A major goal since the completion of the Human Genome Project has been to understand all functional elements in the human genome and the role they play in normal biological processes and disease. To that end, large pooled libraries of RNA interference (RNAi) reagents have been developed for genome-wide loss-of-function screens but have been hindered by 3 problems: 1) the incompleteness of protein depletion inherent in partial knock-down; 2) off-target effects from the seed sequence; and 3) genetic elements that are not transcribed are inaccessible to manipulation. Genome engineering using precisely targeted nucleases has emerged as an innovative technology to modify the genome and causally interrogate the role of different functional elements. Recently, I developed a new technology for functional genomic screening using the RNA- guided CRISPR/Cas9 nuclease (Shalem*, Sanjana*, et al., Science, 2014). Since CRISPR works on the DNA level, it is possible to manipulate non-coding elements that are inaccessible to RNAi. The research goal of this proposal is to develop new biological tools and analysis techniques for functional annotation of non-coding elements using pooled CRISPR screens. Mentored phase: First, I plan to develop and optimize high-throughput CRISPR non-coding mutagenesis libraries targeting introns, UTRs, promoters, non-coding RNAs, and intergenic regions to enable screening at high-resolution with megabase-scale coverage. Next, I will validate functional non-coding elements and use this large dataset to find unifying principles of how non-coding elements regulate gene expression. Independent phase: I plan to develop a novel CRISPR architecture for tiled deletion screens capable of deleting many segments over entire chromosomes or even entire genomes. With this technology and the increased screening throughput it enables, I will be able to develop a long-term independent research program in several possible directions, including further genome biology, personalized functional genomics, and predictive diagnostics for drug-genome interactions. The two primary areas of training needed to help me succeed in my research goals are 1) CRISPR technology development (mentor: Dr. Feng Zhang) and 2) knowledge of human genetics and non-coding variation (mentor: Dr. David Altshuler). Each mentor is an established expert in these fields. My career development plan integrates additional laboratory training, specialized tutorials in human genetics from world experts, local and national presentations of my research, and courses in scientific writing, grantsmanship and job search strategies. To assist with science- and career-related decisions, I have assembled an Advisory Committee with a team of established, senior genomics experts: Drs. Eric Lander, Steven Hyman, and David Root. The Broad Institute is an ideal environment: All Mentors and Advisors are located in one building and there are facilities for high-throughput functional screening in th RNAi Platform (Director: Dr. Root).

Public Health Relevance

This project seeks to transform our understanding of the human genome by developing a new kind of functional assay capable of directly editing the genome and analyzing how this genome editing impacts the growth, development, and drug resistance of human cells. The remarkable feature of this assay is its high capacity, which can test thousands of genome variations in a single experiment. This research will also improve our understanding of which parts of the genome are essential to life and which parts of the genome might be responsible for the proliferation of cancer cells.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Transition Award (R00)
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Study Section
Special Emphasis Panel (NSS)
Program Officer
Pazin, Michael J
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New York Genome Center
Research Institutes
New York
United States
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Li, Li; Tian, E; Chen, Xianwei et al. (2018) GFAP Mutations in Astrocytes Impair Oligodendrocyte Progenitor Proliferation and Myelination in an hiPSC Model of Alexander Disease. Cell Stem Cell 23:239-251.e6
Sanjana, Neville E (2018) A genome-wide net to catch and understand cancer. Sci Transl Med 10:
Joung, Julia; Engreitz, Jesse M; Konermann, Silvana et al. (2017) Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood. Nature 548:343-346
Erb, Michael A; Scott, Thomas G; Li, Bin E et al. (2017) Transcription control by the ENL YEATS domain in acute leukaemia. Nature 543:270-274
Montalbano, Antonino; Canver, Matthew C; Sanjana, Neville E (2017) High-Throughput Approaches to Pinpoint Function within the Noncoding Genome. Mol Cell 68:44-59
Patel, Shashank J; Sanjana, Neville E; Kishton, Rigel J et al. (2017) Identification of essential genes for cancer immunotherapy. Nature 548:537-542
Joung, Julia; Konermann, Silvana; Gootenberg, Jonathan S et al. (2017) Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat Protoc 12:828-863
Sanjana, Neville E (2017) Genome-scale CRISPR pooled screens. Anal Biochem 532:95-99
Meier, Joshua A; Zhang, Feng; Sanjana, Neville E (2017) GUIDES: sgRNA design for loss-of-function screens. Nat Methods 14:831-832
Sanjana, Neville E; Wright, Jason; Zheng, Kaijie et al. (2016) High-resolution interrogation of functional elements in the noncoding genome. Science 353:1545-1549

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