The developmental miRNA profiles of zebrafish as determined by small RNA cloning
The developmental miRNA profiles of zebrafish as determined by small RNA cloning
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DOI：
10.1101/gad.1310605
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发表时间：
2005-06-01
影响因子：
10.5
通讯作者：
Tuschl, T
中科院分区：
文献类型：
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作者：
Chen, PY;Manninga, H;Tuschl, T
微小RNA（miRNAs）是一类在植物和动物中发现的小型调节性非编码RNA。在此，我们描述了以发育和细胞类型特异性方式解析的斑马鱼（Danio rerio）的miRNA图谱。这些图谱是通过对从处于不同发育阶段的斑马鱼以及两种源自尾鳍（ZFL）和肝上皮（SJD）的成年成纤维细胞系制备的小RNA文库进行大规模测序获得的。我们从343个miRNA基因中鉴定出总共154种不同的miRNAs。其他实验/计算来源支持另外19个基因编码的10种miRNAs。这些miRNAs可分为87个不同的家族。跨物种比较表明，81个家族在哺乳动物中是保守的，其中17个家族在无脊椎动物中也至少有一个成员是保守的。我们的分析显示，受精卵基本上没有miRNAs，它们的表达在囊胚期开始，伴随着由紧密排列的多拷贝基因编码的斑马鱼特异性miRNA家族。我们提供了考虑到进化保守程度的斑马鱼miRNA靶标的计算预测。除了miRNAs，我们还鉴定出一类显著的与重复序列相关的小干扰RNA（rasiRNAs）。
MicroRNAs (miRNAs) represent a family of small, regulatory, noncoding RNAs that are found in plants and animals. Here, we describe the miRNA profile of the zebrafish Danio rerio resolved in a developmental and cell-type-specific manner. The profiles were obtained from larger-scale sequencing of small RNA libraries prepared from developmentally staged zebrafish, and two adult fibroblast cell lines derived from the caudal fin (ZFL) and the liver epithelium (SJD). We identified a total of 154 distinct miRNAs expressed from 343 miRNA genes. Other experimental/computational sources support an additional 10 miRNAs encoded by 19 genes. The miRNAs can be classified into 87 distinct families. Cross-species comparison indicates that 81 families are conserved in mammals, 17 of which also have at least one member conserved in an invertebrate. Our analysis reveals that the zygotes are essentially devoid of miRNAs and that their expression begins during the blastula period with a zebrafish-specific family of miRNAs encoded by closely spaced multicopy genes. Computational predictions of zebrafish miRNA targets are provided that take into account the depth of evolutionary conservation. Besides miRNAs, we identified a prominent class of repeat-associated small interfering RNAs (rasiRNAs).