NSF Postdoctoral Fellowship in Biology FY 2021: Analyzing the interplay of chromatin accessibility and transcription factor binding to decipher the cis-regulatory code

这一行动为NSF 2021财年生物学博士后研究奖学金提供了资金，综合研究调查了支配基因组、环境和表型之间相互作用的生命规则。该奖学金支持研究员的研究和培训，这些研究员将以创新的方式为生活规则领域做出贡献。为了使生物体正常运作，其基因的表达必须受到转录因子(Tf)的严格调控，Tf是一种结合特定DNA序列的蛋白质，以控制基因的开启或关闭。DNA序列中的变异会导致转铁蛋白的错误定位，破坏正常的基因表达，并导致疾病。因此，了解Tf结合的精确DNA序列以及周围的DNA序列如何影响Tf结合对于深入了解基因是如何调控的是必要的。然而，目前的方法只检查这些组件中的一个，并且需要大量的起始材料，从而限制了可以研究的模型系统。因此，该项目将专注于开发一种方法(CHIP-NEXT)，该方法将从少量的起始材料提供TF结合序列和周围DNA景观的全面图谱。这个项目的结果将加深我们对TF如何解释DNA序列以及DNA序列的微小变化如何对哺乳动物的发育、疾病和进化产生重大影响的理解。除了研究部分，该研究员还将向俄克拉荷马州代表性较低的美洲原住民群体提供科学推广。ChIP-NEXT将允许从同一样本中收集染色质可获得性和Tf结合数据集。为了研究染色质可及性和转铁蛋白结合的动态相互作用，在不同的时间点进行了小鼠胚胎干细胞分化的CHIP-NEXT实验。此外，利用最近开发的深度学习模型，该研究员将预测在mESC和小鼠胚胎中，哪些DNA碱基对TF结合最重要，以及这些序列的突变如何影响TF结合。然后，这些预测将通过突变实验得到验证。所获得的结果将为转录因子如何解释顺式调控代码以及DNA突变如何影响这种解释提供关键的见解。这位研究员将把他的外展努力集中在俄克拉荷马州的美国原住民高中生身上，提供课堂职业研讨会，参加一个既定的部落STEM博览会，并实施一年一度的科学博览会。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势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. In order for an organism to properly function, expression of its genes must be tightly regulated by transcription factors (TF), proteins that bind a specific DNA sequence to control whether a gene is turned on or off. Variants in DNA sequence can lead to mis-localization of TF, disruption of normal gene expression, and disease. Therefore, knowledge of the precise DNA sequence bound by TF and how the surrounding DNA sequences influence TF binding is necessary to gain a deep understanding of how genes are regulated. However, current methods only examine one of these components and require large amounts of starting material thereby limiting the model systems that can be studied. Therefore, this project will focus on the development of a method (ChIP-next) that will provide comprehensive maps of TF binding sequences and the surrounding DNA landscape from low amounts of starting material. Results from this project will enhance our understanding of how TF interpret DNA sequence and how small changes in DNA sequence can have large impacts on mammalian development, disease, and evolution. In addition to the research component, the Fellow will also provide scientific outreach to underrepresented Native American populations in Oklahoma.ChIP-next will allow for the collection of chromatin accessibility and TF binding datasets from the same sample. In order to examine the dynamic interplay of chromatin accessibility and TF binding, ChIP-next will be performed at different time points on differentiating mouse embryonic stem cells (mESC) in culture. Furthermore, using a recently developed deep learning model, the Fellow will predict which DNA bases are most important for TF binding in both mESC and mouse embryos and how mutation of these sequences affect TF binding. These predictions will then be validated using mutagenesis experiments. Results obtained will provide crucial insights into how TFs interpret the cis-regulatory code and how DNA mutations affect this interpretation. The Fellow will focus his outreach efforts on Native American high school students in Oklahoma by providing classroom career seminars, participation in an established tribal STEM fair, and the implementation of a yearly science fair.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.