Identification and Characterization of Functional lncRNAs in human cells - Project Summary/Abstract: The human transcriptome contains tens of thousands of long noncoding RNAs (lncRNAs). Although lncRNAs are involved in many basic biological processes and their dysregulation implicated in human disease, only a handful have been functionally and mechanistically studied to date. This is largely due to lack of efficient tools for lncRNA knockdown, imaging, and biochemical characterization, combined with evidence suggesting that many lncRNAs may be nonfunctional or function only in a context-specific manner. The overall goal of this proposal is to identify and characterize functional lncRNAs in human cells, deepening our understanding of fundamental RNA biology while laying the foundation for advances in disease diagnosis and treatment. To overcome prior technical limitations in studying lncRNAs, this work will take advantage of my newly developed RNA-targeting CRISPR-Csm methodology. This tool enables highly efficient knockdown of both nuclear and cytoplasmic RNAs with limited off-targets and cytotoxicity. When fused to GFP or other proteins, the tool also enables programmable live-cell RNA imaging or tagging without genetic manipulation. The specific aims of this project are thus to: 1) adapt CRISPR-Csm technology for high-throughput screening to enable investigation of thousands of lncRNAs in parallel; 2) perform an RNA imaging screen to identify candidate functional lncRNAs based on interesting morphology and subcellular localization; 3) perform an RNA knockdown screen to inform lncRNA function based on changes in single-cell transcriptome profile; 4) perform proximity labeling experiments to inform lncRNA mechanism based on interacting protein network. Significant findings relevant to the fields of CRISPR technology, noncoding RNA, and gene regulation are expected. Areas of additional scientific training that will enable successful completion of this work include experience conducting high-throughput CRISPR screens, in situ sequencing technique/image analysis, and single-cell RNA-sequencing analysis. The mentored phase of this award will be supervised by Dr. Jennifer Doudna, a world-renowned leader in RNA biology and CRISPR technology. Professional development activities centered around laboratory management, grant writing, and faculty search preparation will be completed to gain the remaining skills necessary before running my own lab. The excellent research environment of the Innovative Genomics Institute at UC Berkeley, combined with the expertise of my Scientific Advisory Committee, will ensure the successful and timely completion of this work and my transition to independence.
