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ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens.
Nucleic Acids Res
January 2025
School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
Genome-wide identification of binding profiles for DNA-binding proteins from the limited number of intracellular pathogens in infection studies is crucial for understanding virulence and cellular processes but remains challenging, as the current ChIP-exo is designed for high-input bacterial cells (>1010). Here, we developed an optimized ChIP-mini method, a low-input ChIP-exo utilizing a 5,000-fold reduced number of initial bacterial cells and an analysis pipeline, to identify genome-wide binding dynamics of DNA-binding proteins in host-infected pathogens. Applying ChIP-mini to intracellular Salmonella Typhimurium, we identified 642 and 1,837 binding sites of H-NS and RpoD, respectively, elucidating changes in their binding position and binding intensity during infection.
View Article and Find Full Text PDFHybrid Plasmonic Symmetry-Protected Bound state in the Continuum Entering the Zeptomolar Biodetection Range.
Small
January 2025
CNR NANOTEC Institute of Nanotechnology, Via Monteroni, 73100, Lecce, Italy.
Photonics bound states in the continuum (BICs) are peculiar localized states in the continuum of free-space waves, unaffected by far-field radiation loss. Although plasmonic nano-antennas squeeze the optical field to nanoscale volumes, engineering the emergence of quasi-BICs with plasmonic hotspots remains challenging. Here, the origin of symmetry-protected (SP) quasi-BICs in a 2D system of silver-filled dimers, quasi-embedded in a high-index dielectric waveguide, is investigated through the strong coupling between photonic and plasmonic modes.
View Article and Find Full Text PDFIdentification of a novel TOP2B::AFF2 fusion gene in B-cell acute lymphoblastic leukemia.
Sci Rep
January 2025
Department of Hematology and Oncology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatric Metabolism and Inflammatory Diseases, Children's Hospital of Chongqing Medical University, No 136 Zhongshan 2 road, YuZhong district, Chongqing, 400014, China.
Genetic alterations play a pivotal role in leukemic clonal transformation, significantly influencing disease pathogenesis and clinical outcomes. Here, we report a novel fusion gene and investigate its pathogenic role in acute lymphoblastic leukemia (ALL). We engineer a transposon transfection system expressing the TOP2B::AFF2 transcript and introduce it into Ba/F3 cells.
View Article and Find Full Text PDFCytosine Methylation Changes the Preferred Cis-Regulatory Configuration of Arabidopsis WUSCHEL-Related Homeobox 14.
Int J Mol Sci
January 2025
College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
The Arabidopsis transcription factor WUSCHEL-related homeobox 14 (AtWOX14) plays versatile roles in plant growth and development. However, its biochemical specificity of DNA binding, its genome-wide regulatory targets, and how these are affected by DNA methylation remain uncharacterized. To clarify the biochemistry underlying the regulatory function of AtWOX14, using the recently developed 5mC-incorporation strategy, this study performed SELEX and DAP-seq for AtWOX14 both in the presence and absence of cytosine methylation, systematically curated 65 motif models and identified 51,039 genomic binding sites for AtWOX14, and examined how 5mC affects DNA binding of AtWOX14 through bioinformatic analyses.
View Article and Find Full Text PDFRelative Distribution of DnaA and DNA in Cells as a Factor of Their Phenotypic Variability.
Int J Mol Sci
January 2025
Department of Life Sciences, Ben Gurion University of the Negev, Beer-Sheva 8410501, Israel.
Phenotypic variability in isogenic bacterial populations is a remarkable feature that helps them cope with external stresses, yet it is incompletely understood. This variability can stem from gene expression noise and/or the unequal partitioning of low-copy-number freely diffusing proteins during cell division. Some high-copy-number components are transiently associated with almost immobile large assemblies (hyperstructures) and may be unequally distributed, contributing to bacterial phenotypic variability.
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