Single-molecule force spectroscopy is a powerful tool to analyze the architecture and interaction of large macromolecular assemblies that are refractory to high-resolution structural interrogations. Here, we describe an optical tweezers-based platform for extracting the mechanical fingerprints of individual nucleosome arrays bound with chromatin-associated complexes, such as the Polycomb repressive complex 2 (PRC2). This platform comprehensively characterizes the diverse binding modes of PRC2 on chromatin, measures their mechanical strengths, and is broadly applicable to the studies of other epigenetic machineries.
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http://dx.doi.org/10.1007/978-1-0716-2229-2_11 | DOI Listing |
Biochem Cell Biol
January 2025
University of Victoria Faculty of Science, Biochemsitry and Microbiology, Victoria, British Columbia, Canada;
Methyl CpG binding protein 2 (MeCP2) is a chromatin-associated protein that remains enigmatic despite more than 30 years of research, primarily due to the ever-growing list of its molecular functions, and, consequently, its related pathologies. Loss of function MECP2 mutations cause the neurodevelopmental disorder Rett syndrome (RTT); in addition, dysregulation of MeCP2 expression and/or function are involved in numerous other pathologies, but the mechanisms of MeCP2 regulation are unclear. Advancing technologies and burgeoning mechanistic theories assist our understanding of the complexity of MeCP2 but may inadvertently cloud it if not rigorously tested.
View Article and Find Full Text PDFbioRxiv
November 2024
Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology, Baylor College of Medicine, Houston Texas.
Histone proteoforms, often presenting multiple co-occurring post-translational modifications (PTMs), are central to chromatin regulation and gene expression. A proteoform is a specific form of a protein that includes variations arising from genetic changes, alternative RNA splicing, proteolytic processing, and PTMs. Genomic context-dependent histone proteoforms define the histone code, influencing cellular phenotype by dictating interactions with DNA and chromatin-associated proteins.
View Article and Find Full Text PDFNucleic Acids Res
December 2024
Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Many RNAs associate with chromatin, either directly or indirectly. Several technologies for mapping regions where RNAs interact across the genome have been developed to investigate the function of these RNAs. Obtaining information on the proteins involved in these RNA-chromatin interactions is critical for further analysis.
View Article and Find Full Text PDFCell Insight
December 2024
Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, Hubei, China.
Eukaryotic genomes are organized into distinct chromatin compartments, some of which exhibit properties of biomolecular condensates. These condensates primarily form due to chromatin-associated proteins/complexes (CAPs). CAPs play a crucial role in gene expression, functioning as either transcriptional repressors or activators.
View Article and Find Full Text PDFAgeing Res Rev
December 2024
IRCCS Ospedale San Raffaele, Milano, Italy; Università Vita-Salute San Raffaele, Milano, Italy. Electronic address:
Aging is a universal biological process characterized by a progressive, cumulative decline in homeostatic capabilities and physiological functions, which inevitably increases vulnerability to diseases. A number of molecular pathomechanisms and hallmarks of aging have been recognized, yet we miss a thorough understanding of their complex interconnectedness. This review explores the molecular and cellular mechanisms underlying human aging, with a focus on the multiple roles of high mobility group Box 1 protein (HMGB1), the archetypal damage-associated molecular pattern (DAMP) molecule.
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