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

该行动资助了2021财年的NSF生物学博士后研究奖学金，即调查基因组，环境和表型之间相互作用的生命规则的综合研究。该研究金支持研究员的研究和培训，以创新的方式为生活规则领域做出贡献。为了使生物体正常发挥功能，其基因的表达必须受到转录因子（TF）的严格调控，转录因子是一种结合特定DNA序列以控制基因开启或关闭的蛋白质。DNA序列的变异可导致TF的错误定位、正常基因表达的破坏和疾病。因此，了解TF结合的精确DNA序列以及周围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，目前的方法仅检查这些组分中的一种，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），该方法将提供TF结合序列的全面图谱以及来自少量起始材料的周围DNA景观。该项目的结果将增强我们对TF如何解释DNA序列以及DNA序列中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，该研究员还将提供科学推广到代表性不足的美国土著人口在俄克拉荷马州。ChIP-next将允许从同一样本中收集染色质可及性和TF结合数据集。为了检查染色质可及性和TF结合的动态相互作用，将在不同时间点对培养的分化小鼠胚胎干细胞（mESC）进行ChIP-next。此外，使用最近开发的深度学习模型，研究员将预测哪些DNA碱基对mESC和小鼠胚胎中的TF结合最重要，以及这些序列的突变如何影响TF结合。这些预测将使用诱变实验进行验证。所获得的结果将提供关键的见解如何转基因解释顺式调控密码和DNA突变如何影响这种解释。该研究员将通过提供课堂职业研讨会，参加既定的部落STEM博览会以及实施年度科学博览会，将其外展工作重点放在俄克拉荷马州的美洲原住民高中生上。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估来支持。

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.