerable interest as key constituents for the realization of highly robust, ultra-thin ordered layers of metal center oligomers (MCOs) for organic electronics applications. By using molecular simulations and nanotribology investigations, we report on the origins of the surprisingly high mechanical and thermal stability in this type of MCO layers, which finds its expression in nanowear resistance values of up to 1.5 µN for the MCO films, as well as in a thermal stability of two-terminal MCO junctions to temperatures up to ∼100 °C under electrical load. A theoretical analysis of the fundamental cohesive forces among the constituents within the context of an electrostatic model reveal that the cohesive energy is essentially based on Coulomb interactions among the ionic constituents of the oligomers, leading to an estimated cohesive energy per molar mass of 0.0132 eV mol g-1 for MCO layers that advantageously compare to the 0.0061 eV mol g-1 reported for pentacene crystals.

The Fibrin-Derived Peptide Bß15-42 (FX06) Ameliorates Vascular Leakage and Improves Survival and Neurocognitive Recovery: Implications From Two Animal Models of Cardiopulmonary Resuscitation.

OBJECTIVES: The fibrin-derived peptide Bß15-42 (FX06) has been proven to attenuate ischemia/reperfusion injury. We tested the hypothesis that Bß15-42 improves survival rate and neurocognitive recovery after cardiopulmonary resuscitation. DESIGN: Pig and mouse model of cardiopulmonary resuscitation. SETTING: Two university hospitals. SUBJECTS: Pigs and mice. INTERVENTIONS: Pigs (n = 16) were subjected to 8-minute cardiac arrest. Successful resuscitated pigs (n = 12) were randomized either to 3 mg/kg Bß15-42 followed by a continuous infusion of 1 mg/kg/hr for 5 hours (pFX06; n = 6) or the control group (pCONTROL; n = 6). Cardiac damage, function, and hemodynamics were recorded up to 8 hours. Mice (n = 52) were subjected to 4-minute cardiac arrest followed by cardiopulmonary resuscitation, and randomized either to two boli of 2.4 mg/kg Bß15-42 (mFX06; n = 26) or the control group (mCONTROL; n = 26). Fourteen-day survival rate, neurocognitive function, and endothelial integrity (additional experiment with n = 26 mice) were evaluated. MEASUREMENTS AND MAIN RESULTS: Bß15-42 reduced cumulative fluid intake (3,500 [2,600-4,200] vs 6,800 [5,700-7,400] mL; p = 0.004) within 8 hours in pigs. In mice, Bß15-42 improved 14-day survival rate (mFX06 vs mCONTROL; 11/26 vs 6/26; p < 0.05) and fastened neurocognitive recovery in the Water-Maze test (15/26 vs 9/26 mice with competence to perform test; p < 0.05). Bß15-42-treated mice showed a significant higher length of intact pulmonary endothelium and reduced pulmonary leukocyte infiltration. CONCLUSIONS: This study confirms the new concept of an important role of fibrin derivatives in global ischemia/reperfusion injury, which can be attenuated by the fibrin-derived peptide Bß15-42.

A Controlled Route to a Luminescent 3 d10 -5 d10 Sulfido Cluster Containing Unique AuCu2 (µ3 -S) Motifs.

The first examples of gold(I) trimethylsilylchalcogenolate complexes were synthesized and their reactivity showcased in the preparation of a novel gold-copper-sulfur cluster [Au4 Cu4 S4 (dppm)2 ] (dppm=bis(diphenylphosphino)methane). The unprecedented structural chemistry of this compound gives rise to interesting optoelectronic properties, including long-lived orange luminescence in the solid state. Through time-dependent density functional theory calculations, this emission is shown to originate from ligand-to-metal charge transfer facilitated by Au⋅⋅⋅Cu metallophilic bonding.

Multiparticle moves in acceptance rate optimized Monte Carlo.

Molecular Dynamics (MD) and Monte Carlo (MC) based simulation methods are widely used to investigate molecular and nanoscale structures and processes. While the investigation of systems in MD simulations is limited by very small time steps, MC methods are often stifled by low acceptance rates for moves that significantly perturb the system. In many Metropolis MC methods with hard potentials, the acceptance rate drops exponentially with the number of uncorrelated, simultaneously proposed moves. In this work, we discuss a multiparticle Acceptance Rate Optimized Monte Carlo approach (AROMoCa) to construct collective moves with near unit acceptance probability, while preserving detailed balance even for large step sizes. After an illustration of the protocol, we demonstrate that AROMoCa significantly accelerates MC simulations in four model systems in comparison to standard MC methods. AROMoCa can be applied to all MC simulations where a gradient of the potential is available and can help to significantly speed up molecular simulations.

Loading of ionic compounds into metal-organic frameworks: a joint theoretical and experimental study for the case of La³âº.

