Paternal poly(ADP-ribose) metabolism modulates retention of inheritable sperm histones and early embryonic gene expression

To achieve the extreme nuclear condensation necessary for sperm function, most histones are replaced with protamines during spermiogenesis in mammals. Mature sperm retain only a small fraction of nucleosomes, which are, in part, enriched on gene regulatory sequences, and recent findings suggest that these retained histones provide epigenetic information that regulates expression of a subset of genes involved in embryo development after fertilization. We addressed this tantalizing hypothesis by analyzing two mouse models exhibiting abnormal histone positioning in mature sperm due to impaired poly(ADP-ribose) (PAR) metabolism during spermiogenesis and identified altered sperm histone retention in specific gene loci genome-wide using MNase digestion-based enrichment of mononucleosomal DNA. We then set out to determine the extent to which expression of these genes was altered in embryos generated with these sperm. For control sperm, most genes showed some degree of histone association, unexpectedly suggesting that histone retention in sperm genes is not an all-or-none phenomenon and that a small number of histones may remain associated with genes throughout the genome. The amount of retained histones, however, was altered in many loci when PAR metabolism was impaired. To ascertain whether sperm histone association and embryonic gene expression are linked, the transcriptome of individual 2-cell embryos derived from such sperm was determined using microarrays and RNA sequencing. Strikingly, a moderate but statistically significant portion of the genes that were differentially expressed in these embryos also showed different histone retention in the corresponding gene loci in sperm of their fathers. These findings provide new evidence for the existence of a linkage between sperm histone retention and gene expression in the embryo. 9 WT samples in 3 groups of 3. Each group consists of 3 eggs fertilized by the same father. 9 KO samples in the same setup.为实现精子功能所必需的极度核浓缩，哺乳动物在精子发生过程中，多数组蛋白会被鱼精蛋白替换。成熟精子仅保留少量核小体，这类核小体部分富集于基因调控序列；近期研究表明，这些留存的组蛋白可提供表观遗传信息，调控受精后胚胎发育相关基因子集的表达。 我们针对这一引人入胜的假说展开研究：通过分析两种因精子发生过程中多聚ADP核糖（poly(ADP-ribose)，PAR）代谢受损，导致成熟精子组蛋白定位异常的小鼠模型，利用基于微球菌核酸酶（Micrococcal Nuclease，MNase）酶切的单核小体DNA富集技术，在全基因组范围内鉴定出特定基因位点的精子组蛋白留存量发生改变。随后我们着手探究，利用这类精子获得的胚胎中，上述基因的表达改变程度如何。 对于对照精子而言，多数基因均呈现出不同程度的组蛋白结合，这出乎意料地表明，精子中基因的组蛋白留存并非全有或全无的现象，全基因组范围内的基因或许仍会结合少量组蛋白。然而，当PAR代谢受损时，众多基因位点的留存组蛋白数量发生了改变。 为明确精子组蛋白结合与胚胎基因表达之间是否存在关联，我们采用微阵列（microarray）与RNA测序（RNA sequencing）技术，对源自这类精子的单个2-细胞胚胎的转录组进行了检测。值得注意的是，在这些胚胎中差异表达的基因中，有占比中等但经统计学检验具有显著性的部分，在其父代精子的对应基因位点上，也表现出了不同的组蛋白留存量。 上述研究结果为精子组蛋白留存与胚胎基因表达之间存在关联这一论点提供了新的证据。 本数据集包含3组野生型（Wild Type，WT）样本，每组由3枚由同一只雄鼠受精的卵细胞组成，总计9份；同时包含相同实验设置下的9份基因敲除（Knockout，KO）样本。