1
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González-Delgado A, Lopez SC, Rojas-Montero M, Fishman CB, Shipman SL. Simultaneous multi-site editing of individual genomes using retron arrays. Nat Chem Biol 2024:10.1038/s41589-024-01665-7. [PMID: 38982310 DOI: 10.1038/s41589-024-01665-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/06/2024] [Indexed: 07/11/2024]
Abstract
During recent years, the use of libraries-scale genomic manipulations scaffolded on CRISPR guide RNAs have been transformative. However, these existing approaches are typically multiplexed across genomes. Unfortunately, building cells with multiple, nonadjacent precise mutations remains a laborious cycle of editing, isolating an edited cell and editing again. The use of bacterial retrons can overcome this limitation. Retrons are genetic systems composed of a reverse transcriptase and a noncoding RNA that contains an multicopy single-stranded DNA, which is reverse transcribed to produce multiple copies of single-stranded DNA. Here we describe a technology-termed a multitron-for precisely modifying multiple sites on a single genome simultaneously using retron arrays, in which multiple donor-encoding DNAs are produced from a single transcript. The multitron architecture is compatible with both recombineering in prokaryotic cells and CRISPR editing in eukaryotic cells. We demonstrate applications for this approach in molecular recording, genetic element minimization and metabolic engineering.
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Affiliation(s)
| | - Santiago C Lopez
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, San Francisco, CA, USA
| | | | - Chloe B Fishman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Seth L Shipman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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2
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Chen P, Zhang J. The loci of environmental adaptation in a model eukaryote. Nat Commun 2024; 15:5672. [PMID: 38971805 PMCID: PMC11227561 DOI: 10.1038/s41467-024-50002-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 06/25/2024] [Indexed: 07/08/2024] Open
Abstract
While the underlying genetic changes have been uncovered in some cases of adaptive evolution, the lack of a systematic study prevents a general understanding of the genomic basis of adaptation. For example, it is unclear whether protein-coding or noncoding mutations are more important to adaptive evolution and whether adaptations to different environments are brought by genetic changes distributed in diverse genes and biological processes or concentrated in a core set. We here perform laboratory evolution of 3360 Saccharomyces cerevisiae populations in 252 environments of varying levels of stress. We find the yeast adaptations to be primarily fueled by large-effect coding mutations overrepresented in a relatively small gene set, despite prevalent antagonistic pleiotropy across environments. Populations generally adapt faster in more stressful environments, partly because of greater benefits of the same mutations in more stressful environments. These and other findings from this model eukaryote help unravel the genomic principles of environmental adaptation.
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Affiliation(s)
- Piaopiao Chen
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA.
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3
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Yao Y, Zhou Z, Wang X, Liu Z, Zhai Y, Chi X, Du J, Luo L, Zhao Z, Wang X, Xue C, Rao S. SpRY-mediated screens facilitate functional dissection of non-coding sequences at single-base resolution. CELL GENOMICS 2024:100583. [PMID: 38889719 DOI: 10.1016/j.xgen.2024.100583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/28/2024] [Accepted: 05/16/2024] [Indexed: 06/20/2024]
Abstract
CRISPR mutagenesis screens conducted with SpCas9 and other nucleases have identified certain cis-regulatory elements and genetic variants but at a limited resolution due to the absence of protospacer adjacent motif (PAM) sequences. Here, leveraging the broad targeting scope of the near-PAMless SpRY variant, we have demonstrated that saturated SpRY mutagenesis and base editing screens can faithfully identify functional regulatory elements and essential genetic variants for target gene expression at single-base resolution. We further extended this methodology to investigate a genome-wide association study (GWAS) locus at 10q22.1 associated with a red blood cell trait, where we identified potential enhancers regulating HK1 gene expression, despite not all of these enhancers exhibiting typical chromatin signatures. More importantly, our saturated base editing screens pinpoint multiple causal variants within this locus that would otherwise be missed by Bayesian statistical fine-mapping. Our approach is generally applicable to functional interrogation of all non-coding genomic elements while complementing other high-coverage CRISPR screens.
