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Overlooked DNA structures help organize the genome
Overlooked DNA structures help organize the genome Lisa Lock Scientific Editor Robert Egan Associate Editor Northwestern Medicine scientists have discovered that little-studied DNA structures play a central role in organizing the human genome and controlling gene activity, according to a new study published in the Proceedings of the National Academy of Sciences. The study revealed that G-quadruplexes (G4s)—four-stranded DNA structures—directly interact with a key genome-organizing protein...
Learning quality scores for chromatin accessibility bigWig tracks using Machine Learning
High-throughput chromatin accessibility assays such as bulk and single-cell ATAC-seq have generated large collections of processed signal tracks in bigWig format, which are widely used for visualisation, data integration, and Machine Learning (ML)-based analyses. Despite their central role, systematic quality control (QC) frameworks operating directly at the level of bigWig signal tracks remain underdeveloped. This gap limits the ability to assess data reliability and hampers robust...
Nuclear confinement from matrix stiffness drives epigenomic reprogramming of gingival fibroblasts
Periodontal disease is characterized by progressive degradation of the gingival extracellular matrix and loss of the physical confinement it imposes on resident stromal cells. In human periodontal tissue, ECM collagen integrity is inversely correlated with facultative nuclear histone acetylation in stromal cells. We hypothesized that matrix stiffness directly coordinates an epigenomic shift in stromal cells.