Mammalian sperm show an unusual and heavily compacted genomic packaging state. In addition to its role in organizing the compact and hydrodynamic sperm head, it has been proposed that sperm chromatin architecture helps to program gene expression in the early embryo. Scores of genome-wide surveys in sperm have reported patterns of chromatin accessibility, nucleosome localization, histone modification, and chromosome folding. Here, we revisit these studies in light of recent reports that sperm obtained from the mouse epididymis are contaminated with low levels of cell-free chromatin. In the absence of proper sperm lysis, we readily recapitulate multiple prominent genome-wide surveys of sperm chromatin, suggesting that these profiles primarily reflect contaminating cell-free chromatin. Removal of cell-free DNA, and appropriate lysis conditions, are together required to reveal a sperm chromatin state distinct from most previous reports. Using ATAC-seq to explore relatively accessible genomic loci, we identify a landscape of open loci associated with early development and transcriptional control. Histone modification and chromosome folding profiles also strongly support the hypothesis that prior studies suffer from contamination, but technical challenges associated with reliably preserving the architecture of the compacted sperm head prevent us from confidently assaying true localization patterns for these epigenetic marks. Together, our studies show that our knowledge of chromosome packaging in mammalian sperm remains largely incomplete, and motivate future efforts to more accurately characterize genome organization in mature sperm.

中文翻译：

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重新审视小鼠精子中的染色质包装

哺乳动物精子表现出不寻常且高度紧凑的基因组包装状态。除了在组织紧凑且流体动力学的精子头中发挥作用外，有人提出精子染色质结构有助于编程早期胚胎中的基因表达。大量精子全基因组调查报告了染色质可及性、核小体定位、组蛋白修饰和染色体折叠的模式。在这里，我们根据最近的报道重新审视这些研究，即从小鼠附睾获得的精子受到低水平的游离染色质污染。在没有适当的精子裂解的情况下，我们很容易重述精子染色质的多个重要的全基因组调查，表明这些图谱主要反映了污染的无细胞染色质。去除游离 DNA 和适当的裂解条件是揭示精子染色质状态与大多数先前报告不同的必要条件。使用 ATAC-seq 探索相对容易接近的基因组位点，我们确定了与早期发育和转录控制相关的开放位点景观。组蛋白修饰和染色体折叠图谱也有力地支持了这样的假设：之前的研究受到污染，但与可靠保存压缩精子头部结构相关的技术挑战使我们无法自信地分析这些表观遗传标记的真实定位模式。总之，我们的研究表明，我们对哺乳动物精子中染色体包装的了解在很大程度上仍然不完整，并激励未来更加准确地表征成熟精子中基因组组织的努力。