In cattle, several calves born after IVP (“in vitro” embryo production) present similar birthweight to those generated after MOET (multiple ovulation and embryo transfer). However, the underlying molecular patterns in organs involved in the developmental process are unknown and could indicate physiological programming. The objectives of this study were: (1) to compare epigenomic and transcriptomic modifications in the hypothalamus, pituitary, gonadal and adrenal organs between 3 months old ovum pick-up-IVP and MOET male calves (n = 4 per group) and (2) to use blood epigenomic data to proxy methylation of the inner organs. Extracted gDNA and RNA were sequenced through whole-genome bisulfite sequencing and RNA sequencing, respectively. Next, bioinformatic analyses determined differentially methylated cytosines (DMC) and differentially expressed genes (DEG) (FDR < 0.05) in IVP versus MOET samples and the KEGG pathways that were overrepresented by genes associated with DMC or DEG (FDR < 0.1). Pathways related to hypothalamus, pituitary, gonadal (HPG) axis activation (GnRH secretion in the hypothalamus, GnRH signaling in the pituitary, and steroidogenesis in the testicle) were enriched in IVP calves. Modeling the effect of the methylation levels and the group on the expression of all the genes involved in these pathways confirmed their upregulation in HPG organs in IVP calves. The application of the DIABLO method allowed the identification of 15 epigenetic and five transcriptomic biomarkers, which were able to predict the embryo origin using the epigenomic data from the blood. In conclusion, the use of an integrated epigenomic-transcriptomic approach suggested an early activation of the HPG axis in male IVP calves compared to MOET counterparts, and the identification of potential biomarkers allowed the use of blood samples to proxy methylation levels of the relevant internal organs.

中文翻译：

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表观基因组学和转录组学分析揭示了体外生产的雄性奶牛中 HPG 轴的早期激活

在牛中，IVP（“体外”胚胎生产）后出生的几只小牛的出生体重与 MOET（多次排卵和胚胎移植）后出生的小牛相似。然而，参与发育过程的器官的潜在分子模式是未知的，可能表明生理程序。本研究的目的是：(1) 比较 3 个月大的取卵-IVP 和 MOET 雄性小牛在下丘脑、垂体、性腺和肾上腺器官中的表观基因组和转录组修饰 ( n = 每组 4 个）和 (2) 使用血液表观基因组数据来代表内部器官的甲基化。提取的 gDNA 和 RNA 分别通过全基因组亚硫酸氢盐测序和 RNA 测序进行测序。接下来，生物信息学分析确定了 IVP 与 MOET 样本中差异甲基化胞嘧啶 (DMC) 和差异表达基因 (DEG) (FDR < 0.05) 以及与 DMC 或 DEG 相关的基因过度表达的 KEGG 通路 (FDR < 0.1)。与下丘脑、垂体、性腺 (HPG) 轴激活相关的通路（下丘脑中的 GnRH 分泌、垂体中的 GnRH 信号传导和睾丸中的类固醇生成）在 IVP 小牛中得到了丰富。对甲基化水平和组对参与这些途径的所有基因表达的影响进行建模证实了它们在 IVP 小牛的 HPG 器官中的上调。DIABLO 方法的应用允许识别 15 种表观遗传和 5 种转录组生物标志物，它们能够使用来自血液的表观基因组数据预测胚胎起源。总之，与MOET对应物相比，使用综合表观基因组转录组学方法表明雄性IVP小牛HPG轴的早期激活，并且潜在生物标志物的鉴定允许使用血液样本来代表相关内脏器官的甲基化水平. 能够使用来自血液的表观基因组数据预测胚胎起源。总之，与MOET对应物相比，使用综合表观基因组转录组学方法表明雄性IVP小牛HPG轴的早期激活，并且潜在生物标志物的鉴定允许使用血液样本来代表相关内脏器官的甲基化水平. 能够使用来自血液的表观基因组数据预测胚胎起源。总之，与MOET对应物相比，使用综合表观基因组转录组学方法表明雄性IVP小牛HPG轴的早期激活，并且潜在生物标志物的鉴定允许使用血液样本来代表相关内脏器官的甲基化水平.