Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability.
Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability.
复制标题
分析未序列的Axolotl中的胚胎发育：转录组动荡和稳定性的波。
DOI：
10.1016/j.ydbio.2016.05.024
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发表时间：
2017-06-15
影响因子：
2.7
通讯作者：
Stewart R
中科院分区：
文献类型：
--
作者：
Jiang P;Nelson JD;Leng N;Collins M;Swanson S;Dewey CN;Thomson JA;Stewart R
墨西哥蝾螈（Ambystoma mexicanum）长期以来一直是生物学研究的对象，这主要是由于其出色的再生能力。然而，控制其胚胎发育的基因表达程序尚未得到充分研究，特别是与其他两栖动物模型物种相比。因此，我们对胚胎发育的17个阶段进行了全转录组polyA+ RNA测序实验。由于蝾螈基因组未测序且其基因注释不完整，我们为每个阶段构建了从头转录组组件，并通过将表达的重叠群与其他生物体中的已知基因进行比较来获得功能注释。在评估随时间变化的差异表达基因的数量时，我们发现了三波实质性转录组剧变，每波都伴随着一段相对转录组稳定的时期。第一波剧变发生在一细胞阶段和二细胞阶段之间。我们发现，每单位时间差异表达基因的数量在一细胞和二细胞阶段之间高于囊胚中期转变（MBT）（合子基因组激活时期）。我们使用总 RNA 测序来证明，绝大多数在一细胞和二细胞阶段之间具有增强的 PolyA+ 信号的基因是由聚腺苷酸化而不是从头转录引起的。第一个稳定期开始于两细胞期之后，一直持续到囊胚中期转变，对应于两栖动物发育中转录静止的 MBT 前阶段。接下来是与合子基因组激活相对应的差异基因表达峰值，以及从阶段 9 到阶段 11 的转录组稳定阶段。我们观察到阶段 11 和阶段 14 之间的第三波转录组变化，随后是最后的稳定期。最后两个稳定阶段以前在两栖动物中尚未有记录，对应于蝾螈胚胎主要形态发生变化的时间：原肠胚形成和神经形成。这些结果对两栖动物胚胎发生早期阶段的整体基因表达产生了新的见解，并将有助于进一步将蝾螈发展为发育和再生生物学的模型物种。
The axolotl (Ambystoma mexicanum) has long been the subject of biological research, primarily owing to its outstanding regenerative capabilities. However, the gene expression programs governing its embryonic development are particularly underexplored, especially when compared to other amphibian model species. Therefore, we performed whole transcriptome polyA+ RNA sequencing experiments on 17 stages of embryonic development. As the axolotl genome is unsequenced and its gene annotation is incomplete, we built de novo transcriptome assemblies for each stage and garnered functional annotation by comparing expressed contigs with known genes in other organisms. In evaluating the number of differentially expressed genes over time, we identify three waves of substantial transcriptome upheaval each followed by a period of relative transcriptome stability. The first wave of upheaval is between the one and two cell stage. We show that the number of differentially expressed genes per unit time is higher between the one and two cell stage than it is across the mid-blastula transition (MBT), the period of zygotic genome activation. We use total RNA sequencing to demonstrate that the vast majority of genes with increasing polyA+ signal between the one and two cell stage result from polyadenylation rather than de novo transcription. The first stable phase begins after the two cell stage and continues until the mid-blastula transition, corresponding with the pre-MBT phase of transcriptional quiescence in amphibian development. Following this is a peak of differential gene expression corresponding with the activation of the zygotic genome and a phase of transcriptomic stability from stages 9 to 11. We observe a third wave of transcriptomic change between stages 11 and 14, followed by a final stable period. The last two stable phases have not been documented in amphibians previously and correspond to times of major morphogenic change in the axolotl embryo: gastrulation and neurulation. These results yield new insights into global gene expression during early stages of amphibian embryogenesis and will help to further develop the axolotl as a model species for developmental and regenerative biology.