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Affiliation(s)
- Yao Yao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China.
| | - Zhiwei Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Xiaoling Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Zhirui Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Yixin Zhai
- Department of Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Xiaolin Chi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Jingyi Du
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Liheng Luo
- Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Zhigang Zhao
- Department of Medical Oncology, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin 300192, China
| | - Xiaoyue Wang
- Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Chaoyou Xue
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Shuquan Rao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China.
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4
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Li Z, You L, Du X, Yang H, Yang L, Zhu Y, Li L, Jiang Z, Li Q, He N, Lin R, Chen Z, Ni H. New strategies to study in depth the metabolic mechanism of astaxanthin biosynthesis in Phaffia rhodozyma. Crit Rev Biotechnol 2024:1-19. [PMID: 38797672 DOI: 10.1080/07388551.2024.2344578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 04/04/2024] [Indexed: 05/29/2024]
Abstract
Astaxanthin, a ketone carotenoid known for its high antioxidant activity, holds significant potential for application in nutraceuticals, aquaculture, and cosmetics. The increasing market demand necessitates a higher production of astaxanthin using Phaffia rhodozyma. Despite extensive research efforts focused on optimizing fermentation conditions, employing mutagenesis treatments, and utilizing genetic engineering technologies to enhance astaxanthin yield in P. rhodozyma, progress in this area remains limited. This review provides a comprehensive summary of the current understanding of rough metabolic pathways, regulatory mechanisms, and preliminary strategies for enhancing astaxanthin yield. However, further investigation is required to fully comprehend the intricate and essential metabolic regulation mechanism underlying astaxanthin synthesis. Specifically, the specific functions of key genes, such as crtYB, crtS, and crtI, need to be explored in detail. Additionally, a thorough understanding of the action mechanism of bifunctional enzymes and alternative splicing products is imperative. Lastly, the regulation of metabolic flux must be thoroughly investigated to reveal the complete pathway of astaxanthin synthesis. To obtain an in-depth mechanism and improve the yield of astaxanthin, this review proposes some frontier methods, including: omics, genome editing, protein structure-activity analysis, and synthetic biology. Moreover, it further elucidates the feasibility of new strategies using these advanced methods in various effectively combined ways to resolve these problems mentioned above. This review provides theory and method for studying the metabolic pathway of astaxanthin in P. rhodozyma and the industrial improvement of astaxanthin, and provides new insights into the flexible combined use of multiple modern advanced biotechnologies.
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Affiliation(s)
- Zhipeng Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian Province, People's Republic of China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, Fujian Province, People's Republic of China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, Fujian Province, People's Republic of China
- Food Microbial and Enzyme Engineering Research Center of Fujian University, People's Republic of China
| | - Li You
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian Province, People's Republic of China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, Fujian Province, People's Republic of China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, Fujian Province, People's Republic of China
- Food Microbial and Enzyme Engineering Research Center of Fujian University, People's Republic of China
| | - Xiping Du
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian Province, People's Republic of China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, Fujian Province, People's Republic of China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, Fujian Province, People's Republic of China
- Food Microbial and Enzyme Engineering Research Center of Fujian University, People's Republic of China
| | - Haoyi Yang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian Province, People's Republic of China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, Fujian Province, People's Republic of China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, Fujian Province, People's Republic of China
- Food Microbial and Enzyme Engineering Research Center of Fujian University, People's Republic of China
| | - Liang Yang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian Province, People's Republic of China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, Fujian Province, People's Republic of China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, Fujian Province, People's Republic of China
- Food Microbial and Enzyme Engineering Research Center of Fujian University, People's Republic of China
| | - Yanbing Zhu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian Province, People's Republic of China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, Fujian Province, People's Republic of China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, Fujian Province, People's Republic of China
- Food Microbial and Enzyme Engineering Research Center of Fujian University, People's Republic of China
| | - Lijun Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian Province, People's Republic of China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, Fujian Province, People's Republic of China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, Fujian Province, People's Republic of China
