Discovery of craniofacial genes capable of compensation through evolutionary mutant model

通过进化突变模型发现能够补偿的颅面基因

• 批准号: 10606667
• 负责人: Hope M Healey
• 金额: $ 4.12万
• 依托单位: UNIVERSITY OF OREGON
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-01-01 至 2025-12-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10606667
• 关键词: Amaze; Animal Model; Atlases; Biological Assay; Branchial arch structure; CRISPR/Cas technology; Cartilage; Cells; Cephalic; Chromatin; Cleft Palate; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Congenital Abnormality; Craniofacial Abnormalities; Craniosynostosis; Data; Deglutition Disorders; Developmental Gene; Disease; Elements; Enhancers; Ethmoid bone structure; Etiology; Exhibits; Face; Financial compensation; Fishes; Gasterosteidae; Gene Expression; Gene Expression Profile; Gene-Modified; Genes; Genetic; Genetic Transcription; Genus Hippocampus; Goals; Head; Health; Human; In Situ Hybridization; Induced Mutation; Knock-out; Knowledge; Laboratory Study; Lead; Libraries; Microcephaly; Modeling; Morphology; Mutation; Neural Crest; Neural Crest Cell; Odontoma; Outcome; Pathway Analysis; Patients; Phenocopy; Play; Proteins; RNA; Regulatory Element; Research; Resolution; Role; Signal Transduction; Skeleton; Structure; Symptoms; Syndrome; System; Testing; Tooth Loss; Tooth structure; Untranslated RNA; Variant; Vertebrates; Work; Zebrafish; bone; cartilage development; craniofacial; craniofacial bone; craniofacial development; craniofacial disorder; cranium; developmental genetics; epigenomics; gene function; gene network; gene regulatory network; genome-wide; human disease; improved; member; mutant; novel; premature; single cell analysis; single cell sequencing; single-cell RNA sequencing; tool; tumor; whole genome

The craniofacial skeleton of vertebrates develops under the guidance of highly conserved gene regulatory networks active in cranial neural crest cells. Alterations to these networks can lead to numerous human disorders such as cleft palate, premature closing of the skull, and reduced teeth size. Laboratory studies of traditional animal models have contributed to our understanding of the functional role of the core gene networks but have largely involved significant gene modifications through induced mutations. As such, these systems may be less fruitful for discovering how craniofacial gene networks adapt to gene loss and unique morphologies because the abrogation of gene function can have a significant systemic effect. A complementary approach is the study of evolutionary mutant models with adaptations that recapitulate human diseases with similar altered morphology and/or gene changes. Variation that is detrimental in humans may be neutral or even beneficial in evolutionary mutant models, therefore allowing the study of gene regulatory networks in the context of normal organismal function. Previously, limited genetic tools necessitated examining craniofacial models in select animal models. Recent advances in sequencing (e.g. single cell) and functional (e.g. CRISPR) technologies enable fruitful studies in less traditional species. By integrating single cell analysis, whole genome comparisons, and functional assays, gene regulatory networks can be successfully compared across species. My project will evaluate craniofacial gene network conservation and malleability through cross species comparisons and studies of syngnathid fishes (pipefish, seahorses, and seadragons). These amazing fish have elongated ethmoid bones, altered hyoids, and a complete loss of teeth. In addition, we recently discovered that syngnathids have lost key craniofacial developmental genes (fgf3 and fgf4) that we hypothesize has led to rewiring of craniofacial gene regulatory networks. First, I will complete single cell sequencing to capture the RNA and chromatin accessibility of cells in zebrafish and stickleback (fish models with ‘normal’ craniofacial features), and pipefish (evolutionary mutant model). Second, I will build whole genome alignments of these fish and 13 other vertebrates to identify regulatory elements. Third, I will functionally test five identified regulatory elements using zebrafish. These three approaches will reveal how well conserved craniofacial gene expression patterns and sequences are across numerous species. In addition, genes and sequences unique to syngnathids may play a role in adaptation to gene loss and produce altered faces, and may identify novel genes and regulatory factors that can lead to human therapies.

脊椎动物的颅面骨骼是在高度的 在颅神经嵴细胞中活跃的保守基因调控网络。这些改动 网络可以导致许多人类疾病，如腭裂，过早关闭的 头骨和牙齿变小传统动物模型的实验室研究 我们对核心基因网络的功能作用的理解，但在很大程度上涉及 通过诱导突变进行显著的基因修饰。因此，这些系统可能更少 对于发现颅面基因网络如何适应基因丢失和独特的 这是因为基因功能的废除可能具有显著的系统性影响。一 一种互补的方法是研究具有适应性的进化突变模型， 以类似的改变的形态和/或基因变化概括人类疾病。变化 对人类有害的基因在进化突变模型中可能是中性的，甚至是有益的， 因此，允许在正常生物体的背景下研究基因调控网络， 功能以前，有限的遗传工具需要检查颅面模型， 动物模型测序（例如单细胞）和功能（例如CRISPR）的最新进展 技术使对不太传统的物种进行富有成效的研究成为可能。通过整合单细胞分析， 全基因组比较和功能测定，基因调控网络可以是 成功地进行了跨物种的比较。我的项目将评估颅面基因网络 通过对海龙类的跨物种比较和研究， 鱼类（尖嘴鱼、海马和海龙）。这些神奇的鱼有着细长的筛骨 骨头舌骨变形牙齿完全脱落另外，我们最近发现， 我们推测，海龙类已经丢失了关键的颅面发育基因（fgf 3和fgf 4）， 导致了颅面基因调控网络的重组。首先，我将完成单细胞 测序以捕获斑马鱼和棘鱼细胞的RNA和染色质可及性 (fish具有“正常”颅面特征的模型）和海龙（进化突变模型）。 其次，我将建立这些鱼和其他13种脊椎动物的全基因组比对， 监管要素。第三，我将对五个确定的监管要素进行功能测试， 斑马鱼这三种方法将揭示颅面基因表达的保守程度 模式和序列在许多物种中都存在。此外，基因和序列 海龙科特有的一种基因可能在适应基因缺失和改变面孔方面发挥作用， 可能会发现新的基因和调节因子，可以导致人类治疗。