The gene regulatory basis of genetic compensation during neural crest induction
The gene regulatory basis of genetic compensation during neural crest induction
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DOI：
10.1371/journal.pgen.1008213
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发表时间：
2019-06-01
期刊：
影响因子：
4.5
通讯作者：
Busch-Nentwich, Elisabeth M.
中科院分区：
文献类型：
--
作者：
Dooley, Christopher M.;Wali, Neha;Busch-Nentwich, Elisabeth M.
神经嵴（NC）是一种脊椎动物特有的细胞类型，有助于所有三个胚层的各种不同组织。负责神经嵴形成的基因调节网络（GRN）在脊椎动物中是保守的。诱导NC GRN的核心是AP-2和SoxE转录因子。通过这些转录因子中的一些能够补偿基因家族成员的功能丧失来确保NC诱导的稳健性。然而，补偿的基因调控事件知之甚少。我们已经使用基因敲除和RNA测序策略来剖析斑马鱼的NC诱导和补偿。我们使用tfap 2a和tfap 2c的双突变体基因消融NC，或者用sox 10和mitfa敲除去除NC的特定子集，并在多个时间点上降低全基因组的基因表达水平。我们发现，通过一个单一的野生型等位基因的tfap 2c的补偿是能够维持早期NC诱导和分化的tfap 2a功能的情况下，但许多靶基因有异常的表达水平，因此显示敏感性降低tfap 2剂量。这种形态学和分子表型的分离确定了早期NC发育所需的核心基因组。我们还确定了15体节阶段作为分子表型的峰值，其在24 hpf时强烈减少，即使形态表型变得更加明显。使用基因敲除，我们将以前未表征的基因与色素细胞发育联系起来，并建立了母体Hippo信号在黑素细胞分化中的作用。这项工作扩展和完善了NC GRN，同时也揭示了通过旁系同源物进行遗传补偿的转录基础。作者总结胚胎发育是一个复杂的过程，需要基因在正确的时间和地点活跃。生物体已经进化出一种机制，即使基因不能发挥作用，也能确保发育计划的忠实执行。例如，在一个称为遗传补偿的过程中，一个或多个基因被激活以响应另一个基因的功能丧失。在这项工作中，我们使用斑马鱼模型来研究两个相关基因tfap 2a和tfap 2c如何相互作用以确保神经嵴的建立，神经嵴是一种脊椎动物特有的细胞类型，有助于许多不同的组织。失去tfap 2a活性会导致轻微的形态学缺陷，而失去tfap 2c则没有明显的影响。然而，当两者都不活跃时，胚胎由于缺乏神经嵴衍生的组织而严重异常。在这里，我们发现，tfap 2a的损失触发上调tfap 2c，防止神经嵴组织的损失。然而，通常由tfap 2a调控的基因对tfap 2c的反应不同，这使我们能够识别Ap 2网络的第一层和神经嵴生物学的新参与者。我们的工作表明，表达签名的部分，但形态上足够的，遗传补偿提供了一个机会，解剖基因调控网络。
The neural crest (NC) is a vertebrate-specific cell type that contributes to a wide range of different tissues across all three germ layers. The gene regulatory network (GRN) responsible for the formation of neural crest is conserved across vertebrates. Central to the induction of the NC GRN are AP-2 and SoxE transcription factors. NC induction robustness is ensured through the ability of some of these transcription factors to compensate loss of function of gene family members. However the gene regulatory events underlying compensation are poorly understood. We have used gene knockout and RNA sequencing strategies to dissect NC induction and compensation in zebrafish. We genetically ablate the NC using double mutants of tfap2a;tfap2c or remove specific subsets of the NC with sox10 and mitfa knockouts and characterise genome-wide gene expression levels across multiple time points. We find that compensation through a single wild-type allele of tfap2c is capable of maintaining early NC induction and differentiation in the absence of tfap2a function, but many target genes have abnormal expression levels and therefore show sensitivity to the reduced tfap2 dosage. This separation of morphological and molecular phenotypes identifies a core set of genes required for early NC development. We also identify the 15 somites stage as the peak of the molecular phenotype which strongly diminishes at 24 hpf even as the morphological phenotype becomes more apparent. Using gene knockouts, we associate previously uncharacterised genes with pigment cell development and establish a role for maternal Hippo signalling in melanocyte differentiation. This work extends and refines the NC GRN while also uncovering the transcriptional basis of genetic compensation via paralogues.Author summary Embryonic development is an intricate process that requires genes to be active at the right time and place. Organisms have evolved mechanisms that ensure faithful execution of developmental programmes even if genes fail to function. For example, in a process called genetic compensation, one or more genes become activated in response to loss of function of another. In this work we use the zebrafish model to investigate how two related genes, tfap2a and tfap2c, interact to ensure establishment of the neural crest, a vertebrate-specific cell type that contributes to many different tissues. Losing tfap2a activity causes mild morphological defects and losing tfap2c has no visible effect. Yet when both are inactive, embryos are severely abnormal due to lack of neural crest-derived tissues. Here we show that loss of tfap2a triggers upregulation of tfap2c which prevents the loss of neural crest tissue. However, the genes normally regulated by tfap2a respond differently to tfap2c allowing us to identify the first tier of the Ap2 network and new players in neural crest biology. Our work demonstrates that the expression signature of partial, but morphologically sufficient, genetic compensation provides an opportunity to dissect gene regulatory networks.