NSF Postdoctoral Fellowship in Biology FY 2021: Deciphering grammatical rules of notochord enhancers and their role in notochord development in Ciona intestinalis

该行动资助2021财年NSF生物学博士后研究奖学金，研究基因组，环境和表型之间相互作用的生命规则的综合研究。该奖学金支持将以创新方式为《生活规则》领域作出贡献的研究员的研究和培训。早期发育阶段的细胞分化成生物体成体中存在的所有细胞类型。这些转变是基因表达变化以及随后RNA和蛋白质产物变化的结果。增强子是对基因表达的位置和时间指令进行编码的遗传元件，确保组织在发育过程中在正确的时间和地点产生；增强子序列的变异与在许多方面影响生物体的结果有关。然而，数以百万计的增强子序列变异使得确定增强子基因型与其表达（表型）之间的因果关系变得困难。该研究员将研究基因表达的控制是如何在增强子内编码的，以及增强子与这些有机性状之间的联系。研究成果将由研究员通过本科生研究人员的指导和公共科学推广计划传达给不同的受众。这项研究将检查脊索中的组织特异性增强子，脊索是一种为邻近组织提供结构支持和发育模式信号的胚胎组织。为了研究脊索特异性增强子如何编码脊索活性，研究员将创建合成脊索增强子变异报告DNA结构，并将其引入海鞘（Ciona ninteinalis）的受精卵中。Ciona胚胎将通过显微镜测量荧光报告子活性和RNA测序独特的DNA条形码表达来筛选增强子活性。研究员将使用增强子活动屏幕生成的数据来识别脊索增强子的共同特征。这些脊索增强子特征将被用于现有的计算管道，以识别Ciona基因组中潜在的脊索增强子。此外，研究员将在受精卵中使用靶向基因编辑来研究脊索特异性增强子内的遗传变异如何影响基因表达（由选定的增强子控制的基因）和脊索发育（表型）。本研究产生的数据将被纳入本科生的互动客座讲座；研究员还将获得大学水平的教学和指导、分析大数据集的计算方法和科学交流方面的培训和经验。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2021, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment and Phenotypes. The fellowship supports research and training of the Fellow that will contribute to the area of Rules of Life in innovative ways. Early developmental stage cells differentiate into all of the cell types present in an organism’s adult body. These transitions are the result of changes in gene expression and the subsequent changes in RNA and protein products. Enhancers are genetic elements that encode instructions for the location and timing of gene expression, which ensures that tissues are created at the right time and place during development; variations in enhancer sequences are associated with outcomes that impact organisms in many ways. However, the millions of enhancer sequence variations have made it difficult to determine causal links between enhancer genotype and its expression (phenotype). The Fellow will investigate how control of gene expression is encoded within enhancers and the links between enhancers and these organismal traits. Research findings will be communicated by the Fellow to diverse audiences through mentorship of undergraduate student researchers and public science outreach programs.This research will examine tissue-specific enhancers in the notochord, an embryonic tissue that provides structural support and developmental patterning signals to adjacent tissues. To study how notochord activity is encoded within notochord-specific enhancers, the Fellow will create synthetic notochord enhancer variant reporter DNA constructs, which will be introduced into fertilized eggs of the sea squirt, Ciona intestinalis (Ciona). Ciona embryos will be screened for enhancer activity by measuring fluorescent reporter activity with microscopy and unique DNA barcode expression with RNA sequencing. The Fellow will use data generated from enhancer activity screens to identify common features of notochord enhancers. These notochord enhancer features will then be used to inform an existing computational pipeline to identify potential notochord enhancers within the Ciona genome. Additionally, the Fellow will use targeted gene editing in fertilized Ciona eggs to examine how genetic variations within notochord-specific enhancers impact gene expression (of genes controlled by selected enhancers) and notochord development (phenotype). Data generated from this research will be incorporated into interactive guest lectures for undergraduates; the Fellow will also gain training and experience in university-level teaching and mentorship, computational methods to analyze large data sets, and scientific communication.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.