Hill Jonathon T, Demarest Bradley, Gorsi Bushra, Smith Megan, Yost H Joseph
Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112, USA
Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA.
Development. 2017 Oct 1;144(19):3487-3498. doi: 10.1242/dev.154146. Epub 2017 Aug 14.
During embryogenesis the heart forms as a linear tube that then undergoes multiple simultaneous morphogenetic events to obtain its mature shape. To understand the gene regulatory networks (GRNs) driving this phase of heart development, during which many congenital heart disease malformations likely arise, we conducted an RNA-seq timecourse in zebrafish from 30 hpf to 72 hpf and identified 5861 genes with altered expression. We clustered the genes by temporal expression pattern, identified transcription factor binding motifs enriched in each cluster, and generated a model GRN for the major gene batteries in heart morphogenesis. This approach predicted hundreds of regulatory interactions and found batteries enriched in specific cell and tissue types, indicating that the approach can be used to narrow the search for novel genetic markers and regulatory interactions. Subsequent analyses confirmed the GRN using two mutants, and , and identified sets of duplicated zebrafish genes that do not show temporal subfunctionalization. This dataset provides an essential resource for future studies on the genetic/epigenetic pathways implicated in congenital heart defects and the mechanisms of cardiac transcriptional regulation.
在胚胎发生过程中，心脏最初形成一条线性管，随后经历多个同时发生的形态发生事件以获得其成熟形态。为了理解驱动心脏发育这一阶段的基因调控网络（GRN），在此阶段可能会出现许多先天性心脏病畸形，我们在斑马鱼中进行了从30小时胚胎期（hpf）到72 hpf的RNA测序时间进程研究，并鉴定出5861个表达发生改变的基因。我们根据时间表达模式对基因进行聚类，确定每个聚类中富集的转录因子结合基序，并生成了心脏形态发生中主要基因簇的GRN模型。这种方法预测了数百种调控相互作用，并发现了在特定细胞和组织类型中富集的基因簇，表明该方法可用于缩小对新型遗传标记和调控相互作用的搜索范围。随后的分析使用两个突变体 和 证实了GRN，并鉴定出未表现出时间亚功能化的斑马鱼重复基因集。该数据集为未来关于先天性心脏缺陷所涉及的遗传/表观遗传途径以及心脏转录调控机制的研究提供了重要资源。
