Characterization of differential transcript abundance through time during Nematostella vectensis development.
Characterization of differential transcript abundance through time during Nematostella vectensis development.
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DOI：
10.1186/1471-2164-14-266
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发表时间：
2013-04-19
期刊：
影响因子：
4.4
通讯作者：
Dunn CW
中科院分区：
文献类型：
--
作者：
Helm RR;Siebert S;Tulin S;Smith J;Dunn CW
凹线海葵（Nematostella vectensis）是一种穴居海葵，已成为研究刺胞动物发育的热门物种。在以前的研究中，各种基因的表达已被描述在N。vectensismRNA原位杂交。这提供了详细的空间分辨率和表达变化的定性视角。然而，很少有人知道广泛的转录组水平模式的基因表达随着时间的推移。在这里，我们检查N的表达式。通过定量RNA-seq.我们提供了一个在转录组的变化，通过发展的概述，并检查母系合子的过渡，这是很难调查与其他工具。我们测量了N.在发育的六个时间点，用RNA-seq对vectensis进行检测：受精卵（受精后2小时（HPF））、早期囊胚（7 HPF）、中期囊胚（12 HPF）、原肠胚（24 HPF）、浮胚（受精后5天（DPF））和年轻息肉（10 DPF）。合子表达的主要波出现在7-12 HPF之间，但在2-7 HPF之间也有一些变化。转录丰度的最动态变化发生在囊胚晚期和原肠胚早期阶段之间。在原肠胚和浮胚之间有更多的转录本被上调，而在浮胚和息肉之间有相对较低数量的转录本发生显著变化。在母体到合子的转变中，我们确定了一个在发育早期减少的母体因素的子集，并且可能在抑制合子基因表达中起作用。在第一个合子表达的基因中，有一些基因的蛋白质可能参与母体RNA的降解。这里提出的方法是高度互补的基因表达的空间模式的先前研究，因为它提供了一个广泛的基因组通过时间的定量视角，但缺乏空间分辨率。除了解决上述问题，我们的工作提供了一个注释矩阵，其他研究人员可以使用它来检查基因和发育事件，我们没有在这里详细检查。
Nematostella vectensis, a burrowing sea anemone, has become a popular species for the study of cnidarian development. In previous studies, the expression of a variety of genes has been characterized during N. vectensis development with in situ mRNA hybridization. This has provided detailed spatial resolution and a qualitative perspective on changes in expression. However, little is known about broad transcriptome-level patterns of gene expression through time. Here we examine the expression of N. vectensis genes through the course of development with quantitative RNA-seq. We provide an overview of changes in the transcriptome through development, and examine the maternal to zygotic transition, which has been difficult to investigate with other tools. We measured transcript abundance in N. vectensis with RNA-seq at six time points in development: zygote (2 hours post fertilization (HPF)), early blastula (7 HPF), mid-blastula (12 HPF), gastrula (24 HPF), planula (5 days post fertilization (DPF)) and young polyp (10 DPF). The major wave of zygotic expression appears between 7–12 HPF, though some changes occur between 2–7 HPF. The most dynamic changes in transcript abundance occur between the late blastula and early gastrula stages. More transcripts are upregulated between the gastrula and planula than downregulated, and a comparatively lower number of transcripts significantly change between planula and polyp. Within the maternal to zygotic transition, we identified a subset of maternal factors that decrease early in development, and likely play a role in suppressing zygotic gene expression. Among the first genes to be expressed zygotically are genes whose proteins may be involved in the degradation of maternal RNA. The approach presented here is highly complementary to prior studies on spatial patterns of gene expression, as it provides a quantitative perspective on a broad set of genes through time but lacks spatial resolution. In addition to addressing the problems identified above, our work provides an annotated matrix that other investigators can use to examine genes and developmental events that we do not examine in detail here.
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