•The current model of UsnRNA biogenesis is discussed.•Perspective is provided on how the RNAPII CTD is recognized by Integrator.•CTD kinases and binding proteins influence RNAPII CTD–Integrator ...association.•Integrator has a new role in pause-release of RNAPII at mRNA-encoding genes.•Integrator has modular properties opening the possibility of new roles.
The discovery of the metazoan-specific Integrator (INT) complex represented a breakthrough in our understanding of noncoding U-rich small nuclear RNA (UsnRNA) maturation and has triggered a reevaluation of their biosynthesis mechanism. In the decade since, significant progress has been made in understanding the details of its recruitment, specificity, and assembly. While some discrepancies remain on how it interacts with the C-terminal domain (CTD) of the RNA polymerase II (RNAPII) and the details of its recruitment to UsnRNA genes, preliminary models have emerged. Recent provocative studies now implicate INT in the regulation of protein-coding gene transcription initiation and RNAPII pause-release, thereby broadening the scope of INT functions in gene expression regulation. We discuss the implications of these findings while putting them into the context of what is understood about INT function at UsnRNA genes.
The reaction of hydroxyl radical (HO•) with thymine in DNA generates 5-(uracilyl)-methyl radicals (T•) and the corresponding methylperoxyl radical (TOO•) in the presence of O2, which in turn ...propagates damage by reacting with a vicinal nucleobase. This leads to so-called double or tandem lesions. Because methyl oxidation products of thymine are major products, we investigated the reactivity of TOO• using a photolabile precursor: 5-(phenylthiomethyl)uracil (TSPh). The precursor was prepared and incorporated into a DNA trinucleotide: 5′-d(GpTSPhpA)-3′ (G-TSPh-A). Upon photolysis, the resulting products were characterized by LC-MS/MS. Thereby, we identified four tandem lesions involving GpT, which include either 2,6-diamino-4-hydroxy-5-formamidopyrimidine (fapyG) or 8-oxo-7,8-dihydroguanine (oxoG) in tandem with either 5-formyluracil (fU) or 5-hydroxymethyluracil (hmU). The formation of these tandem lesions is explained by initial addition of TOO• to the C8 of guanine moiety, giving an N7-guanine cross-linked radical. The latter radical undergoes either reduction to an 7,8-saturated endoperoxide or oxidation to an 7,8-unsaturated endoperoxide, which transform into fapyG-fU-A and oxoG-fU-A, respectively. This is supported by the effect of a reducing (dithiothreitol) and oxidizing agent (Fe3+) on product formation. This study expands the repertoire of tandem lesions that can occur at GpT sequences and underlines the importance of redox environment.
The unpaired electron impacts the binding between radicals and ordinary closed-shell molecules in noncovalent complexes. Conversely, the complexation partner can enhance, decrease, or even control ...the reactivity of the interacting radical. Previously, such radical–molecule (and especially radical–water) complexes were studied by controlled assembly of the interacting partners which mostly leads to formation of the thermodynamically most stable species. Here, we show that UV photolysis of the resonance-stabilized carboxymethyl radical isolated in a cryogenic argon matrix at 4 K leads to the intermediary formation of a metastable, noncovalent complex of the ketenyl radical with a water molecule. In this complex, the ketenyl radical binds water at its terminal carbon atom, although a more stable isomer exists in which water interacts with the C–H bond of the radical. Rigorous W1 theory computations confirm that the ketenyl radical is a stronger donor in C–H···O interactions than ketene itself, while it performs comparably well as an acceptor. We propose that complex formation proceeds via an initial excited-state C–O bond breaking reaction in carboxymethyl under release of an OH radical, which is supported by multireference QD-NEVPT2 computations.
Constraint-induced movement therapy (CIMT) is among the most developed training approaches for motor restoration of the upper extremity (UE).
Very Early Constraint-Induced Movement during Stroke ...Rehabilitation (VECTORS) was a single-blind phase II trial of CIMT during acute inpatient rehabilitation comparing traditional UE therapy with dose-matched and high-intensity CIMT protocols. Participants were adaptively randomized on rehabilitation admission, and received 2 weeks of study-related treatments. The primary endpoint was the total Action Research Arm Test (ARAT) score on the more affected side at 90 days after stroke onset. A mixed model analysis was performed.
A total of 52 participants (mean age 63.9 +/- 14 years) were randomized 9.65 +/- 4.5 days after onset. Mean NIHSS was 5.3 +/- 1.8; mean total ARAT score was 22.5 +/- 15.6; 77% had ischemic stroke. Groups were equivalent at baseline on all randomization variables. As expected, all groups improved with time on the total ARAT score. There was a significant time x group interaction (F = 3.1, p < 0.01), such that the high intensity CIT group had significantly less improvement at day 90. No significant differences were found between the dose-matched CIMT and control groups at day 90. MRI of a subsample showed no evidence of activity-dependent lesion enlargement.
Constraint-induced movement therapy (CIMT) was equally as effective but not superior to an equal dose of traditional therapy during inpatient stroke rehabilitation. Higher intensity CIMT resulted in less motor improvement at 90 days, indicating an inverse dose-response relationship. Motor intervention trials should control for dose, and higher doses of motor training cannot be assumed to be more beneficial, particularly early after stroke.
The canonical histone proteins are encoded by replication-dependent genes and must rapidly reach high levels of expression during S phase. In metazoans the genes that encode these proteins produce ...mRNAs that, instead of being polyadenylated, contain a unique 3' end structure. By contrast, the synthesis of the variant, replication-independent histones, which are encoded by polyadenylated mRNAs, persists outside of S phase. Accurate positioning of both histone types in chromatin is essential for proper transcriptional regulation, the demarcation of heterochromatic boundaries and the epigenetic inheritance of gene expression patterns. Recent results suggest that the coordinated synthesis of replication-dependent and variant histone mRNAs is achieved by signals that affect formation of the 3' end of the replication-dependent histone mRNAs.
