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Among the pervasive transcripts from eukaryotic genomes, a novel subset, referred to as architectural RNAs (arcRNAs), has an essential role in assembling membraneless organelles (MLOs). These arcRNAs sequester specific RNA-binding proteins (RBPs) and promote phase separation through multivalent interactions. NEAT1_2, an archetypal arcRNA, serves as a blueprint for paraspeckle architecture, characterized by a shell-and-core micelle-like configuration and immiscibility with other MLOs, relying on the cooperative contributions of distinct modular RNA domains. arcRNAs regulate gene expression through three of MLO action modes (crucible, sponge, and hub), guided by the functional blueprints embedded in arcRNA sequences. Advanced high-throughput analyses have identified thousands of arcRNA candidates, underscoring their potential in organizing transient intracellular compartments and driving dynamic cellular processes.
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http://dx.doi.org/10.1016/j.tig.2025.05.007 | DOI Listing |
Int J Biol Macromol
September 2025
Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau. Electronic address:
Protein-nucleic acid interactions (PNI) play crucial roles in various life processes, including gene expression regulation, DNA replication, repair, recombination, and RNA processing and translation. However, accurately predicting these interactions remains challenging due to their complexity. This paper proposes a deep learning-based multi-task learning framework for predicting protein-nucleic acid interactions.
View Article and Find Full Text PDFJ Biol Chem
September 2025
Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802; Center for Structural Biology, Penn State University, University Park, PA 16802; Center for RNA Molecular Biology, Penn State University, University Park, PA 16802. Electronic address:
Despite the overall conservation of ribosomes across all domains of life, differences in their 3D architecture, rRNA sequences, ribosomal protein composition, and translation factor requirements reflect lineage-specific adaptations to environmental niches. In the domain Archaea, structural studies have primarily focused on non-methanogenic thermophiles and halophiles, leaving it unclear whether these represent the broader archaeal domain. Here, we report the cryo-electron microscopy (cryo-EM) structure of the ribosome from Methanosarcina acetivorans, a previously unreported high-resolution structure from a model mesophilic methanogenic archaeon.
View Article and Find Full Text PDFWater Res
September 2025
Department of Civil and Architecture, School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan. Electronic address:
Ammonia (NH), a naturally occurring disinfectant in wastewater, plays an important role in inactivating pathogens, including viruses. Despite its importance in non-sewered sanitation systems, the inactivation rate constant attributed solely to ammonia ( [Formula: see text] ) remains unclear, owing to the diverse range of disinfection conditions in existing studies. Determining [Formula: see text] is critical for quantifying the contribution of ammonia to viral inactivation and distinguishing it from other environmental factors.
View Article and Find Full Text PDFJ Cell Mol Med
September 2025
Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan City, Hubei Province, China.
Glioblastoma (GBM) exhibits remarkable intra-tumoral heterogeneity, which contributes to therapeutic resistance and poor clinical outcomes. In this study, we employed integrative single-cell RNA sequencing analysis across two complementary public datasets encompassing diverse cellular populations from GBM centre and periphery regions to elucidate potential spatial molecular programmes driving tumour progression. Our analyses revealed substantial transcriptomic divergence between anatomically distinct tumour regions, with NUCB2 emerging as significantly upregulated in centre-residing neural progenitor cell-like (NPC-like) tumour cells.
View Article and Find Full Text PDFNpj Viruses
September 2025
Faculty of Veterinary Medicine, Institute of Virology, Freie Universität Berlin, Berlin, Germany.
Porcine reproductive and respiratory syndrome virus (PRRSV), an Arteriviridae family enveloped RNA virus, is a major swine pathogen. Using yeast transformation-associated recombination (TAR) cloning, we efficiently generated infectious PRRSV and GFP-expressing clones, identifying transcription-regulating sequences as essential for stable foreign gene expression. Screening SARS-CoV-2 antivirals showed potent inhibition by the multitarget drug ribavirin, the polymerase inhibitors remdesivir and its metabolite GS-441524.
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