- Food Microbial and Enzyme Engineering Research Center of Fujian University, People's Republic of China
| | - Zedong Jiang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian Province, People's Republic of China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, Fujian Province, People's Republic of China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, Fujian Province, People's Republic of China
- Food Microbial and Enzyme Engineering Research Center of Fujian University, People's Republic of China
| | - Qingbiao Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian Province, People's Republic of China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, Fujian Province, People's Republic of China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, Fujian Province, People's Republic of China
- Food Microbial and Enzyme Engineering Research Center of Fujian University, People's Republic of China
| | - Ning He
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian Province, People's Republic of China
| | - Rui Lin
- College of Ocean and Earth Sciences, and Research and Development Center for Ocean Observation Technologies, Xiamen University, Xiamen, China
| | - Zhen Chen
- College of Life Science, Xinyang Normal University, Xinyang, China
| | - Hui Ni
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian Province, People's Republic of China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, Fujian Province, People's Republic of China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, Fujian Province, People's Republic of China
- Food Microbial and Enzyme Engineering Research Center of Fujian University, People's Republic of China
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5
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Deng L, Zhou YL, Cai Z, Zhu J, Li Z, Bao Z. Massively parallel CRISPR-assisted homologous recombination enables saturation editing of full-length endogenous genes in yeast. SCIENCE ADVANCES 2024; 10:eadj9382. [PMID: 38748797 PMCID: PMC11095455 DOI: 10.1126/sciadv.adj9382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 04/10/2024] [Indexed: 05/19/2024]
Abstract
Performing saturation editing of chromosomal genes will enable the study of genetic variants in situ and facilitate protein and cell engineering. However, current in vivo editing of endogenous genes either lacks flexibility or is limited to discrete codons and short gene fragments, preventing a comprehensive exploration of genotype-phenotype relationships. To enable facile saturation editing of full-length genes, we used a protospacer adjacent motif-relaxed Cas9 variant and homology-directed repair to achieve above 60% user-defined codon replacement efficiencies in Saccharomyces cerevisiae genome. Coupled with massively parallel DNA design and synthesis, we developed a saturation gene editing method termed CRISPR-Cas9- and homology-directed repair-assisted saturation editing (CHASE) and achieved highly saturated codon swapping of long genomic regions. By applying CHASE to massively edit a well-studied global transcription factor gene, we found known and unreported genetic variants affecting an industrially relevant microbial trait. The user-defined codon editing capability and wide targeting windows of CHASE substantially expand the scope of saturation gene editing.
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Affiliation(s)
- Lei Deng
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yi-Lian Zhou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Zhenkun Cai
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jie Zhu
- Bota Biosciences, Hangzhou 311222, Zhejiang, China
| | - Zenan Li
- Bota Biosciences, Hangzhou 311222, Zhejiang, China
| | - Zehua Bao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, Zhejiang, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China
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6
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Cachera P, Kurt NC, Røpke A, Strucko T, Mortensen UH, Jensen MK. Genome-wide host-pathway interactions affecting cis-cis-muconic acid production in yeast. Metab Eng 2024; 83:75-85. [PMID: 38428729 DOI: 10.1016/j.ymben.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/11/2024] [Accepted: 02/23/2024] [Indexed: 03/03/2024]
Abstract
The success of forward metabolic engineering depends on a thorough understanding of the behaviour of a heterologous metabolic pathway within its host. We have recently described CRI-SPA, a high-throughput gene editing method enabling the delivery of a metabolic pathway to all strains of the Saccharomyces cerevisiae knock-out library. CRI-SPA systematically quantifies the effect of each modified gene present in the library on product synthesis, providing a complete map of host:pathway interactions. In its first version, CRI-SPA relied on the colour of the product betaxanthins to quantify strains synthesis ability. However, only a few compounds produce a visible or fluorescent phenotype limiting the scope of our approach. Here, we adapt CRI-SPA to onboard a biosensor reporting the interactions between host genes and the synthesis of the colourless product cis-cis-muconic acid (CCM). We phenotype >9,000 genotypes, including both gene knock-out and overexpression, by quantifying the fluorescence of yeast colonies growing in high-density agar arrays. We identify novel metabolic targets belonging to a broad range of cellular functions and confirm their positive impact on CCM biosynthesis. In particular, our data suggests a new interplay between CCM biosynthesis and cytosolic redox through their common interaction with the oxidative pentose phosphate pathway. Our genome-wide exploration of host:pathway interaction opens novel strategies for improved production of CCM in yeast cell factories.
