基因组分析揭示了增强子在鸡胚胎发育过程中介导的肝转录重编程变化。

Genome analysis reveals hepatic transcriptional reprogramming changes mediated by enhancers during chick embryonic development.

机构信息

College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.

出版信息

Poult Sci. 2023 Apr;102(4):102516. doi: 10.1016/j.psj.2023.102516. Epub 2023 Jan 20.

DOI:10.1016/j.psj.2023.102516

PMID:36764138

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9929590/

Abstract

The liver undergoes a slow process for lipid deposition during chick embryonic period. However, the underlying physiological and molecular mechanisms are still unclear. Therefore, the aim of the current study was to reveal the epigenetic mechanism of hepatic transcriptional reprogramming changes based on the integration analysis of RNA-seq and H3K27ac labeled CUT&Tag. Results showed that lipid contents increased gradually with the embryonic age (E) 11, E15, and E19 based on morphological analysis of Hematoxylin-eosin and Oil Red O staining as well as total triglyceride and cholesterol detection. The hepatic protein level of SREBP-1c was higher in E19 when compared with that in E11 and E15, while H3K27ac and H3K4me2 levels declined from E11 to E19. Differential expression genes (DEGs) among these 3 embryonic ages were determined by transcriptome analysis. A total of 107 and 46 genes were gradually upregulated and downregulated respectively with the embryonic age. Meanwhile, differential H3K27ac occupancy in chromatin was investigated. But the integration analysis of RNA-seq and CUT&Tag data showed that the overlap genes were less between DEGs and target genes of differential peaks in the promoter regions. Further, some KEGG pathways enriched from target genes of typical enhancer were overlapped with those from DEGs in transcriptome analysis such as insulin, FoxO, MAPK signaling pathways which were related to lipid metabolism. DNA motif analysis identify 8 and 10 transcription factors (TFs) based on up and down differential peaks individually among E11, E15, and E19 stages where 7 TFs were overlapped including COUP-TFII, FOXM1, FOXA1, HNF4A, RXR, ERRA, FOXA2. These results indicated that H3K27ac histone modification is involved in the transcriptional reprogramming regulation during embryonic development, which could recruit TFs binding to mediate differential enhancer activation. Differential activated enhancer impels dynamic transcriptional reprogramming towards lipid metabolism to promote the occurrence of special phenotype of hepatic lipid deposition.

摘要

鸡胚胎期肝脏的脂质沉积是一个缓慢的过程。然而，其潜在的生理和分子机制尚不清楚。因此，本研究旨在基于 RNA-seq 和 H3K27ac 标记的 CUT&Tag 整合分析，揭示肝转录重编程变化的表观遗传机制。结果表明，基于 H&E 和油红 O 染色以及总甘油三酯和胆固醇检测的形态学分析，脂质含量随着胚胎龄 (E)11、E15 和 E19 的增加而逐渐增加。与 E11 和 E15 相比，E19 时肝 SREBP-1c 蛋白水平较高，而 H3K27ac 和 H3K4me2 水平从 E11 下降到 E19。通过转录组分析确定这 3 个胚胎龄之间的差异表达基因 (DEGs)。共有 107 个基因逐渐上调，46 个基因逐渐下调。同时，对染色质中差异 H3K27ac 占有率进行了研究。但 RNA-seq 和 CUT&Tag 数据的整合分析表明，DEGs 与启动子区差异峰的靶基因之间的重叠基因较少。此外，一些来自典型增强子靶基因的 KEGG 通路与转录组分析中的 DEGs 重叠，如胰岛素、FoxO、MAPK 信号通路等与脂质代谢有关。基于 E11、E15 和 E19 阶段的上调和下调差异峰，分别鉴定出 8 个和 10 个转录因子 (TF) 的 DNA 基序，其中包括 COUP-TFII、FOXM1、FOXA1、HNF4A、RXR、ERRA 和 FOXA2 等 7 个 TF。这些结果表明，H3K27ac 组蛋白修饰参与了胚胎发育过程中的转录重编程调控，可募集 TF 结合介导差异增强子激活。差异激活的增强子促使动态转录重编程向脂质代谢方向发展，促进肝脏脂质沉积特殊表型的发生。