Decoding the dynamics and regulation of parental allelic expression at single-cell resolution

项目摘要 母系和父系基因的遗传是正常发育所必需的。然而， 我们不是父母双方基因的平等产物。只有一个特定基因的排他性表达 在亲本中，等位基因效应已被认为影响遗传结构和疾病风险，但几乎没有。 了解他们对发展的贡献。全面认识的根本障碍 亲本遗传及其发育调控是不完全覆盖的局限性 发育中胚胎内每个细胞的差异，以及等位基因序列之间区分的准确性。作为 脊椎动物现存的近亲，肠囊藻属和萨维尼亚囊藻属提供了适当程度的 多细胞生物体之间的简单性和母体和父体基因组的极端差异 克服这些限制。在这里，我建议使用杂交海鞘来阐明 发育过程中的等位基因在单细胞分辨率下的表达。 在K99阶段，我将致力于目标1并启动目标2。 利用单细胞重建杂交胚胎时间表达谱的参考谱系图 RNA-Seq技术。由于海鞘细胞数量很少，我希望获得全面的覆盖。 发育过程中的每一种细胞类型，包括罕见的神经元亚型。在目标1中，基于极端 杂交胚胎中亲本基因组序列之间的差异，我将描述等位基因特异性 表达每个已定义的细胞谱系，并开发能够同时分析 单细胞中的基因表达和染色质可及性，这将把父母的表达模式与 推测为顺式调控的DNA序列。在目标1完成后，我希望建立潜力 等位基因特异性表达与单个细胞和细胞的规格和形态发生的关系 血统。 在R00阶段，基于我在K99阶段获得的培训，我将致力于高度创新 目标2，其中我计划开发空间转录技术，以增加另一个维度 在细胞-细胞接触的背景下，剖析等位基因特异的表达模式及其调控。vt.在.的基础上 成功完成目标1和目标2，这种数据丰富的方法将极大地增强我们对 父母的遗传及其调控，最终让我们更接近整体性和数量化 对胚胎发育的理解。它还为我勾勒出一份广泛的职业发展计划 在莱文教授的指导下完成我的培训，并过渡到一名独立的学者 通过建立一个多学科的研究计划来定位。

Project Summary The inheritance of both the maternal and paternal genes is required for normal development to proceed. Yet, we are not equal products of both parents’ genes. With exclusive expression of specific genes from only one parent, allelic effects have been suggested to influence genetic architecture and disease risk, but little is known about their contributions to development. Fundamental obstacles of comprehensively understanding the parental genetic inheritance and its regulation during development are limitations in incomplete coverage of each cell within developing embryos, and the accuracy of differentiation between allele sequences. As the closest living relatives of vertebrates, the ascidians C. intestinalis and C. savignyi provide the right degree of simplicity among multicellular organisms and extreme divergence of the maternal and paternal genomes for overcoming these limitations. Here I propose to use hybrid ascidians to elucidate the regulatory grammar of allele-specific gene expression during development at single cell resolution. During the K99 phase, I will work on Aim 1 and initiate Aim 2. Based on my preliminary results, I have reconstructed the reference lineage map of temporal expression profiles for hybrid embryos using single cell RNA-Seq technology. Due to the small cell numbers of ascidians, I expect to obtain comprehensive coverage of every cell type during development, including rare neuronal subtypes. In Aim 1, based on the extreme divergence between parental genomic sequences in hybrid embryos, I will characterize allele-specific expression of each defined cell lineage, and develop novel approaches that are able to simultaneously profile gene expression and chromatin accessibility in single cells, which will link parental expression patterns with putative cis-regulatory DNA sequences. Upon the completion of Aim 1, I expect to establish potential associations of allelic-specific expression and the specification and morphogenesis of individual cells and cell lineages. During the R00 phase, based on my training gained during the K99 phase, I will work on the highly innovative Aim 2, in which I plan to develop the spatial transcriptomics technique in order to add another dimension to dissect the allele-specific expression pattern and its regulation in the context of cell-cell contacts. Upon successful completion of Aim 1 and Aim 2, this data-rich approach will greatly enhance our understanding of parental genetic inheritance and its regulation, and eventually let us move closer to a holistic and quantitative understanding of embryonic development. It also outlines an extensive career development plan for me to complete my training under the mentorship of Prof. Levine and the transition to an independent academic position by establishing a multi-disciplinary research program.