Ontogeny-Driven rDNA Rearrangement, Methylation, and Transcription, and Paternal Influence

Gene rearrangement occurs during development in some cell types and this genome dynamics is modulated by intrinsic and extrinsic factors, including growth stimulants and nutrients. This raises a possibility that such structural change in the genome and its subsequent epigenetic modifications may also take place during mammalian ontogeny, a process undergoing finely orchestrated cell division and differentiation. We tested this hypothesis by comparing single nucleotide polymorphism-defined haplotype frequencies and DNA methylation of the rDNA multicopy gene between two mouse ontogenic stages and among three adult tissues of individual mice. Possible influences to the genetic and epigenetic dynamics by paternal exposures were also examined for Cr(III) and acid saline extrinsic factors. Variables derived from litters, individuals, and duplicate assays in large mouse populations were examined using linear mixed-effects model. We report here that active rDNA rearrangement, represented by changes of haplotype frequencies, arises during ontogenic progression from day 8 embryos to 6-week adult mice as well as in different tissue lineages and is modifiable by paternal exposures. The rDNA methylation levels were also altered in concordance with this ontogenic progression and were associated with rDNA haplotypes. Sperm showed highest level of methylation, followed by lungs and livers, and preferentially selected haplotypes that are positively associated with methylation. Livers, maintaining lower levels of rDNA methylation compared with lungs, expressed more rRNA transcript. In vitro transcription demonstrated haplotype-dependent rRNA expression. Thus, the genome is also dynamic during mammalian ontogeny and its rearrangement may trigger epigenetic changes and subsequent transcriptional controls, that are further influenced by paternal exposures.

部分细胞类型在发育进程中会发生基因重排，此类基因组动态性会受到内在与外在因素（包括生长刺激剂与营养素）的调控。这提示，哺乳动物个体发生过程中或许也会出现此类基因组结构改变及其后续的表观遗传修饰——这一进程伴随精细调控的细胞分裂与分化。我们通过对比两种小鼠发育阶段之间、以及单只小鼠的三种成年组织之间的由单核苷酸多态性（single nucleotide polymorphism, SNP）界定的单倍型频率与核糖体DNA（rDNA）多拷贝基因的DNA甲基化水平，对该假说进行了验证。我们还针对三价铬（Cr(III)）与酸性盐水这两种外在因素，检测了父本暴露对遗传与表观遗传动态性的潜在影响。本研究采用线性混合效应模型（linear mixed-effects model），对来自同窝小鼠、个体以及重复实验的大型小鼠种群变量开展了分析。本研究结果显示：以单倍型频率变化为表征的活跃rDNA重排，既会在小鼠从胚胎第8天到6周龄成年个体的发育进程中发生，也存在于不同的组织谱系中，且可被父本暴露所调控。rDNA甲基化水平也会随该发育进程发生一致性改变，并与rDNA单倍型相关联。精子的甲基化水平最高，其次为肺与肝脏组织；精子还会优先选择与甲基化水平呈正相关的单倍型。与肺组织相比，肝脏的rDNA甲基化水平更低，但rRNA转录产物更多。体外转录实验证实了单倍型依赖的rRNA表达模式。综上，哺乳动物个体发育过程中基因组同样具有动态性，其重排可能会触发表观遗传改变与后续的转录调控，且这一过程会进一步受到父本暴露的影响。