Malhotra, F. | bioRxiv Science

bioRxiv2026

Visualizing the Epigenetic Landscape of Aging and Cellular Reprogramming: Optimized ATAC-see for Cells and Tissues

Spatial chromatin organization dictates cellular function and resilience, yet scalable imaging methods to quantify chromatin states in situ across aging and interventions are lacking. While ATAC-see can visualize accessible chromatin, its broader application is hindered by protocol variability, low throughput, and incompatibility with complex tissues. Here, we systematically optimize the ATAC-see workflow for robust, high-throughput quantitative imaging in fixed, adherent mammalian cells and fresh frozen tissues. We validate the platforms sensitivity to pharmacologic remodeling and apply it to replicative, chronological, and pathological aging in primary human fibroblasts, revealing progressive age-associated chromatin opening and heterochromatin remodeling. Furthermore, we demonstrate that our optimized ATAC-see captures rapid, reversible chromatin reorganization during OSK(M)-driven partial reprogramming of aged fibroblasts. Finally, we extend a cost-effective and accessible protocol to murine tissue sections, quantifying in situ age-dependent remodeling. This standardized framework establishes chromatin accessibility as a highly scalable, sequencing-compatible imaging biomarker for evaluating aging and rejuvenation. Summary StatementATAC-see was optimized for scalable, quantitative imaging of chromatin remodeling during aging and cellular reprogramming, and extended to characterize age-associated epigenetic changes across organs.

cell biology↗

bioRxiv2025

The development of FEDUPP: Feeding Experimentation Device Users Processing Package to Assess Learning and Cognitive Flexibility

Cognitive flexibility, the ability to adapt behavior in response to changing contingencies, is a key component of adaptive decision-making and is impaired in multiple neuropsychiatric disorders. Traditional rodent assays of cognitive flexibility are conducted in experimenter-controlled sessions in restrictive environments, limiting ecological validity and temporal resolution. Here, we developed a fully automated, home-cage paradigm using the Feeding Experimentation Device 3 (FED3) and a companion open-source analysis pipeline, the Feeding Experimentation Device Users Processing Package (FEDUPP), to assess learning and cognitive flexibility with minimal experimenter intervention. The paradigm combines a single-day fixed-ratio 1 (FR1) task with a multi-day, reversal learning task in which active port assignment switches every 25 pellets collected. FEDUPP implements multi-scale learning metrics, including overall accuracy, an 80% accuracy milestone, and a machine learning-based classification of meal accuracy to capture motivated, goal-directed feeding. In wild-type mice, the paradigm detected rapid FR1 acquisition and progressive within-block adaptation during reversal. Application to mice with dorsal hippocampal knockdown of the scaffolding protein CASK revealed faster FR1 acquisition and higher accuracy than controls but a delayed onset of the first accurate meal after reversal, suggesting a selective deficit in updating goal-directed feeding behavior. These findings demonstrate that FEDUPP enables high-resolution, continuous assessment of learning and cognitive flexibility in ethologically relevant settings, and that meal-based accuracy provides a sensitive metric for detecting subtle flexibility impairments not captured by traditional measures.

animal behavior and cognition↗