Computational identification of microRNAs in Anatid herpesvirus 1 genome.
Computational identification of microRNAs in Anatid herpesvirus 1 genome.
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DOI：
10.1186/1743-422x-9-93
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发表时间：
2012-05-14
期刊：
影响因子：
4.8
通讯作者：
Chen X
中科院分区：
文献类型：
--
作者：
Xiang J;Cheng A;Wang M;Zhang S;Zhu D;Jia R;Chen S;Zhou Y;Wang X;Chen X
MicroRNAs （miRNAs）是一组短的（~22 nt）非编码rna，在转录后水平特异性调节基因表达。miRNA前体（pre-miRNA）是一种不完善的~70 nt的茎环结构，由细胞RNases III加工成成熟的miRNA。迄今为止，已经在不同的生物体中发现了数千种mirna。据报道，有几种病毒编码mirna。在这里，我们将mirna编码潜力的分析扩展到Anatid herpesvirus 1 （AHV-1）。通过计算方法，我们发现AHV-1可能编码12个成熟的mirna。然后，我们将12个成熟的候选mirna与所有已知的疱疹病毒家族mirna进行比较。有趣的是，预测2个mirna的“种子序列”（nt 2 ~ 8）与马立克病病毒1型（MDV-1）的2个mirna在位置和/或序列上具有高度的保守性。此外，我们从病毒mrna中搜索目标。通过计算方法，我们发现AHV-1可能编码12个成熟mirna，其中2个mirna与MDV-1的2个mirna具有高度保守性。结果提示AHV-1与MDV-1具有密切的进化关系，为AHV-1的分类提供了有价值的依据。此外，还发现了7个病毒基因靶点，这表明AHV-1 mirna可以影响其自身基因的表达。
MicroRNAs (miRNAs) are a group of short (~22 nt) noncoding RNAs that specifically regulate gene expression at the post-transcriptional level. miRNA precursors (pre-miRNAs), which are imperfect stem loop structures of ~70 nt, are processed into mature miRNAs by cellular RNases III. To date, thousands of miRNAs have been identified in different organisms. Several viruses have been reported to encode miRNAs. Here, we extended the analysis of miRNA-encoding potential to the Anatid herpesvirus 1 (AHV-1). Using computational approaches, we found that AHV-1 putatively encodes 12 mature miRNAs. We then compared the 12 mature miRNAs candidates with the all known miRNAs of the herpesvirus family. Interestingly, the “seed sequences” (nt 2 to 8) of 2 miRNAs were predicted to have the high conservation in position and/or sequence with the 2 miRNAs of Marek’s disease virus type 1 (MDV-1). Additionally, we searched the targets from viral mRNAs. Using computational approaches, we found that AHV-1 putatively encodes 12 mature miRNAs and 2 miRNAs have the high conservation with the 2 miRNAs of MDV-1. The result suggested that AHV-1 and MDV-1 should have closed evolutionary relation, which provides a valuable evidence of classification of AHV-1. Additionally, seven viral gene targets were found, which suggested that AHV-1 miRNAs could affect its own gene expression.