Graphitic carbon nitride (g-C3N4) has recently emerged as a promising visible-light-responsive polymeric photocatalyst; however, a molecular-level understanding of material properties and its ...application for water purification were underexplored. In this study, we rationally designed nonmetal doped, supramolecule-based g-C3N4 with improved surface area and charge separation. Density functional theory (DFT) simulations indicated that carbon-doped g-C3N4 showed a thermodynamically stable structure, promoted charge separation, and had suitable energy levels of conduction and valence bands for photocatalytic oxidation compared to phosphorus-doped g-C3N4. The optimized carbon-doped, supramolecule-based g-C3N4 showed a reaction rate enhancement of 2.3–10.5-fold for the degradation of phenol and persistent organic micropollutants compared to that of conventional, melamine-based g-C3N4 in a model buffer system under the irradiation of simulated visible sunlight. Carbon-doping but not phosphorus-doping improved reactivity for contaminant degradation in agreement with DFT simulation results. Selective contaminant degradation was observed on g-C3N4, likely due to differences in reactive oxygen species production and/or contaminant-photocatalyst interfacial interactions on different g-C3N4 samples. Moreover, g-C3N4 is a robust photocatalyst for contaminant degradation in raw natural water and (partially) treated water and wastewater. In summary, DFT simulations are a viable tool to predict photocatalyst properties and oxidation performance for contaminant removal, and they guide the rational design, fabrication, and implementation of visible-light-responsive g-C3N4 for efficient, robust, and sustainable water treatment.
One goal of modeling for metal Additive Manufacturing (AM) is to predict the resultant mechanical properties from given manufacturing process parameters and intrinsic material properties, thereby ...reducing uncertainty in the material built. This can dramatically reduce the time and cost for the development of new products using AM. We have realized the seamless linking of models for the manufacturing process, material structure formation, and mechanical response through an integrated multi-physics modeling framework. The sequentially coupled modeling framework relies on the concept that the results from each model used in the framework are contained in space-filling volume elements using a prescribed structure. This framework is implemented to show a prediction of the decrease in fatigue life caused by insufficient fusion resulting from low laser power relative to the hatch spacing. In this demonstration, powder spreading and thermal-fluid flow models are used to predict the thermal history and void formation in a multilayer, multi-track build with different processing conditions. The results of these predictions are passed to a cellular automaton-based prediction of grain structure. Finally, the predicted grain and void structure is passed to a reduced-order micromechanics-based model to predict mechanical properties and fatigue life arising from the different processing conditions used in the process model. The simulation results from this combination of models demonstrate qualitative agreement with experimental observations from literature, showing the appealing potential of an integrated framework.
The transition of RNA polymerase II (Pol II) from initiation to productive elongation is a central, regulated step in metazoan gene expression. At many genes, Pol II pauses stably in early ...elongation, remaining engaged with the 25- to 60-nt-long nascent RNA for many minutes while awaiting signals for release into the gene body. However, 15%–20% of genes display highly unstable promoter Pol II, suggesting that paused polymerase might dissociate from template DNA at these promoters and release a short, non-productive mRNA. Here, we report that paused Pol II can be actively destabilized by the Integrator complex. Specifically, we present evidence that Integrator utilizes its RNA endonuclease activity to cleave nascent RNA and drive termination of paused Pol II. These findings uncover a previously unappreciated mechanism of metazoan gene repression, akin to bacterial transcription attenuation, wherein promoter-proximal Pol II is prevented from entering productive elongation through factor-regulated termination.
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•Integrator inhibits transcription elongation at ∼15% of mRNA genes and enhancers•Integrator targets promoter-proximally paused Pol II for termination•The RNA endonuclease of Integrator subunit 11 is critical for gene repression•Integrator depletion increases productive elongation and histone H3 K4 methylation
Here, Elrod et al. demonstrate that the Integrator complex associates with paused RNA polymerase II at promoters and enhancers to terminate RNA synthesis. This attenuation mechanism potently represses expression of both stress- and growth-responsive genes in Drosophila and mammalian cells.
In this paper, a parallelized 3D cellular automaton computational model is developed to predict grain morphology for solidification of metal during the additive manufacturing process. Solidification ...phenomena are characterized by highly localized events, such as the nucleation and growth of multiple grains. As a result, parallelization requires careful treatment of load balancing between processors as well as interprocess communication in order to maintain a high parallel efficiency. We give a detailed summary of the formulation of the model, as well as a description of the communication strategies implemented to ensure parallel efficiency. Scaling tests on a representative problem with about half a billion cells demonstrate parallel efficiency of more than 80% on 8 processors and around 50% on 64; loss of efficiency is attributable to load imbalance due to near-surface grain nucleation in this test problem. The model is further demonstrated through an additive manufacturing simulation with resulting grain structures showing reasonable agreement with those observed in experiments.
The Cover Feature shows a molecule of oxalyl diisothiocyanate trapped in an argon matrix. After irradiation with UV‐light carbon monoxide is cleaved off, leaving carbonyl diisothiocyanate in a ...rotationally excited state. Subsequent annealing at 30 K leads to a relaxation of the structure into its ground state. Cover art by Cristina Ripoll. More information can be found in the Research Article by J. Pfeiffer, J. P. Wagner, and F. Tambornino.
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