Tong Xinyu, Lei Chao, Liu Yilin, Yin Mei, Peng Huan, Qiu Qunnan, Feng Yongjie, Hu Xiaolong, Gong Chengliang, Zhu Min
School of Life Sciences, Soochow University, Suzhou 215123, China.
Int J Mol Sci. 2025 Jan 19;26(2):818. doi: 10.3390/ijms26020818.
Extrachromosomal circular DNAs (eccDNAs) has been found to be widespread and functional in various organisms. However, comparative analyses of pre- and post-infection of virus are rarely known. Herein, we investigated the changes in expression patterns of eccDNA following infection with cytoplasmic polyhedrosis virus (BmCPV) and explore the role of eccDNA in viral infection. Circle-seq was used to analyze eccDNAs in the midgut of BmCPV-infected and BmCPV-uninfected silkworms. A total of 5508 eccDNAs were identified, with sizes varying from 72 bp to 17 kb. Most of eccDNAs are between 100 to 1000 bp in size. EccDNA abundance in BmCPV-infected silkworms was significantly higher than in BmCPV-uninfected silkworms. GO and KEGG analysis of genes carried by eccDNAs reveals that most are involved in microtubule motor activity, phosphatidic acid binding, cAMP signaling pathway, and pancreatic secretion signaling pathways. Several eccDNAs contain sequences of the transcription factor SOX6, sem-2, sp8b, or Foxa2. Association analysis of eccDNA-mRNA/miRNA/circRNA revealed that some highly expressed genes are transcribed from relevant sequences of eccDNA and the transcription of protein coding genes influenced the frequency of eccDNA. BmCPV infection resulted in changes in the expression levels of six miRNAs, but no known miRNAs with altered expression levels due to changes in eccDNA abundance were identified. Moreover, it was found that 1287 and 924 sequences representing back-spliced junctions of circRNAs were shared by the junctions of eccDNAs in the BmCPV-infected and uninfected silkworms, respectively, and some eccDNAs loci were shared by circRNAs on Chromosomes 2, 7, 11, 14, and 24, suggesting some eccDNAs may exert its function by being transcribed into circRNAs. These findings suggest that BmCPV infection alter the expression pattern of eccDNAs, leading to changes in RNA transcription levels, which may play roles in regulating BmCPV replication. In the future, further experiments are needed to verify the association between eccDNA-mRNA/miRNA/circRNA and its function in BmCPV infection.
染色体外环状DNA（eccDNA）已被发现在各种生物体中广泛存在且具有功能。然而，关于病毒感染前后的比较分析却鲜为人知。在此，我们研究了感染细胞质多角体病毒（BmCPV）后eccDNA表达模式的变化，并探讨了eccDNA在病毒感染中的作用。利用Circle-seq分析BmCPV感染和未感染的家蚕中肠中的eccDNA。共鉴定出5508个eccDNA，大小从72 bp到17 kb不等。大多数eccDNA的大小在100到1000 bp之间。BmCPV感染的家蚕中eccDNA丰度显著高于未感染的家蚕。对eccDNA携带的基因进行GO和KEGG分析表明，大多数基因参与微管运动活性、磷脂酸结合、cAMP信号通路和胰腺分泌信号通路。一些eccDNA包含转录因子SOX6、sem-2、sp8b或Foxa2的序列。eccDNA与mRNA/miRNA/circRNA的关联分析表明，一些高表达基因是从eccDNA的相关序列转录而来的，蛋白质编码基因的转录影响了eccDNA的频率。BmCPV感染导致6种miRNA的表达水平发生变化，但未鉴定出因eccDNA丰度变化而表达水平改变的已知miRNA。此外，发现BmCPV感染和未感染的家蚕中，分别有1287和924个代表circRNA反向剪接连接的序列与eccDNA的连接共享，并且2号、7号、11号、14号和24号染色体上的circRNA共享一些eccDNA位点，这表明一些eccDNA可能通过转录成circRNA发挥其功能。这些发现表明，BmCPV感染改变了eccDNA的表达模式，导致RNA转录水平发生变化，这可能在调节BmCPV复制中发挥作用。未来，需要进一步的实验来验证eccDNA与mRNA/miRNA/circRNA之间的关联及其在BmCPV感染中的功能。
