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

Lian, Jiazhang; Schultz, Carl; Cao, Mingfeng; HamediRad, Mohammad; Zhao, Huimin

doi:10.1038/s41467-019-13621-4

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

Abstract

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, to the best of our knowledge, 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:

;

; Cao, Mingfeng;

;

Publication Date:: Thu Dec 19 00:00:00 EST 2019

Research Org.:: Univ. of Illinois at Urbana-Champaign, IL (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

OSTI Identifier:: 1619764

Alternate Identifier(s):: OSTI ID: 1581091

Grant/Contract Number:: SC0018260

Resource Type:: Published Article

Journal Name:: Nature Communications

Additional Journal Information:: Journal Name: Nature Communications Journal Volume: 10 Journal Issue: 1; Journal ID: ISSN 2041-1723

Publisher:: Nature Publishing Group

Country of Publication:: United Kingdom

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 Kingdom: N. p., 2019. 
Web.  doi:10.1038/s41467-019-13621-4.

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                    Lian, Jiazhang, Schultz, Carl, Cao, Mingfeng, HamediRad, Mohammad, & Zhao, Huimin. Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping.  United Kingdom.  https://doi.org/10.1038/s41467-019-13621-4

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                    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 Kingdom.  https://doi.org/10.1038/s41467-019-13621-4.

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@article{osti_1619764,

  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 = {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, to the best of our knowledge, 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 Kingdom},

  year         = {Thu Dec 19 00:00:00 EST 2019},

  month        = {Thu Dec 19 00:00:00 EST 2019}

}

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

Abstract

Citation Formats

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Activation of the mitochondrial signaling pathway in response to organic solvent stress in yeast journal, December 2014

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CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells journal, December 2016

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Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance journal, June 2018

Genome-wide RNAi screen reveals the E3 SUMO-protein ligase gene SIZ1 as a novel determinant of furfural tolerance in Saccharomyces cerevisiae journal, January 2014

High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method journal, January 2007

Combined genome editing and transcriptional repression for metabolic pathway engineering in Corynebacterium glutamicum using a catalytically active Cas12a journal, October 2019

Construction of a GAL1-regulated yeast cDNA expression library and its application to the identification of genes whose overexpression causes lethality in yeast. journal, November 1992

An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance journal, April 2018

Rcf1 Mediates Cytochrome Oxidase Assembly and Respirasome Formation, Revealing Heterogeneity of the Enzyme Complex journal, March 2012

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Sfh1p, a component of a novel chromatin-remodeling complex, is required for cell cycle progression. journal, June 1997

Ubc9p Is the Conjugating Enzyme for the Ubiquitin-like Protein Smt3p journal, October 1997

High-throughput functional genomics using CRISPR–Cas9 journal, April 2015

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds journal, January 2015

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RNAi assisted genome evolution unveils yeast mutants with improved xylose utilization journal, March 2018

Mitochondrial ribosomal proteins (MRPs) of yeast journal, February 1998

Ubiquitin-specific proteases of Saccharomyces cerevisiae. Cloning of UBP2 and UBP3, and functional analysis of the UBP gene family journal, November 1992

Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision journal, May 2018

Functional profiling of the Saccharomyces cerevisiae genome journal, July 2002

Genome-wide binding map of the histone deacetylase Rpd3 in yeast journal, June 2002

Development of a Synthetic Malonyl-CoA Sensor in Saccharomyces cerevisiae for Intracellular Metabolite Monitoring and Genetic Screening journal, July 2015

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering journal, December 2016

Enabling Graded and Large-Scale Multiplex of Desired Genes Using a Dual-Mode dCas9 Activator in Saccharomyces cerevisiae journal, June 2017

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Engineering Cellular Metabolism journal, March 2016

Genetic Analysis Connects SLX5 and SLX8 to the SUMO Pathway in Saccharomyces cerevisiae journal, December 2005

Design and engineering of intracellular-metabolite-sensing/regulation gene circuits in Saccharomyces cerevisiae : Engineering Gene Circuits in journal, July 2015

Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast
journal, August 2015

CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering
journal, May 2016

Rapid prototyping of microbial cell factories via genome-scale engineering
journal, November 2015

CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing
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Automated multiplex genome-scale engineering in yeast
journal, May 2017

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
journal, December 2014

Homology-Integrated CRISPR–Cas (HI-CRISPR) System for One-Step Multigene Disruption in Saccharomyces cerevisiae
journal, September 2014

Metabolic engineering of Saccharomyces cerevisiae for improvement in stresses tolerance
journal, December 2016

Microbial production of indolylglucosinolate through engineering of a multi-gene pathway in a versatile yeast expression platform
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Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells
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Genome‐scale engineering for systems and synthetic biology
journal, January 2013

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation
journal, October 2014

Cas9 gRNA engineering for genome editing, activation and repression
journal, September 2015

Discovery and engineering of a 1-butanol biosensor in Saccharomyces cerevisiae
journal, December 2017

Activation of the mitochondrial signaling pathway in response to organic solvent stress in yeast
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journal, November 2018

Yeast Mitochondria: Subcellular Units involved in the Synthesis of Respiratory Enzymes in Yeast
journal, December 1955

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journal, December 2016

Development and Applications of CRISPR-Cas9 for Genome Engineering
journal, June 2014

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journal, September 2013

Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance
journal, June 2018

Genome-wide RNAi screen reveals the E3 SUMO-protein ligase gene SIZ1 as a novel determinant of furfural tolerance in Saccharomyces cerevisiae
journal, January 2014

High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method
journal, January 2007

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journal, October 2019

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journal, November 1992

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journal, April 2018

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journal, March 2012

Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease
journal, October 2015

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journal, November 2017

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journal, April 2018

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journal, July 2017

Sfh1p, a component of a novel chromatin-remodeling complex, is required for cell cycle progression.
journal, June 1997

Ubc9p Is the Conjugating Enzyme for the Ubiquitin-like Protein Smt3p
journal, October 1997

High-throughput functional genomics using CRISPR–Cas9
journal, April 2015

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds
journal, January 2015

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening
journal, March 2017

RNAi assisted genome evolution unveils yeast mutants with improved xylose utilization
journal, March 2018

Mitochondrial ribosomal proteins (MRPs) of yeast
journal, February 1998

Ubiquitin-specific proteases of Saccharomyces cerevisiae. Cloning of UBP2 and UBP3, and functional analysis of the UBP gene family
journal, November 1992

Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision
journal, May 2018

Functional profiling of the Saccharomyces cerevisiae genome
journal, July 2002

Genome-wide binding map of the histone deacetylase Rpd3 in yeast
journal, June 2002

Development of a Synthetic Malonyl-CoA Sensor in Saccharomyces cerevisiae for Intracellular Metabolite Monitoring and Genetic Screening
journal, July 2015

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering
journal, December 2016

Enabling Graded and Large-Scale Multiplex of Desired Genes Using a Dual-Mode dCas9 Activator in Saccharomyces cerevisiae
journal, June 2017

N-hypermannose glycosylation disruption enhances recombinant protein production by regulating secretory pathway and cell wall integrity in Saccharomyces cerevisiae
journal, May 2016

Engineering Cellular Metabolism
journal, March 2016

Genetic Analysis Connects SLX5 and SLX8 to the SUMO Pathway in Saccharomyces cerevisiae
journal, December 2005

Design and engineering of intracellular-metabolite-sensing/regulation gene circuits in Saccharomyces cerevisiae : Engineering Gene Circuits in
journal, July 2015