Molecular anatomy of palate development

Background: The FACEBASE consortium was established in part to create a central resource for craniofacial researchers. One purpose is to provide a molecular anatomy of craniofacial development. To this end we have used a combination of laser capture microdissection and RNA-Seq to define the gene expression programs driving development of the murine palate. Results: We focused on the E14.5 palate, soon after medial fusion of the two palatal shelves. The palate was divided into multiple compartments, including medial and lateral, as well as oral and nasal, for both the anterior and posterior domains. A total of 25 RNA-Seq datasets were generated. The results provide a comprehensive view of the region specific expression of all transcription factors, growth factors and receptors. Paracrine interactions can be inferred from flanking compartment growth factor/receptor expression patterns. The results are validated primarily through very high concordance with extensive previously published gene expression data for the developing palate. In addition selected immunostain validations were carried out. Conclusions: This report provides an RNA-Seq based atlas of gene expression patterns driving palate development at microanatomic resolution. This FACEBASE resource is designed to fuel discovery by the craniofacial research community. Laser capture microdissection and RNA-seq were used to generate gene expression profiles of different compartments of the mouse E14.5 developing palate背景：FACEBASE联盟（FACEBASE）的成立初衷之一是为颅面研究人员构建核心资源库。其核心目标之一是提供颅面发育的分子解剖学图谱。为此，本研究结合激光捕获显微切割（laser capture microdissection）与RNA测序（RNA-Seq）技术，明确了驱动小鼠腭部发育的基因表达调控程序。 结果：本研究聚焦于双侧腭突内侧融合后不久的E14.5小鼠腭部样本。将腭部按前后区域划分为内侧、外侧、口腔侧与鼻腔侧多个亚解剖分区。最终共生成25组RNA-Seq数据集。研究结果全面呈现了所有转录因子、生长因子及受体的区域特异性表达模式。可通过相邻亚区的生长因子/受体表达谱，推断腭部发育中的旁分泌相互作用。本研究结果主要通过与既往发表的大量发育腭部基因表达数据的高度一致性得到验证，此外还开展了部分免疫染色验证实验。 结论：本报告提供了具备微观解剖分辨率的、基于RNA-Seq技术的腭部发育驱动基因表达图谱。该FACEBASE资源库旨在助力颅面研究群体开展探索性研究。本研究通过激光捕获显微切割与RNA测序技术，获取了小鼠E14.5发育阶段腭部不同亚区的基因表达谱。