Botman Daniel, Jansson Fredrik, Röttinger Eric, Martindale Mark Q, de Jong Johann, Kaandorp Jaap A
Computational Science, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands.
Université Nice Sophia Antipolis, Institute for Research on Cancer and Aging, Nice (IRCAN), UMR 7284, Nice, France.
BMC Syst Biol. 2015 Sep 24;9:63. doi: 10.1186/s12918-015-0209-4.
The spatial distribution of many genes has been visualized during the embryonic development in the starlet sea anemone Nematostella vectensis in the last decade. In situ hybridization images are available in the Kahi Kai gene expression database, and a method has been developed to quantify spatial gene expression patterns of N. vectensis. In this paper, gene expression quantification is performed on a wide range of gene expression patterns from this database and descriptions of observed expression domains are stored in a separate database for further analysis.
Spatial gene expression from suitable in situ hybridization images has been quantified with the GenExp program. A correlation analysis has been performed on the resulting numerical gene expression profiles for each stage. Based on the correlated clusters of spatial gene expression and detailed descriptions of gene expression domains, various mechanisms for developmental gene expression are proposed.
In the blastula and gastrula stages of development in N. vectensis, its continuous sheet of cells is partitioned into correlating gene expression domains. During progressing development, these regions likely correspond to different fates. A statistical analysis shows that genes generally remain expressed during the planula stages in those major regions that they occupy at the end of gastrulation.
Observed shifts in gene expression domain boundaries suggest that elongation in the planula stage mainly occurs in the vegetal ring under the influence of the gene Rx. The secondary body axis in N. vectensis is proposed to be determined at the mid blastula transition.
Early gene expression domains in N. vectensis appear to maintain a positional order along the primary body axis. Early determination in N. vectensis occurs in two stages: expression in broad circles and rings in the blastula is consolidated during gastrulation, and more complex expression patterns appear in the planula within these broad regions. Quantification and comparison of gene expression patterns across a database can generate hypotheses about collective cell movements before these movements are measured directly.
在过去十年中，人们已经观察到许多基因在星状海葵（Nematostella vectensis）胚胎发育过程中的空间分布情况。原位杂交图像可在卡希凯伊基因表达数据库中获取，并且已经开发出一种方法来量化星状海葵的空间基因表达模式。在本文中，我们对该数据库中广泛的基因表达模式进行了基因表达定量分析，并将观察到的表达域描述存储在一个单独的数据库中以便进一步分析。
使用GenExp程序对合适的原位杂交图像中的空间基因表达进行了定量分析。对每个阶段得到的数字基因表达谱进行了相关性分析。基于空间基因表达的相关聚类以及基因表达域的详细描述，提出了发育基因表达的各种机制。
在星状海葵发育的囊胚期和原肠胚期，其连续的细胞片层被划分为相关的基因表达域。在发育过程中，这些区域可能对应不同的命运。统计分析表明，在原肠胚后期占据的那些主要区域中，基因在浮浪幼虫阶段通常仍保持表达。
观察到的基因表达域边界的变化表明，浮浪幼虫阶段的伸长主要发生在基因Rx影响下的植物环中。星状海葵的次生体轴被认为是在囊胚中期转变时确定的。
星状海葵早期的基因表达域似乎沿着主要体轴保持位置顺序。星状海葵的早期确定分两个阶段进行：囊胚期广泛的圆圈和环中的表达在原肠胚期得到巩固，在这些广泛区域内的浮浪幼虫中出现更复杂的表达模式。跨数据库对基因表达模式进行定量和比较，可以在直接测量这些细胞运动之前生成关于集体细胞运动的假设。
