Spermatogenesis is a highly coordinated developmental process governed by precise epigenetic regulation. However, the exact chromatin dynamics during human spermatogenesis and their systemic failure in non-obstructive azoospermia (NOA)—the most severe form of male infertility—remain largely elusive due to the complexity of the meiotic process and the fleeting nature of epigenetic remodeling.
To bridge this gap, we profiled the single-cell chromatin accessibility of testicular tissues from 16 individuals with relatively normal spermatogenesis and 15 NOA patients across different subtypes. This generated a comprehensive atlas comprising over 810,000 candidate cis-regulatory elements (cCREs).
In normal spermatogenesis, we uncovered a wave-like, highly synchronized phasing of master transcription factor (TF) networks that precisely orchestrates meiotic progression. Furthermore, we tracked the dynamic opening and closing of meiotic DNA double-strand break (DSB) hotspots at single-cell resolution. Our data revealed a transient "epigenetic licensing" window during which thousands of pre-determined DSB hotspots, significantly enriched in sub-telomeric regions, become accessible for recombination.
In NOA patients, this delicate epigenetic architecture systematically collapses, resulting in severe meiotic arrest at the zygotene stage. We delineated this pathology as the dephasing and decoupling of master TF networks, alongside the failure of DSB hotspot activation. Crucially, we established a functional paradigm for interpreting non-coding genetic variants in sporadic NOA cases. We demonstrated that single nucleotide variants (SNVs) within non-coding regulatory regions—such as the enhancer of the PITX2 gene—disrupt key TF binding motifs (e.g., the NFY complex). This disruption leads to targeted epigenetic silencing and a cascaded failure of downstream spermatogenic networks.
Collectively, this study provides an unprecedented epigenetic roadmap of human spermatogenesis, advancing our understanding of NOA etiology from descriptive cellular phenotypes to network-level regulatory failures, and offering novel targets for precise molecular diagnosis.
Protein & Cell
Experimental study
Not applicable
Epigenetic Dynamics of Human Spermatogenesis and Their Dysregulation in Non-Obstructive Azoospermia
22-May-2026