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Title: Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping

Abstract

Genome-scale engineering is an indispensable tool to understand genome functions due to our limited knowledge of cellular networks. Unfortunately, most existing methods for genome-wide genotype-phenotype mapping are limited to a single mode of genomic alteration, i.e. overexpression, repression, or deletion. Here we report a multi-functional genome-wide CRISPR (MAGIC) system to precisely control the expression level of defined genes to desired levels throughout the whole genome. By combining the tri-functional CRISPR system and array-synthesized oligo pools, MAGIC is used to create one of the most comprehensive and diversified genomic libraries in yeast ever reported. The power of MAGIC is demonstrated by the identification of previously uncharacterized genetic determinants of complex phenotypes, particularly those having synergistic interactions when perturbed to different expression levels. MAGIC represents a powerful synthetic biology tool to investigate fundamental biological questions as well as engineer complex phenotypes for biotechnological applications.

Authors:
ORCiD logo [1]; ORCiD logo [2];  [2]; ORCiD logo [3]; ORCiD logo [2]
  1. Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States); Zhejiang Univ., Hangzhou (China)
  2. Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States)
  3. Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States); Lifefoundry Inc., Champaign, IL (United States)
Publication Date:
Research Org.:
Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23). Biological Systems Science Division
OSTI Identifier:
1581091
Grant/Contract Number:  
SC0018260
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Related Information: For Supplementary Information and Source Data, please see https://www.nature.com/articles/s41467-019-13621-4#Sec24.; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Lian, Jiazhang, Schultz, Carl, Cao, Mingfeng, HamediRad, Mohammad, and Zhao, Huimin. Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping. United States: N. p., 2019. Web. doi:10.1038/s41467-019-13621-4.
Lian, Jiazhang, Schultz, Carl, Cao, Mingfeng, HamediRad, Mohammad, & Zhao, Huimin. Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping. United States. doi:10.1038/s41467-019-13621-4.
Lian, Jiazhang, Schultz, Carl, Cao, Mingfeng, HamediRad, Mohammad, and Zhao, Huimin. Thu . "Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping". United States. doi:10.1038/s41467-019-13621-4. https://www.osti.gov/servlets/purl/1581091.
@article{osti_1581091,
title = {Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping},
author = {Lian, Jiazhang and Schultz, Carl and Cao, Mingfeng and HamediRad, Mohammad and Zhao, Huimin},
abstractNote = {Genome-scale engineering is an indispensable tool to understand genome functions due to our limited knowledge of cellular networks. Unfortunately, most existing methods for genome-wide genotype-phenotype mapping are limited to a single mode of genomic alteration, i.e. overexpression, repression, or deletion. Here we report a multi-functional genome-wide CRISPR (MAGIC) system to precisely control the expression level of defined genes to desired levels throughout the whole genome. By combining the tri-functional CRISPR system and array-synthesized oligo pools, MAGIC is used to create one of the most comprehensive and diversified genomic libraries in yeast ever reported. The power of MAGIC is demonstrated by the identification of previously uncharacterized genetic determinants of complex phenotypes, particularly those having synergistic interactions when perturbed to different expression levels. MAGIC represents a powerful synthetic biology tool to investigate fundamental biological questions as well as engineer complex phenotypes for biotechnological applications.},
doi = {10.1038/s41467-019-13621-4},
journal = {Nature Communications},
number = 1,
volume = 10,
place = {United States},
year = {2019},
month = {12}
}

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