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Increasing the flanking DNA from 40 to 80 base pairs (bp) causes ~100-fold faster nucleosome sliding by INO80. A prevalent hypothesis posits that the Arp8 module within INO80 enables a ruler-like activity. Using cryogenic electron microscopy, we show that on nucleosomes with 40 bp of flanking DNA, the Arp8 module rotates 180° away from the DNA. Deleting the Arp8 module enables rapid sliding irrespective of flanking DNA length. Thus, rather than enabling a ruler-like activity, the Arp8 module acts as a brake on INO80 remodeling when flanking DNA is short. This autoinhibition-based mechanism has broad implications for understanding how primitive nucleosome mobilization enzymes may have evolved into sophisticated remodelers.
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http://dx.doi.org/10.1126/science.adr3831 | DOI Listing |
Microbiol Spectr
September 2025
Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto, Japan.
Kaposi's sarcoma-associated herpesvirus (KSHV) belongs to the Gammaherpesvirinae subfamily. During the lytic phase of herpesviruses, viral capsids form in the host cell nucleus, and the replicated viral genome is packaged into these capsids. The herpesviral genome is replicated as a precursor head-to-tail concatemer consisting of tandemly repeated genomic units, each flanked by terminal repeats (TRs).
View Article and Find Full Text PDFMol Plant Pathol
September 2025
Área de Genética, Facultad de Ciencias, Campus Teatinos s/n, Universidad de Málaga, Málaga, Spain.
The type III secretion system in Pseudomonas syringae complex pathogens delivers type III effectors (T3Es) into plant cells to manipulate host processes, enhance survival, and promote disease. While substantial research has focused on herbaceous pathogens, T3Es in strains infecting woody hosts are less understood. This study investigates the HopBL family of effectors in Pseudomonas savastanoi, a pathogen of woody plants.
View Article and Find Full Text PDFNature
September 2025
Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Transcription factors (TFs) regulate gene expression by interacting with DNA in a sequence-specific manner. High-throughput in vitro technologies, such as protein-binding microarrays and HT-SELEX (high-throughput systematic evolution of ligands by exponential enrichment), have revealed the DNA-binding specificities of hundreds of TFs. However, they have limited ability to reliably identify lower-affinity DNA binding sites, which are increasingly recognized as important for precise spatiotemporal control of gene expression.
View Article and Find Full Text PDFNature
September 2025
Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
Prokaryotes create adaptive immune memories by acquiring foreign DNA snippets, known as spacers, into the CRISPR array. In type II CRISPR-Cas systems, the RNA-guided effector Cas9 also assists the acquisition machinery by selecting spacers from protospacer adjacent motif (PAM)-flanked DNA. Here, we uncover the first biological role for Cas9 that is independent of its dual RNA partners.
View Article and Find Full Text PDFRes Sq
August 2025
Graduate Program in Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, TX, USA.
Bacterial gyrase, unique among type II topoisomerases, introduces negative supercoils into DNA. Mechanistic details of gyrase still must be elucidated because of the complexity of the process and the difficulty in visualizing it. Specifically, the interplay among base sequence, local DNA deformability, and global DNA topology for gyrase site selection is unclear.
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