Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA.
San Diego Zoo Global, Institute for Conservation Research, Reproductive Sciences, Escondido, CA, 92027, USA.
Mol Hum Reprod. 2020 Nov 1;26(11):866-878. doi: 10.1093/molehr/gaaa064.
The preimplantation stage of development is exquisitely sensitive to environmental stresses, and changes occurring during this developmental phase may have long-term health effects. Animal studies indicate that IVF offspring display metabolic alterations, including hypertension, glucose intolerance and cardiac hypertrophy, often in a sexual dimorphic fashion. The detailed nature of epigenetic changes following in-vitro culture is, however, unknown. This study was performed to evaluate the epigenetic (using whole-genome bisulfite sequencing (WGBS) and assay for transposase-accessible chromatin using sequencing (ATAC-seq)) and transcriptomic changes (using RNA-seq) occurring in the inner cell mass (ICM) of male or female mouse embryos generated in vivo or by IVF. We found that the ICM of IVF embryos, compared to the in-vivo ICM, differed in 3% of differentially methylated regions (DMRs), of which 0.1% were located on CpG islands. ATAC-seq revealed that 293 regions were more accessible and 101 were less accessible in IVF embryos, while RNA-seq revealed that 21 genes were differentially regulated in IVF embryos. Functional enrichment analysis revealed that stress signalling (STAT and NF-kB signalling), developmental processes and cardiac hypertrophy signalling showed consistent changes in WGBS and ATAC-seq platforms. In contrast, male and female embryos showed minimal changes. Male ICM had an increased number of significantly hyper-methylated DMRs, while only 27 regions showed different chromatin accessibility and only one gene was differentially expressed. In summary, this study provides the first comprehensive analysis of DNA methylation, chromatin accessibility and RNA expression changes induced by IVF in male and female ICMs. This dataset can be of value to all researchers interested in the developmental origin of health and disease (DOHaD) hypothesis and might lead to a better understanding of how early embryonic manipulation may affect adult health.
胚胎植入前阶段的发育对环境压力非常敏感，在此发育阶段发生的变化可能会对长期健康产生影响。动物研究表明，体外受精（IVF）后代表现出代谢改变，包括高血压、葡萄糖不耐受和心脏肥大，通常具有性别二态性。然而，体外培养后发生的表观遗传变化的详细性质尚不清楚。本研究旨在评估体内或通过 IVF 产生的雄性或雌性小鼠胚胎内细胞团（ICM）中发生的表观遗传（使用全基因组亚硫酸氢盐测序（WGBS）和转座酶可及染色质测序（ATAC-seq））和转录组变化（使用 RNA-seq）。我们发现，与体内 ICM 相比，IVF 胚胎的 ICM 在 3%的差异甲基化区域（DMR）中存在差异，其中 0.1%位于 CpG 岛。ATAC-seq 显示，IVF 胚胎中有 293 个区域的可及性增加，101 个区域的可及性降低，而 RNA-seq 显示，IVF 胚胎中有 21 个基因的表达受到差异调控。功能富集分析显示，应激信号（STAT 和 NF-kB 信号）、发育过程和心脏肥大信号在 WGBS 和 ATAC-seq 平台上显示出一致的变化。相比之下，雄性和雌性胚胎的变化很小。雄性 ICM 中存在大量显著超甲基化 DMR，而只有 27 个区域的染色质可及性不同，只有一个基因的表达存在差异。总之，本研究首次全面分析了 IVF 对雄性和雌性 ICM 中 DNA 甲基化、染色质可及性和 RNA 表达变化的影响。该数据集对所有关注健康和疾病的发育起源（DOHaD）假说的研究人员都具有重要价值，并可能有助于更好地理解早期胚胎操作如何影响成年健康。
