Computational approaches for protein functional analysis using CRISPR screens

摘要 高通量生物技术的发展高度依赖于相关的计算方法 系统优化和数据分析。另一方面，生物信息学方法的发展 需要对生物系统和实验方案有深入的了解。长期目标 我们实验室的主要任务是开发能够与高吞吐量无缝集成的计算方法 解决生物学问题的实验，重点是转录和表观遗传调控。 了解蛋白质的功能是生物学的一个基本目标。CRISPR筛选的最新进展 技术使高通量的蛋白质功能研究成为可能，从而导致了新的发现 超出了传统方法的能力。今后五年，我们的短期目标是发展 提高用于蛋白质功能分析的高通量CRISPR筛查利用率的解决方案。要实现 为了实现这一目标，我们提出了三个研究课题： 1)预测CRSIPR筛选中改进的sgRNA文库设计的sgRNA敲除效应。这将是 解决CRISPR屏幕设计中的生物信息学需求； 2)使用CRISPR平铺-sgRNA筛选进行蛋白质结构域分析。这将带来创新的解决方案 蛋白质结构域和结构的研究。 3)从CRISPR筛查和基因组数据推断转录调控网络。这将导致 开发新的方法学来解决涉及蛋白质-蛋白质相互作用和 转录因子和表观遗传调控因子的调控。 总的来说，拟议的项目将为丰富蛋白质功能工具箱贡献新的方法 分析，并将为转录和表观遗传调控领域提供新的见解。

Abstract The development of a high-throughput biotechnology highly relies on relevant computational methods for systematic optimization and data analysis. On the other hand, the development of bioinformatics methods requires in-depth understanding of the biological systems and the experimental protocols. The long-term goal of our lab is to develop computational methods that can be seamlessly integrated with high-throughput experiments to address biological questions, with a focus on transcriptional and epigenetic regulations. Understanding protein functions is a fundamental aim in biology. The recent advances of CRISPR screening techniques have enabled functional studies of proteins in a high-throughput manner, leading to novel discoveries beyond the capacity of traditional methods. During the next five years, our short-term goal is to develop solutions to boost the utilization of high-throughput CRISPR screens for protein functional analysis. To achieve this goal, we propose three research topics: 1) Prediction of sgRNA knockout effects for improved sgRNA library design in CRSIPR screens. This will address the bioinformatics needs in the design of CRISPR screens; 2) Protein domain analysis using CRISPR tiling-sgRNA screens. This will lead to innovative solutions for the studies of protein domain and structure. 3) Inference of transcriptional regulatory networks from CRISPR screen and -omic data. This will lead to the development of new methodology to address an open problem involving protein-protein interactions and regulations of transcription factors and epigenetic regulators. Collectively, the proposed project will contribute new methods to enrich the toolbox for protein functional analysis, and will provide novel insights into the fields of transcriptional and epigenetic regulations.