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Affiliation(s)
- Paul Cachera
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nikolaj Can Kurt
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andreas Røpke
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tomas Strucko
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Uffe H Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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Hwang J, Ye DY, Jung GY, Jang S. Mobile genetic element-based gene editing and genome engineering: Recent advances and applications. Biotechnol Adv 2024; 72:108343. [PMID: 38521283 DOI: 10.1016/j.biotechadv.2024.108343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 03/25/2024]
Abstract
Genome engineering has revolutionized several scientific fields, ranging from biochemistry and fundamental research to therapeutic uses and crop development. Diverse engineering toolkits have been developed and used to effectively modify the genome sequences of organisms. However, there is a lack of extensive reviews on genome engineering technologies based on mobile genetic elements (MGEs), which induce genetic diversity within host cells by changing their locations in the genome. This review provides a comprehensive update on the versatility of MGEs as powerful genome engineering tools that offers efficient solutions to challenges associated with genome engineering. MGEs, including DNA transposons, retrotransposons, retrons, and CRISPR-associated transposons, offer various advantages, such as a broad host range, genome-wide mutagenesis, efficient large-size DNA integration, multiplexing capabilities, and in situ single-stranded DNA generation. We focused on the components, mechanisms, and features of each MGE-based tool to highlight their cellular applications. Finally, we discussed the current challenges of MGE-based genome engineering and provided insights into the evolving landscape of this transformative technology. In conclusion, the combination of genome engineering with MGE demonstrates remarkable potential for addressing various challenges and advancing the field of genetic manipulation, and promises to revolutionize our ability to engineer and understand the genomes of diverse organisms.
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Affiliation(s)
- Jaeseong Hwang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Sungho Jang
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; Division of Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; Research Center for Bio Materials & Process Development, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea.
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8
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Kaur N, Pati PK. Retron Library Recombineering: Next Powerful Tool for Genome Editing after CRISPR/Cas. ACS Synth Biol 2024; 13:1019-1025. [PMID: 38480006 DOI: 10.1021/acssynbio.3c00667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Retron library recombineering (RLR) is a powerful tool in the field of genome editing that exceeds the scope and specificity of the CRISPR/Cas technique. In RLR, single-stranded DNA produced in vivo by harnessing the in-built potential of bacterial retrons is used for replication-dependent genome editing. RLR introduces several genomic variations at once, resulting in pooled and barcoded variant libraries, thus permitting multiplexed applications. Retron-generated RT-DNA has already shown promise for use in genome editing. Thus, this new tool will result in fresh, intriguing, and surprising developments in molecular biology and its juncture with other disciplines of research, including medicine, agriculture, and microbiology. In this review, we discuss the current state of this brand-new tool that could eventually boost genome editing research.
