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The Ku heterodimer plays an essential role in non-homologous end-joining and other cellular processes including transcription, telomere maintenance and apoptosis. While the function of Ku is regulated through its association with other proteins and nucleic acids, the specific composition of these macromolecular complexes and their dynamic response to endogenous and exogenous cellular stimuli are not well understood. Here we use quantitative proteomics to define the composition of Ku multicomponent complexes and demonstrate that they are dramatically altered in response to UV radiation. Subsequent biochemical assays revealed that the presence of DNA ends leads to the substitution of RNA-binding proteins with DNA and chromatin associated factors to create a macromolecular complex poised for DNA repair. We observed that dynamic remodeling of the Ku complex coincided with exit of Ku and other DNA repair proteins from the nucleolus. Microinjection of sheared DNA into live cells as a mimetic for double strand breaks confirmed these findings in vivo.
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http://dx.doi.org/10.1074/mcp.M111.013581 | DOI Listing |
Cell Rep Methods
July 2025
Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China; Key Laboratory of Smart Farming for Agricultural Animals, Ministry of Agriculture and Rural Affairs, Beijing, P.R. China; College of Informatics, Huazhong Agricult
We introduce a cell-free DNA (cfDNA) fragmentation pattern: the fragment dispersity index (FDI), which integrates information on the distribution of cfDNA fragment ends with the variation in fragment coverage, enabling precise characterization of chromatin accessibility in specific regions. The FDI shows a strong correlation with chromatin accessibility and gene expression, and regions with high FDI are enriched in active regulatory elements. Using whole-genome cfDNA data from five datasets, we developed and validated the FDI-oncology model, which demonstrates robust performance in early cancer diagnosis, subtyping, and prognosis.
View Article and Find Full Text PDFVirology
August 2025
Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, 108-8477, Japan; Institute for Aquaculture Biotechnology (IAB), Tokyo University of Marine Science and Technology, Tokyo, 108-8477, Japan. Electronic address:
Atypical cellular gill disease (ACGD) in ayu (Plecoglossus altivelis) caused by P. altivelis poxvirus (PaPV) infection has led to significant economic losses in Japanese aquaculture. The propagation of PaPV has not yet been successfully achieved in cultured cells.
View Article and Find Full Text PDFKinesin-1 is a robust motor that carries intracellular cargos towards the plus ends of microtubules. However, optical trapping studies reported that kinesin-1 is a slippery motor that quickly detaches from the microtubule, and multiple kinesins are incapable of teaming up to generate large collective forces. This may be due to the vertical (z) forces that the motor experiences in a single bead trapping assay, accelerating the detachment of the motor from a microtubule.
View Article and Find Full Text PDFCircular Rep-encoding single-stranded DNA (CRESS-DNA) virus Rep proteins are multidomain enzymes that mediate viral DNA rolling-circle replication. Reps nick viral DNA to expose a 3' end for polymerase extension, provide an NTP-dependent helicase activity for DNA unwinding, and join nicked ends to form circular viral genomes. Here, we present the first structures of a Rep protein from the family, a newly discovered family of human-associated CRESS-DNA viruses that replicates within the oral protozoan .
View Article and Find Full Text PDFTelomeres are DNA-protein structures that protect chromosome ends. The DNA component of telomeres shortens as cells divide, and telomere length (TL) is a key biomarker of aging and disease risk. Most previous studies in humans of TL have analyzed average TL; thus, our knowledge of TL variability across chromosome arms remains limited.
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