Crystalline, highly orientated surface-anchored MOF thin films, grown on Au substrates, were prepared using liquid-phase epitaxy (LPE). The successful loading of La(3+) ions into the Cu3(BTC)2 (HKUST-1) SURMOFs (surface-mounted metal-organic frameworks) was monitored using X-ray diffraction (XRD). Theoretical calculations using classical force-field based Monte Carlo simulations yield a structure with two La(3+) ions within the large Cu3(BTC)2 pores, in full agreement with experimental results on the composition of these films and the relative intensities of the XRD peaks. Implications of these findings for using MOF thin films for electronic applications are briefly discussed.

Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework.

Nucleotide conversion RNA sequencing techniques interrogate chemical RNA modifications in cellular transcripts, resulting in mismatch-containing reads. Biases in mapping the resulting reads to reference genomes remain poorly understood. We present splice_sim, a splice-aware RNA-seq simulation and evaluation pipeline that introduces user-defined nucleotide conversions at set frequencies, creates mixture models of converted and unconverted reads, and calculates mapping accuracies per genomic annotation. By simulating nucleotide conversion RNA-seq datasets under realistic experimental conditions, including metabolic RNA labeling and RNA bisulfite sequencing, we measure mapping accuracies of state-of-the-art spliced-read mappers for mouse and human transcripts and derive strategies to prevent biases in the data interpretation.

Modeling disordered morphologies in organic semiconductors.

Organic thin film devices are investigated for many diverse applications, including light emitting diodes, organic photovoltaic and organic field effect transistors. Modeling of their properties on the basis of their detailed molecular structure requires generation of representative morphologies, many of which are amorphous. Because time-scales for the formation of the molecular structure are slow, we have developed a linear-scaling single molecule deposition protocol which generates morphologies by simulation of vapor deposition of molecular films. We have applied this protocol to systems comprising argon, buckminsterfullerene, N,N-Di(naphthalene-1-yl)-N,N'-diphenyl-benzidine, mer-tris(8-hydroxy-quinoline)aluminum(III), and phenyl-C61-butyric acid methyl ester, with and without postdeposition relaxation of the individually deposited molecules. The proposed single molecule deposition protocol leads to formation of highly ordered morphologies in argon and buckminsterfullerene systems when postdeposition relaxation is used to locally anneal the configuration in the vicinity of the newly deposited molecule. The other systems formed disordered amorphous morphologies and the postdeposition local relaxation step has only a small effect on the characteristics of the disordered morphology in comparison to the materials forming crystals.

Release of Hyaluronan in Aneurysmal Subarachnoid Hemorrhage and Cerebral Vasospasm: A Pilot Study Indicating a Shedding of the Endothelial Glycocalyx.

BACKGROUND: This pilot study investigated plasma concentrations of hyaluronan, heparan sulfate, and syndecan-1 as possible biomarkers for glycocalyx integrity after aneurysmal subarachnoid hemorrhage (aSAH). METHODS: Daily blood samples for biomarker assay were obtained in aSAH patients on the intensive care unit stay and compared with samples from a historic cohort of 40 healthy controls. In post hoc subgroup analyses in patients with and without cerebral vasospasm, we explored the influence of aSAH-related cerebral vasospasm on biomarker levels. RESULTS: A total of 18 aSAH patients and 40 historic controls were included in the study. Median (interquartile range) plasma levels of hyaluronan were higher in aSAH patients compared with controls (131 [84 to 179] vs. 92 [82 to 98] ng/mL, respectively; P=0.009), whereas heparan sulfate (mean±SD: 754±428 vs. 1329±316 ng/mL; P<0.001) and syndecan-1 (median: 23 [17 to 36] vs. 30 [23 to 52] ng/mL; P=0.02) levels were lower. Patients who developed vasospasm had significantly higher median hyaluronan concentrations at day 7 (206 [165 to 288] vs. 133 [108 to 164] ng/mL, respectively; P=0.009) and at day of first vasospasm detection (203 [155 to 231] vs. 133 [108 to 164] ng/mL, respectively; P=0.01) compared with those without vasospasm. Heparan sulfate and syndecan-1 concentrations were similar in patients with and without vasospasm. CONCLUSIONS: The increased plasma concentrations of hyaluronan after aSAH suggest selective shedding of this component of the glycocalyx. Increased levels of hyaluronan in patients with cerebral vasospasm, underlines a potential role for hyaluronan in vasospasm processes.

Controlling doping efficiency in organic semiconductors by tuning short-range overscreening.

Conductivity doping has emerged as an indispensable method to overcome the inherently low conductivity of amorphous organic semiconductors, which presents a great challenge in organic electronics applications. While tuning ionization potential and electron affinity of dopant and matrix is a common approach to control the doping efficiency, many other effects also play an important role. Here, we show that the quadrupole moment of the dopant anion in conjunction with the mutual near-field host-dopant orientation have a crucial impact on the conductivity. In particular, a large positive quadrupole moment of a dopant leads to an overscreening in host-dopant integer charge transfer complexes. Exploitation of this effect may enhance the conductivity by several orders of magnitude. This finding paves the way to a computer-aided systematic and efficient design of highly conducting amorphous small molecule doped organic semiconductors.