Publisher Correction: Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition
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Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition
Metazoan gene transcription by RNA polymerase II (Pol II) is regulated in the promoter-proximal region. Pol II can undergo termination in the promoter-proximal region but whether this can contribute to transcription regulation in cells remains unclear. Here we extend our previous multiomics analysis to quantify changes in transcription kinetics during a human cell type transition event. We observe that upregulation of transcription involves an increase in initiation frequency and, at a set of genes, a decrease in promoter-proximal termination. In turn, downregulation of transcription involves a decrease in initiation frequency and an increase in promoter-proximal termination. Thus, promoter-proximal termination of Pol II contributes to the regulation of human gene transcription.
Chalcogen and halogen surface termination coverage in MXenes—structure, stability, and properties
MXenes are a diverse family of two-dimensional (2D) transition metal carbides, nitrides, and carbonitrides. They can be synthesized through both top-down approaches, such as selective etching of A-layers from MAX phases using acids or molten salts, and bottom-up approaches, such as direct synthesis using chemical vapor deposition. However, the degree of the surface termination coverage depends on the synthesis route and is one key parameter for controlling its properties. This study focuses on halogen- and chalcogen-terminated MXenes, particularly M2CTx where M = Ti, Zr, V, Nb, Ta, and T = S, Se, Te, Cl, Br, I, and with surface termination coverage ranging from 100% (ideal, x = 2) to 50% (x = 1). The incorporation of oxygen on vacant termination sites was also evaluated. Using density functional theory (DFT) calculations, we investigated the structural, electronic, and mechanical properties of these MXenes. Our findings reveal that non-ideal termination coverage (x < 2) is more favorable for MXenes terminated with a larger size of T, such as Ti2CBrx, Nb2CClx, and Ta2CClx, and leads to mixed termination sites and lower binding energies. A reduced binding energy may facilitate delamination into single sheets, however, too low termination coverage may also cause structural collapse. Electronic properties showed an increased number of states at the Fermi level under non-ideal coverage, potentially enhancing the conductivity. Mechanically, we find the moduli of MXenes to be comparable to other 2D materials, such as transition metal chalcogenides and hexagonal boron nitride, indicating their suitability for applications requiring flexibility and durability. This study underscores the potential of tailoring MXene properties through precise control of termination coverage and composition, paving the way for enhanced application-specific performance.
First-principles and machine-learning approaches for interpreting and predicting the properties of MXenes
MXenes are a versatile family of 2D inorganic materials with applications in energy storage, shielding, sensing, and catalysis. This review highlights computational studies using density functional theory and machine-learning approaches to explore their structure (stacking, functionalization, doping), properties (electronic, mechanical, magnetic), and application potential. Key advances and challenges are critically examined, offering insights into applying computational research to transition these materials from the lab to practical use.
Mechanism of expression regulation of head-to-head overlapping protein-coding genes INO80E and HIRIP3
Although the existence of overlapping protein-coding genes in eukaryotic genomes is known for decades, their role in regulating expression remains far from fully understood. Here, the mechanism regulating the expression of head-to-head overlapping genes, a pair of INO80E and HIRIP3 genes is presented. Based on a series of experiments, we show that the expression of these genes is strongly dependent on sense/antisense interactions. The overlapping transcripts form an RNA:RNA duplex that has a stabilizing effect on the mRNAs involved, and this stabilization may be mediated by the ELAVL1 protein. We also show that the transcription factor RARG is important for the transcription of both genes studied. In addition, we demonstrate that the overlapping isoform of INO80E forms an R-loop that may positively regulate HIRIP3 isoforms. We propose that both structures, dsRNA and R-loops, help to keep the DNA loop open to allow the transcription of the remaining variants of both genes. However, experiments suggest that RNA:RNA duplex formation plays a major role, while R-loops play only a complementary one. The absence of this dsRNA structure leads to the loss of a stable DNA opening and consequently to transcriptional interference.
Structural basis for the activation of plant bunyavirus replication machinery and its dual-targeted inhibition by ribavirin
Despite the discovery of plant viruses as a new class of pathogens over a century ago, the structure of plant virus replication machinery and antiviral pesticide remains lacking. Here we report five cryogenic electron microscopy structures of a ~330-kDa RNA-dependent RNA polymerase (RdRp) from a devastating plant bunyavirus, tomato spotted wilt orthotospovirus (TSWV), including the apo, viral-RNA-bound, base analogue ribavirin-bound and ribavirin-triphosphate-bound states. They reveal that a flexible loop of RdRp’s motif F functions as ‘sensor’ to perceive viral RNA and further acts as an ‘adaptor’ to promote the formation of a complete catalytic centre. A ten-base RNA ‘hook’ structure is sufficient to trigger major conformational changes and activate RdRp. Chemical screening showed that ribavirin is effective against TSWV, and structural data revealed that ribavirin disrupts both hook-binding and catalytic core formation, locking polymerase in its inactive state. This work provides structural insights into the mechanisms of plant bunyavirus RdRp activation and its dual-targeted site inhibition, facilitating the development of pesticides against plant viruses.
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