Rué Olivier, Fuandila Nurul Novelia, Hammoumi Saliha, Gaspin Christine, Avarre Jean-Christophe
Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France.
Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, Jouy-en-Josas, France.
Data Brief. 2025 Jun 18;61:111800. doi: 10.1016/j.dib.2025.111800. eCollection 2025 Aug.
MicroRNAs (miRNAs) are small non-coding RNAs capable of altering gene expression. In viruses, miRNAs may significantly influence the interaction between the virus and its host. Among all the viruses that have been reported to encode miRNAs, those belonging to the order encode the largest number of pre-miRNAs. (CyHV-3) is a member of the family and is recognised as a significant threat for the common carp and ornamental koi aquaculture. The present study aimed to identify miRNAs involved in the lytic cycle of CyHV-3 and monitor their expression from 1 h to 10 days post-infection (dpi), at two different temperatures: a permissive temperature (22 °C) and a non-permissive temperature (30 °C) (Fig. 1). This is the first study that describes the expression kinetics of predicted miRNAs from CyHV-3-infected carp cells. Alignment of reads against a CyHV-3 reference genome led to the identification of 81 putative pre-miRNAs. Although this data mainly focused on CyHV-3 miRNAs, an alignment of reads against the genome led to the identification of 3025 miRNA that could be annotated. Of note, the 7 miRNAs previously identified in CyHV-3 were retrieved among the 81 putative pre-miRNAs found here. The number of putative miRNAs identified is far higher than in the two previous studies, probably because of the high number of reads obtained across the 36 individual samples that represented all stages of viral infection. A constant increase in the expression of virus-predicted miRNAs was observed along the viral infection at 22 °C, with a maximum at 6 dpi (Fig. 2). Interestingly, cytopathic effects started to be observed after 3 dpi, and all the cells were lysed after 10 days. In contrast, no cyctopathic effects were recorded at 30 °C; at this temperature, no difference could be observed between samples in terms of miRNA expression (Fig. 2).
微小RNA（miRNA）是一类能够改变基因表达的小型非编码RNA。在病毒中，miRNA可能会显著影响病毒与其宿主之间的相互作用。在所有已报道编码miRNA的病毒中，属于该目的病毒编码的前体miRNA数量最多。鲤疱疹病毒3型（CyHV-3）是该科的成员，被认为是对鲤鱼和观赏锦鲤养殖的重大威胁。本研究旨在鉴定参与CyHV-3裂解周期的miRNA，并在两个不同温度下监测其感染后1小时至10天（dpi）的表达：允许温度（22°C）和非允许温度（30°C）（图1）。这是第一项描述CyHV-3感染鲤鱼细胞中预测的miRNA表达动力学的研究。将读数与CyHV-3参考基因组进行比对，鉴定出81个假定的前体miRNA。尽管该数据主要集中在CyHV-3 miRNA上，但将读数与该基因组进行比对后，鉴定出了3025个可注释的miRNA。值得注意的是，在本文发现的81个假定前体miRNA中检索到了先前在CyHV-3中鉴定出的7个miRNA。鉴定出的假定miRNA数量远高于前两项研究，这可能是因为在代表病毒感染所有阶段的36个个体样本中获得了大量读数。在22°C下，随着病毒感染的进行，观察到病毒预测的miRNA表达持续增加，在6 dpi时达到最大值（图2）。有趣的是，在3 dpi后开始观察到细胞病变效应，10天后所有细胞均裂解。相比之下，在30°C下未记录到细胞病变效应；在此温度下，样本之间在miRNA表达方面没有差异（图2）。