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Affiliation(s)
- Navdeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
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Siddiq MA, Duveau F, Wittkopp PJ. Plasticity and environment-specific relationships between gene expression and fitness in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589130. [PMID: 38659876 PMCID: PMC11042213 DOI: 10.1101/2024.04.12.589130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Phenotypic evolution is shaped by interactions between organisms and their environments. The environment influences how an organism's genotype determines its phenotype and how this phenotype affects its fitness. To better understand this dual role of the environment in the production and selection of phenotypic variation, we empirically determined and compared the genotype-phenotype-fitness relationship for mutant strains of the budding yeast Saccharomyces cerevisiae in four environments. Specifically, we measured how mutations in the promoter of the metabolic gene TDH3 modified its expression level and affected its growth on media with four different carbon sources. In each environment, we observed a clear relationship between TDH3 expression level and fitness, but this relationship differed among environments. Genetic variants with similar effects on TDH3 expression in different environments often had different effects on fitness and vice versa. Such environment-specific relationships between phenotype and fitness can shape the evolution of phenotypic plasticity. The set of mutants we examined also allowed us to compare the effects of mutations disrupting binding sites for key transcriptional regulators and the TATA box, which is part of the core promoter sequence. Mutations disrupting the binding sites for the transcription factors had more variable effects on expression among environments than mutations disrupting the TATA box, yet mutations with the most environmentally variable effects on fitness were located in the TATA box. This observation suggests that mutations affecting different molecular mechanisms are likely to contribute unequally to regulatory sequence evolution in changing environments.
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Affiliation(s)
- Mohammad A. Siddiq
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan
- Authors contributed equally to this work
| | - Fabien Duveau
- Department of Ecology and Evolutionary Biology, University of Michigan
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon, Université de Lyon, France
- Authors contributed equally to this work
| | - Patricia J. Wittkopp
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan
- Department of Ecology and Evolutionary Biology, University of Michigan
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Brettner L, Eder R, Schmidlin K, Geiler-Samerotte K. An ultra high-throughput, massively multiplexable, single-cell RNA-seq platform in yeasts. Yeast 2024; 41:242-255. [PMID: 38282330 PMCID: PMC11146634 DOI: 10.1002/yea.3927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 01/04/2024] [Accepted: 01/16/2024] [Indexed: 01/30/2024] Open
Abstract
Yeasts are naturally diverse, genetically tractable, and easy to grow such that researchers can investigate any number of genotypes, environments, or interactions thereof. However, studies of yeast transcriptomes have been limited by the processing capabilities of traditional RNA sequencing techniques. Here we optimize a powerful, high-throughput single-cell RNA sequencing (scRNAseq) platform, SPLiT-seq (Split Pool Ligation-based Transcriptome sequencing), for yeasts and apply it to 43,388 cells of multiple species and ploidies. This platform utilizes a combinatorial barcoding strategy to enable massively parallel RNA sequencing of hundreds of yeast genotypes or growth conditions at once. This method can be applied to most species or strains of yeast for a fraction of the cost of traditional scRNAseq approaches. Thus, our technology permits researchers to leverage "the awesome power of yeast" by allowing us to survey the transcriptome of hundreds of strains and environments in a short period of time and with no specialized equipment. The key to this method is that sequential barcodes are probabilistically appended to cDNA copies of RNA while the molecules remain trapped inside of each cell. Thus, the transcriptome of each cell is labeled with a unique combination of barcodes. Since SPLiT-seq uses the cell membrane as a container for this reaction, many cells can be processed together without the need to physically isolate them from one another in separate wells or droplets. Further, the first barcode in the sequence can be chosen intentionally to identify samples from different environments or genetic backgrounds, enabling multiplexing of hundreds of unique perturbations in a single experiment. In addition to greater multiplexing capabilities, our method also facilitates a deeper investigation of biological heterogeneity, given its single-cell nature. For example, in the data presented here, we detect transcriptionally distinct cell states related to cell cycle, ploidy, metabolic strategies, and so forth, all within clonal yeast populations grown in the same environment. Hence, our technology has two obvious and impactful applications for yeast research: the first is the general study of transcriptional phenotypes across many strains and environments, and the second is investigating cell-to-cell heterogeneity across the entire transcriptome.
