Biology subjects

Kirkland, N. J.

Publications and source records attributed to Kirkland, N. J..

4 recordsLinked to original sources

bioRxiv2026

Targeted ATAC-see (tATAC-see): A Visual Assay for Target-Specific Chromatin Profiling

We present targeted ATAC-see (tATAC-see), a visual genomics assay for site-specific chromatin profiling. By integrating the in situ visualization of ATAC-see with antibody-tethered tagmentation, tATAC-see captures chromatin states at defined protein-occupied domains with the simplicity of standard immunofluorescence. Modulating the spatial interaction radius of Tn5 via salt titration enables extended tagmentation of local chromatin environments near the target. We validated this imaging-based method by capturing the expanded chromatin neighborhoods of active euchromatin (H3K27ac, H3K4me3) alongside the dense structural lamina-associated domains (LADs) of lamin A/C and lamin B1. Using an HDAC inhibitor, we tested the assays sensitivity to detect dynamic structural remodeling. We not only tracked chromatin decompaction but also demonstrated the robust structural resistance of LADs. As a proof-of-principle biological application, we applied tATAC-see to models of replicative, chronological, and pathological (Hutchinson-Gilford progeria syndrome) aging to assess its ability to detect well-characterized peripheral heterochromatin and LAD remodeling. We observed divergent chromatin trajectories at the nuclear envelope, reflective of the lamins distinct roles. lamin B1 domains exhibit increased local accessibility consistent with age-associated heterochromatin erosion, while lamin A/C-associated domains physically detach from their scaffold. Ultimately, tATAC-see provides a robust, accessible platform for mechanistic and population-level studies to uncover spatial epigenome dynamics. Summary StatementtATAC-see is a tunable visual genomics assay that can capture target-specific chromatin remodeling across diverse biological contexts.

cell biology↗

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↗

bioRxiv2019

Tissue mechanics regulate mitotic nuclear dynamics during epithelial development

Cell divisions are essential for tissue growth. In pseudostratified epithelia, where nuclei are staggered across the tissue, each nucleus migrates apically before undergoing mitosis. Successful apical nuclear migration is critical to preserve tissue integrity during cell division. Most previous investigations have focused on the local cellular mechanisms controlling nuclear migration. Yet, inter-species and inter-organ comparisons of different pseudostratified epithelia suggest global tissue architecture may influence nuclear dynamics, but the underlying mechanisms remain elusive. Here, we use the developing Drosophila wing disc to systematically investigate, in a single epithelial type, how changes in tissue architecture during growth influence mitotic nuclear migration. We observe distinct nuclear dynamics at discrete developmental stages, as epithelial morphology changes. We then use genetic and physical perturbations to show a direct effect of cell density on mitotic nuclear positioning. We also find Rho kinase and Diaphanous, which facilitate mitotic cell rounding in confined cell conditions, are essential for efficient apical nuclear movement. Strikingly, perturbation of Diaphanous causes increasing defects in apical nuclear migration as the tissue grows, and these defects can be reversed by acute physical reduction of cell density. Our findings reveal how the mechanical environment imposed on cells within a tissue alters the molecular and cellular mechanisms adopted by single cells for mitosis. We speculate that mechanical regulation of apical mitotic positioning could be a global mechanism for tissue growth control.

developmental biology↗

bioRxiv2019

Planar differential growth rates determine the position of folds in complex epithelia

Folding is a fundamental process shaping epithelial sheets into 3D architectures of organs. Initial positioning of folds is the foundation for the emergence of correct tissue morphology. Mechanisms forming individual folds have been studied, yet the precise positioning of the folds in complex, multi-folded epithelia is an open question. We present a model of morphogenesis, encompassing local differential growth, and tissue mechanics to investigate tissue fold positioning. We use Drosophila melanogaster wing imaginal disc as our model system, and show that there is spatial and temporal heterogeneity in its planar growth rates. This planar differential growth is the main driver for positioning the folds. Increased stiffness of the apical layer and confinement by the basement membrane drive fold formation. These influence fold positions to a lesser degree. The model successfully predicts the emergent morphology of wingless spade mutant in vivo, via perturbations solely on planar differential growth rates in silico.

biophysics↗