Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements.
Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements.
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DOI：
10.1101/gr.144469.112
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发表时间：
2014-01
期刊：
影响因子：
7
通讯作者：
Hill CS
中科院分区：
文献类型：
--
作者：
Harding JL;Horswell S;Heliot C;Armisen J;Zimmerman LB;Luscombe NM;Miska EA;Hill CS
小RNA基因表达的控制对脊椎动物胚胎的发育过程至关重要。为了确定小RNA表达的动态并揭示早期脊椎动物胚胎中的新型小RNA，我们对热带爪蟾胚胎在三个发育时间点和解剖半原胚中的所有小RNA进行了高通量测序。这一分析使我们能够鉴定出新的microRNA，我们发现microRNA的表达在早期胚胎中是高度动态和空间定位的。此外，我们已经开发了一个microRNA预测管道，并证明它具有预测在青蛙，小鼠和人类实验中可检测到的新mirna的能力。通过将不同发育阶段的小RNA测序与mRNA分析相结合，我们确定了一类新的小非编码RNA，我们将其命名为siteRNAs，它们与蛋白质编码基因的内含子成簇排列。我们发现siterna来源于内含子中存在的转座因子的残余物。我们发现，与所有基因相比，含有siteRNAs簇的基因在转录上受到抑制。此外，我们还表明，对于含有siteRNA簇的单个基因来说，这是正确的，并且这些基因在特定的抑制性组蛋白修饰中富集。因此，我们的数据提示了脊椎动物中siterna介导的基因沉默的新机制，并提供了一个移动元件如何影响基因调控的例子。
Small RNA control of gene expression is critical for developmental processes in vertebrate embryos. To determine the dynamics of small RNA expression and to uncover novel small RNAs in the early vertebrate embryo, we performed high-throughput sequencing of all small RNAs in Xenopus tropicalis embryos at three developmental time points and in dissected halves of gastrula embryos. This analysis allowed us to identify novel microRNAs and we show that microRNA expression is highly dynamic and spatially localized in early embryos. In addition, we have developed a microRNA prediction pipeline and demonstrate that it has the power to predict new miRNAs that are experimentally detectable in frogs, mice, and humans. By combining the small RNA sequencing with mRNA profiling at the different developmental stages, we identify a new class of small noncoding RNAs that we name siteRNAs, which align in clusters to introns of protein-coding genes. We show that siteRNAs are derived from remnants of transposable elements present in the introns. We find that genes containing clusters of siteRNAs are transcriptionally repressed as compared with all genes. Furthermore, we show that this is true for individual genes containing siteRNA clusters, and that these genes are enriched in specific repressive histone modifications. Our data thus suggest a new mechanism of siteRNA-mediated gene silencing in vertebrates, and provide an example of how mobile elements can affect gene regulation.
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影响因子：
64.8
作者：
Baek, Daehyun;Villen, Judit;Shin, Chanseok;Camargo, Fernando D.;Gygi, Steven P.;Bartel, David P.
通讯作者：
Bartel, David P.
影响因子：
14.9
作者：
Griffiths-Jones, S;Bateman, A;Eddy, SR
通讯作者：
Eddy, SR
影响因子：
10.5
作者：
Babiarz, Joshua E.;Ruby, J. Graham;Blelloch, Robert
通讯作者：
Blelloch, Robert
影响因子：
64.8
作者：
Gonzalez, S;Klatt, P;Serrano, M
通讯作者：
Serrano, M
影响因子：
56.9
作者：
Giraldez, AJ;Mishima, Y;Schier, AF
通讯作者：
Schier, AF