College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
J Agric Food Chem. 2024 Nov 13;72(45):25403-25413. doi: 10.1021/acs.jafc.4c06867. Epub 2024 Nov 1.
The excessive deposition of abdominal fat tissue (AFT) in broilers has emerged as a major concern in the poultry industry. Despite some progress in recent years, the molecular mechanisms underlying AFT development remain ambiguous. The current study combined RNA-seq with transposase-accessible chromatin sequencing (ATAC-seq) to map the dynamic profiling of chromatin accessibility and transcriptional reprogramming in AFT adipocyte differentiation in broilers at day 3 (D3) and D14. Our results found that the levels of CDK1 and PCNA were down-regulated at D14, D28, and D42 compared to D3, while the levels of C/EBPα and FABP4 were up-regulated at D14 and D42 compared to D3. Meanwhile, PPARγ was significantly up-regulated at D28 and D42. RNA-seq of AFT identified 1705 up-regulated and 1112 down-regulated differential expression genes (DEGs) between D3 and D14. Pathways based on up-regulated DEGs mainly enriched some pathways related to adipocyte differentiation, while down-regulated DEGs pointed to DNA replication, cell cycle, and gap junction. Gene set enrichment analysis (GSEA) revealed that DNA replication and the cell cycle were down-regulated at D14, while the insulin signaling pathway was up-regulated. In the OA-induced immortalized chicken preadipocyte (ICP2) model, protein dynamic changes were consistent with AFT from D3 to D14. Same pathways were enriched in ICP2. In addition, based on overlapped DEGs from AFT and ICP2, enriched pathways related to adipocyte differentiation or proliferation mentioned above were all involved. A total of 1600 gain and 16727 loss differential peaks (DPs) were identified in ICP2 by ATAC-seq. Predicted genes from DPs at the promoter regions were enriched in glycerophospholipid metabolism, TGF-β signaling, FoxO signaling, and ubiquitin-mediated proteolysis. DNA motifs predicted 159 transcription factors (TFs) based on gain and loss peaks from the promoter regions, where 1 and 10 TFs were overlapped with up or down TFs from DEGs. Overall, this study presents a framework for the comprehension of the epigenetic regulatory mechanisms of adipocyte differentiation and identifies candidate genes and potential TFs involved in AFT adipocyte differentiation in broilers.
肉鸡腹部脂肪组织（AFT）过度沉积已成为家禽业的主要关注点。尽管近年来取得了一些进展，但 AFT 发育的分子机制仍不清楚。本研究结合 RNA-seq 和转座酶可及染色质测序（ATAC-seq），绘制了肉鸡 AFT 脂肪细胞分化第 3 天（D3）和第 14 天（D14）染色质可及性和转录重编程的动态图谱。我们的结果发现，与 D3 相比，CDK1 和 PCNA 的水平在 D14、D28 和 D42 时下调，而 C/EBPα 和 FABP4 的水平在 D14 和 D42 时上调。同时，PPARγ 在 D28 和 D42 时显著上调。AFT 的 RNA-seq 在 D3 和 D14 之间鉴定出 1705 个上调和 1112 个下调的差异表达基因（DEGs）。基于上调 DEGs 的通路主要富集了一些与脂肪细胞分化相关的通路，而下调 DEGs 则指向 DNA 复制、细胞周期和间隙连接。基因集富集分析（GSEA）显示，D14 时 DNA 复制和细胞周期下调，而胰岛素信号通路上调。在 OA 诱导的鸡原代脂肪细胞（ICP2）模型中，蛋白质的动态变化与 AFT 从 D3 到 D14 的变化一致。ICP2 中也富集了相同的通路。此外，基于 AFT 和 ICP2 之间重叠的 DEGs，上述与脂肪细胞分化或增殖相关的富集通路均有涉及。通过 ATAC-seq 在 ICP2 中鉴定出 1600 个获得和 16727 个丢失的差异峰（DP）。在启动子区域的 DP 预测基因富集在甘油磷脂代谢、TGF-β 信号、FoxO 信号和泛素介导的蛋白水解途径中。基于启动子区域的增益和损失峰预测的 DNA 基序，根据增益和损失峰预测了 159 个转录因子（TFs），其中 1 个和 10 个 TFs与 DEGs 中的上调或下调 TF 重叠。总的来说，本研究为理解脂肪细胞分化的表观遗传调控机制提供了一个框架，并确定了候选基因和潜在的 TF 参与肉鸡 AFT 脂肪细胞分化。
