Biology subjects

Sahu, Y.

Publications and source records attributed to Sahu, Y..

3 recordsLinked to original sources

bioRxiv2025

Deep Neurite Analysis Tool (DeNAT): A machine-learning framework for precise automated neurite outgrowth measurement

Accurate quantification of neurite sprouting after injury is a critical step in axon regeneration research. Yet it remains a major bottleneck, as the current gold standard relies on manual counting by multiple blinded observers. This process is slow, labor-intensive, and prone to variability. While some software can measure total neurite length, they arent made to specifically measure new growth in complicated images from real-life injury models, like the thoracic crush and pyramidotomy model. Existing software can measure total neurite length in culture, but it is not designed to capture new growth in complex images from injury models, such as thoracic crush or pyramidotomy. Crucially, these tools lack the ability to selectively analyze growth within user-defined regions, a key requirement for injury paradigms. To address this need, we developed the Deep Neurite Analysis Tool (DeNAT), an accessible deep-learning-based platform that automatically measures neurite outgrowth after injury. DeNAT allows users to define regions of interest to specifically quantify sprouting in images from common spinal cord injury paradigms. We benchmarked its performance against manual scoring and conventional automated approaches. DeNAT achieved 87 percent accuracy in detecting neurite sprouts relative to manual counts, while reducing variability and labor. By combining user-guided region selection with automated deep learning analysis, DeNAT offers an accurate, reproducible, and efficient solution for measuring neurite outgrowth in injury models.

bioinformatics↗

bioRxiv2025

Nuclear Receptor Transcription factors promote axon regeneration in the Adult Corticospinal Tract

Transcription factors are potent levers for neural repair, but which factors govern regenerative capacity in the corticospinal tract remains largely unknown. By intersecting developmental RNA-seq with ATAC-seq footprinting, we identified two nuclear-receptor transcription factors, NR2F1 and NR2F6, neither previously linked to CNS axon growth, whose chromatin occupancy at pro-growth enhancers is progressively lost as neurons mature. Forced expression of either factor significantly increased neurite outgrowth in single-neuron tracing assays, and each drove strong cross-midline sprouting after pyramidotomy and long-tract CST regeneration after complete thoracic crush, with concordant recovery of hip-rise kinematics and grip strength. Parallel multi-omic profiling (CUT&RUN, snRNA-seq and Ribo-seq) of both factors together with NR2F6 Hi-C revealed distinct mechanisms: NR2F1 reactivated chromatin-remodeling and cytoskeletal programs, whereas NR2F6, via a conserved corepressor domain, re-occupied developmental enhancers, reorganized three-dimensional chromatin architecture into new topologically associating domains, and imposed a transient translational down-shift in which growth-relevant modules were selectively preserved through translational buffering. Together, these data identify NR2F nuclear receptors as regulators of corticospinal regeneration, acting through enhancer redeployment, translational reprogramming and three-dimensional genome reorganization.

neuroscience↗

bioRxiv2025

PATZ1 Reinstates a Growth-Permissive Chromatin Landscape in Adult Corticospinal Neurons After Injury

BackgroundThe failure of axon regeneration in the adult central nervous system represents a major barrier to recovery from spinal cord injury and neurodegenerative disease. Pro-growth transcription factors can promote regenerative responses, but their effects remain partial, suggesting that additional restraints must be relieved for these factors to achieve their full potential. The chromatin landscape of adult neurons has emerged as a candidate mechanism, yet we lack a developmental map of when and how this epigenetic restriction occurs, whether injury can reverse it, and how to therapeutically target it. ResultsWe assembled a comprehensive chromatin accessibility atlas spanning mouse forebrain development from embryonic day 11 through adulthood using bulk and single-nucleus ATAC-seq. This revealed progressive restriction of growth-gene promoters and enhancers across postnatal development, leaving over 95% of growth-associated regulatory elements substantially inaccessible in mature neurons. We found that the distance between injury site and neuronal cell body determines the magnitude of chromatin reopening: intracortical lesions proximal to motor cortex soma triggered ten-fold greater enhancer reactivation compared to distal thoracic spinal cord crush. Motif analysis identified PATZ1, a chromatin-remodeling transcription factor, as correlated with this proximity effect. Viral delivery of PATZ1 to adult cortex converted the limited epigenomic response to distal injury into a profile approaching that of proximal injury, selectively reopening enhancers at growth-associated loci and depositing active H3K27ac marks. Hi-C analysis demonstrated that PATZ1 additionally reorganizes higher-order chromatin architecture, inducing compartment switching at growth loci and remodeling topologically associating domain boundaries. Integration with single-nucleus transcriptomics revealed that while PATZ1 selectively opens chromatin at growth genes, transcriptional output and axon regeneration remain modest, indicating that combinatorial approaches pairing epigenetic priming with pro-growth transcription factors may be required for functional repair. ConclusionsThis study provides a developmental timeline of chromatin closure at regeneration-associated genes and identifies PATZ1 as a molecular tool capable of reversing this epigenetic barrier in adult neurons. Our findings indicate that chromatin accessibility functions as a gatekeeping mechanism that must be addressed before transcription factor-based therapies can achieve their full effect, establishing epigenetic priming as a targetable component of CNS repair strategies.

neuroscience↗