Epigenetic Association Study Uncovered H3K27 Acetylation Enhancers and Dysregulated Genes in High-Fat-Diet-Induced Nonalcoholic Fatty Liver Disease in Rats

Abstract

Aim: To evaluate the regulatory landscape underlying the active enhancer marked by H3K27ac in high-fat diet (HFD)-induced nonalcoholic fatty liver disease (NAFLD) in rats. Materials & methods: H3K27ac chromatin immunoprecipitation and high-throughput RNA sequencing to construct regulatory profiles and transcriptome of liver from NAFLD rat model induced by HFD. De novo motif analysis for differential H3K27ac peaks. Functional enrichment, Kyoto Encyclopedia of Genes and Genomes pathway and protein–protein interaction network were examined for differential peak–genes. The mechanism was further verified by western blot, chromatin immunoprecipitation-quantitative PCR and real-time PCR. Results: A total of 1831 differential H3K27ac peaks were identified significantly correlating with transcription factors and target genes (CYP8B1, PLA2G12B, SLC27A5, CYP7A1 and APOC3) involved in lipid and energy homeostasis. Conclusion: Altered acetylation induced by HFD leads to the dysregulation of gene expression, further elucidating the epigenetic mechanism in the etiology of NAFLD.

Plain language summary

What is this summary about? Nonalcoholic fatty liver disease (NAFLD) is a typical metabolic disease, which is becoming the most common liver disease in the world. Despite its high prevalence and morbidity, there is currently no effective diagnostic or approved therapy, and the molecular mechanisms for NAFLD have not been fully clarified, especially for epigenetics. Herein, we focused on histone modification and investigated the impact of active enhancer to explore the epigenetic regulation of NAFLD, seeking new targets for the prevention and treatment of the disease.

What were the results? We identified the alteration of H3K27 acetylation and differential gene expression, enriched potential transcription-factor binding motifs and highlighted the hub risk genes of CYP8B1, PLA2G12B, SLC27A5, CYP7A1 and APOC3 in a NAFLD rat model.

What do the results mean? This work emphasized the vital roles of histone modification of H3K27ac in a high-fat-diet-induced NAFLD model, which could regulate the expression of key genes and transcription factor binding motifs, and H3K27ac induced the formation of NAFLD. Targeting the H3K27ac modification, dysregulated target genes and enriched pathways may be of great importance for NAFLD prediction and prevention, and serve as a valuable resource for genome-wide studies of epigenomic regulation in lipid metabolic disease.

Keywords::

• ChIP-seq
• H3K27ac
• nonalcoholic fatty liver disease
• RNA-seq
• target genes

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/suppl/10.2217/epi-2022-0362

Y Zhu, J Huang and X Wei conceived and designed the experiments. J Ma, S Chen, N Fang, X Yi, X Lu and X Li performed the experiments. D You, Y Wang and M Zhu analyzed the data. D You and J Ma wrote and revised the manuscript. Y Zhu and Y Tang revised the manuscript. ​All authors read and approved the final manuscript.

Acknowledgments

We are grateful to colleagues in College of Animal Science and Technology, Jiangxi Agricultural University for data collection and experiments.

Financial & competing interests disclosure

This work was supported by the National Natural Science Foundation of China (grant no. 31960690), Natural Science Foundation of the Anhui Higher Education Institutions (grant no. KJ2021A0205) and Basic and Clinical cooperative research program of Anhui Medical University (grant no. 2022xkjT013). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval for all animal experimental investigations.

Data sharing statement

All the sequencing data of high-throughput RNA sequencing and chromatin immunoprecipitation will be deposited at the Genome Sequence Archive (https://ngdc.cncb.ac.cn/gsa/) upon acceptance. Three sets of control data of RNA-seq have been deposited at the Genome Sequence Archive repository (https://bigd.big.ac.cn/gsa/browse/ CRA002638). The Gene Expression Omnibus dataset used for this study can be found at https://www.ncbi.nlm.nih.gov/, GSE135251.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China (grant no. 31960690), Natural Science Foundation of the Anhui Higher Education Institutions (grant no. KJ2021A0205) and Basic and Clinical cooperative research program of Anhui Medical University (grant no. 2022xkjT013). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.