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Affiliation(s)
- Leandra Brettner
- Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
| | - Rachel Eder
- Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Kara Schmidlin
- Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Kerry Geiler-Samerotte
- Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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11
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Gould SI, Wuest AN, Dong K, Johnson GA, Hsu A, Narendra VK, Atwa O, Levine SS, Liu DR, Sánchez Rivera FJ. High-throughput evaluation of genetic variants with prime editing sensor libraries. Nat Biotechnol 2024:10.1038/s41587-024-02172-9. [PMID: 38472508 DOI: 10.1038/s41587-024-02172-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024]
Abstract
Tumor genomes often harbor a complex spectrum of single nucleotide alterations and chromosomal rearrangements that can perturb protein function. Prime editing has been applied to install and evaluate genetic variants, but previous approaches have been limited by the variable efficiency of prime editing guide RNAs. Here we present a high-throughput prime editing sensor strategy that couples prime editing guide RNAs with synthetic versions of their cognate target sites to quantitatively assess the functional impact of endogenous genetic variants. We screen over 1,000 endogenous cancer-associated variants of TP53-the most frequently mutated gene in cancer-to identify alleles that impact p53 function in mechanistically diverse ways. We find that certain endogenous TP53 variants, particularly those in the p53 oligomerization domain, display opposite phenotypes in exogenous overexpression systems. Our results emphasize the physiological importance of gene dosage in shaping native protein stoichiometry and protein-protein interactions, and establish a framework for studying genetic variants in their endogenous sequence context at scale.
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Affiliation(s)
- Samuel I Gould
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexandra N Wuest
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kexin Dong
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- University of Chinese Academy of Sciences, Beijing, China
| | - Grace A Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alvin Hsu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Varun K Narendra
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ondine Atwa
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stuart S Levine
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Francisco J Sánchez Rivera
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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12
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Hurabielle C, LaFlam TN, Gearing M, Ye CJ. Functional genomics in inborn errors of immunity. Immunol Rev 2024; 322:53-70. [PMID: 38329267 PMCID: PMC10950534 DOI: 10.1111/imr.13309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Inborn errors of immunity (IEI) comprise a diverse spectrum of 485 disorders as recognized by the International Union of Immunological Societies Committee on Inborn Error of Immunity in 2022. While IEI are monogenic by definition, they illuminate various pathways involved in the pathogenesis of polygenic immune dysregulation as in autoimmune or autoinflammatory syndromes, or in more common infectious diseases that may not have a significant genetic basis. Rapid improvement in genomic technologies has been the main driver of the accelerated rate of discovery of IEI and has led to the development of innovative treatment strategies. In this review, we will explore various facets of IEI, delving into the distinctions between PIDD and PIRD. We will examine how Mendelian inheritance patterns contribute to these disorders and discuss advancements in functional genomics that aid in characterizing new IEI. Additionally, we will explore how emerging genomic tools help to characterize new IEI as well as how they are paving the way for innovative treatment approaches for managing and potentially curing these complex immune conditions.
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Affiliation(s)
- Charlotte Hurabielle
- Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Taylor N LaFlam
- Division of Pediatric Rheumatology, Department of Pediatrics, UCSF, San Francisco, California, USA
| | - Melissa Gearing
- Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics, UCSF, San Francisco, California, USA
- Institute of Computational Health Sciences, UCSF, San Francisco, California, USA
- Gladstone Genomic Immunology Institute, San Francisco, California, USA
- Parker Institute for Cancer Immunotherapy, UCSF, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, California, USA
- Arc Institute, Palo Alto, California, USA
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13
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Zheng Y, Li Y, Zhou K, Li T, VanDusen NJ, Hua Y. Precise genome-editing in human diseases: mechanisms, strategies and applications. Signal Transduct Target Ther 2024; 9:47. [PMID: 38409199 PMCID: PMC10897424 DOI: 10.1038/s41392-024-01750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.
