Department of Genetics, Eötvös Loránd University, Budapest, Hungary.
PLoS One. 2013 Jul 29;8(7):e70053. doi: 10.1371/journal.pone.0070053. Print 2013.
Understanding the molecular interactions that lead to the establishment of the major body axes during embryogenesis is one of the main goals of developmental biology. Although the past two decades have revolutionized our knowledge about the genetic basis of these patterning processes, the list of genes involved in axis formation is unlikely to be complete. In order to identify new genes involved in the establishment of the dorsoventral (DV) axis during early stages of zebrafish embryonic development, we employed next generation sequencing for full transcriptome analysis of normal embryos and embryos lacking overt DV pattern. A combination of different statistical approaches yielded 41 differentially expressed candidate genes and we confirmed by in situ hybridization the early dorsal expression of 32 genes that are transcribed shortly after the onset of zygotic transcription. Although promoter analysis of the validated genes suggests no general enrichment for the binding sites of early acting transcription factors, most of these genes carry "bivalent" epigenetic histone modifications at the time when zygotic transcription is initiated, suggesting a "poised" transcriptional status. Our results reveal some new candidates of the dorsal gene regulatory network and suggest that a plurality of the earliest upregulated genes on the dorsal side have a role in the modulation of the canonical Wnt pathway.
理解导致胚胎发生过程中主要身体轴建立的分子相互作用是发育生物学的主要目标之一。尽管过去二十年极大地改变了我们对这些模式形成过程遗传基础的认识，但参与轴形成的基因列表不太可能完整。为了鉴定新的基因参与斑马鱼胚胎发育早期背腹（DV）轴的建立，我们采用下一代测序对正常胚胎和明显缺乏 DV 模式的胚胎进行全转录组分析。不同统计方法的组合产生了 41 个差异表达的候选基因，我们通过原位杂交证实了 32 个基因的早期背侧表达，这些基因在合子转录开始后不久转录。尽管验证基因的启动子分析表明没有早期作用的转录因子结合位点的一般富集，但这些基因中的大多数在合子转录开始时携带“双重”表观遗传组蛋白修饰，表明存在“预备”转录状态。我们的结果揭示了背侧基因调控网络的一些新候选基因，并表明背侧最早上调的基因中的大多数在调节经典 Wnt 途径中起作用。
