Transcriptome-wide analysis of small RNA expression in early zebrafish development.
Transcriptome-wide analysis of small RNA expression in early zebrafish development.
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DOI：
10.1261/rna.029090.111
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发表时间：
2012-05
期刊：
影响因子：
4.5
通讯作者：
Chunyao Wei;Leonidas Salichos;Carli M. Wittgrove;A. Rokas;J. G. Patton
中科院分区：
文献类型：
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作者：
Chunyao Wei;Leonidas Salichos;Carli M. Wittgrove;A. Rokas;J. G. Patton
在脊椎动物早期发育过程中，大量非编码rna通过母系遗传或合子转录激活表达。这些非编码rna的确切身份、表达水平和功能在很大程度上仍然未知。miRNAs （microRNAs）和piRNAs （piwi-interacting RNAs）是两类小的非编码rna，在胚胎早期发育过程中发挥重要的基因调控作用。在这里，我们利用下一代测序技术来确定mirna和pirna在早期脊椎动物发育的四个不同阶段的时间表达模式，以斑马鱼为模型系统。对于miRNA，确定了122个不同miRNA家族中的198个已知miRNA和8个新miRNA的表达模式。在miRNAs的5‘和3’端观察到显著的序列变化，大多数额外的核苷酸以非模板定向的方式添加在3'端。对于miR-430家族，腺苷和尿嘧啶残基的添加受到发育调控，可能在母体合子过渡期间对miRNA的稳定性起作用。在大量mirna的3'端存在类似的修饰，表明在早期发育过程中对稳定性进行了广泛的调控。除了mirna，我们还发现了在早期发育过程中表达的大量且出乎意料地多样化的pirna。
During early vertebrate development, a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity, expression levels, and function for most of these noncoding RNAs remain largely unknown. miRNAs (microRNAs) and piRNAs (piwi-interacting RNAs) are two classes of small noncoding RNAs that play important roles in gene regulation during early embryonic development. Here, we utilized next-generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system. For miRNAs, the expression patterns for 198 known miRNAs within 122 different miRNA families and eight novel miRNAs were determined. Significant sequence variation was observed at the 5' and 3'ends of miRNAs, with most extra nucleotides added at the 3' end in a nontemplate directed manner. For the miR-430 family, the addition of adenosine and uracil residues is developmentally regulated and may play a role in miRNA stability during the maternal zygotic transition. Similar modification at the 3' ends of a large number of miRNAs suggests widespread regulation of stability during early development. Beside miRNAs, we also identified a large and unexpectedly diverse set of piRNAs expressed during early development.