Adverse maternal environments perturb hepatic DNA methylome and transcriptome prior to the adult-onset non-alcoholic fatty liver disease in mouse offspring [RRBS]

Exposure to adverse early-life environment (AME) increases the incidence of developing adult-onset non-alcoholic fatty liver disease (NAFLD). DNA methylation has been postulated to link AME and late-onset diseases. The objective was to investigate whether and to what extent hepatic DNA methylome was perturbed prior to the development of NAFLD in offspring exposed to AME in mice. AME constituted maternal western diet and late-gestational stress. Male offspring livers at birth (d0) and weaning (d21) were used for evaluating DNA methylome and transcriptome using reduced representation of bisulfite sequencing and RNA-seq, respectively. We found AME caused 5,879 differentially methylated regions (DMRs) and zero differentially expressed gene (DEG) at d0, and 2,970 and 123, respectively at d21. Majority of the DMRs were distal from gene transcription start sites and did not correlate with DEGs. The DEGs at d21 were significantly en-riched in GO biological processes characteristic of liver metabolic functions. In conclusion, AME drove changes in hepatic DNA methylome which preceded perturbations in the hepatic metabolic transcriptome, which preceded the onset of NAFLD. We speculate that subtle impacts in dynamic enhancers lead to long-range regulatory changes that manifest over time as gene network alter-nations to increase the incidence of NAFLD later in life. Comparative analysis of RRBS and RNA-seq data from the livers of C57bl/6 male mouse offspring (at birth and weaning) of dams experienced adverse maternal

早期不良环境（Adverse early-life environment, AME）暴露会提升成年发病非酒精性脂肪肝病（Non-alcoholic fatty liver disease, NAFLD）的发生风险。已有假说提出DNA甲基化可能是连接AME与迟发性疾病的纽带。本研究旨在探究：暴露于AME的小鼠子代在NAFLD发病前，其肝脏DNA甲基化组是否发生扰动，以及扰动的程度如何。本研究中的AME由母体西式饮食与妊娠晚期应激共同构成。我们分别采用简化亚硫酸氢盐测序（Reduced Representation Bisulfite Sequencing, RRBS）与RNA测序（RNA-seq），检测子代小鼠出生时（d0）与断乳期（d21）的肝脏组织DNA甲基化组与转录组。研究发现，AME在d0时可诱导产生5879个差异甲基化区域（Differentially methylated regions, DMRs），但未检测到差异表达基因（Differentially expressed gene, DEG）；在d21时则分别产生2970个DMRs与123个DEG。绝大多数DMRs位于基因转录起始位点远端，且与DEGs无显著相关性。d21时的DEGs显著富集于以肝脏代谢功能为特征的基因本体（Gene Ontology, GO）生物学过程。综上，AME可引发肝脏DNA甲基化组的改变，该改变先于肝脏代谢转录组的扰动，而后者又先于NAFLD的发病。我们推测，动态增强子的细微影响会引发远距离调控改变，随时间推移表现为基因网络紊乱，进而增加晚年NAFLD的发病风险。本研究对经历不良母体环境的孕鼠所产C57BL/6雄性子代小鼠（出生时与断乳期）的肝脏RRBS与RNA-seq数据进行了比较。