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Affiliation(s)
- Yanjiang Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tiange Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nathan J VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yimin Hua
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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14
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Roy KR, Smith JD, Li S, Vonesch SC, Nguyen M, Burnett WT, Orsley KM, Lee CS, Haber JE, St Onge RP, Steinmetz LM. Dissecting quantitative trait nucleotides by saturation genome editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.577784. [PMID: 38352467 PMCID: PMC10862795 DOI: 10.1101/2024.02.02.577784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Genome editing technologies have the potential to transform our understanding of how genetic variation gives rise to complex traits through the systematic engineering and phenotypic characterization of genetic variants. However, there has yet to be a system with sufficient efficiency, fidelity, and throughput to comprehensively identify causal variants at the genome scale. Here we explored the ability of templated CRISPR editing systems to install natural variants genome-wide in budding yeast. We optimized several approaches to enhance homology-directed repair (HDR) with donor DNA templates, including donor recruitment to target sites, single-stranded donor production by bacterial retrons, and in vivo plasmid assembly. We uncovered unique advantages of each system that we integrated into a single superior system named MAGESTIC 3.0. We used MAGESTIC 3.0 to dissect causal variants residing in 112 quantitative trait loci across 32 environmental conditions, revealing an enrichment for missense variants and loci with multiple causal variants. MAGESTIC 3.0 will facilitate the functional analysis of the genome at single-nucleotide resolution and provides a roadmap for improving template-based genome editing systems in other organisms.
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Affiliation(s)
- Kevin R Roy
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Justin D Smith
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Shengdi Li
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Sibylle C Vonesch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Laboratory for Genome Editing and Systems Genetics, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- KU Leuven Center for Microbial and Plant Genetics, Department M2S, Leuven, Belgium
| | - Michelle Nguyen
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Wallace T Burnett
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Kevin M Orsley
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Cheng-Sheng Lee
- Brandeis University, Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Waltham, MA
| | - James E Haber
- Brandeis University, Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Waltham, MA
| | - Robert P St Onge
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
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15
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Liu S, Liu H, Wang X, Shi L. The immune system of prokaryotes: potential applications and implications for gene editing. Biotechnol J 2024; 19:e2300352. [PMID: 38403433 DOI: 10.1002/biot.202300352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/30/2023] [Accepted: 12/28/2023] [Indexed: 02/27/2024]
Abstract
Gene therapy has revolutionized the treatment of genetic diseases. Spearheading this revolution are sophisticated genome editing methods such as TALENs, ZFNs, and CRISPR-Cas, which trace their origins back to prokaryotic immune systems. Prokaryotes have developed various antiviral defense systems to combat viral attacks and the invasion of genetic elements. The comprehension of these defense mechanisms has paved the way for the development of indispensable tools in molecular biology. Among them, restriction endonuclease originates from the innate immune system of bacteria. The CRISPR-Cas system, a widely applied genome editing technology, is derived from the prokaryotic adaptive immune system. Single-base editing is a precise editing tool based on CRISPR-Cas system that involves deamination of target base. It is worth noting that prokaryotes possess deamination enzymes as part of their defense arsenal over foreign genetic material. Furthermore, prokaryotic Argonauts (pAgo) proteins, also function in anti-phage defense, play an important role in complementing the CRISPR-Cas system by addressing certain limitations it may have. Recent studies have also shed light on the significance of Retron, a reverse transcription transposon previously showed potential in genome editing, has also come to light in the realm of prokaryotic immunity. These noteworthy findings highlight the importance of studying prokaryotic immune system for advancing genome editing techniques. Here, both the origin of prokaryotic immunity underlying aforementioned genome editing tools, and potential applications of deaminase, pAgo protein and reverse transcriptase in genome editing among prokaryotes were introduced, thus emphasizing the fundamental mechanism and significance of prokaryotic immunity.
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Affiliation(s)
- Siyang Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Hongling Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xue Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lei Shi
- School of Life Sciences, Chongqing University, Chongqing, China
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16
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Sapède E, Sugawara N, Tyers RG, Nakajima Y, Afreen MF, Romero Escobar J, Haber JE. Nonhomologous tails direct heteroduplex rejection and mismatch correction during single-strand annealing in Saccharomyces cerevisiae. PLoS Genet 2024; 20:e1010527. [PMID: 38315739 PMCID: PMC10868807 DOI: 10.1371/journal.pgen.1010527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/15/2024] [Accepted: 12/28/2023] [Indexed: 02/07/2024] Open
Abstract
Single-strand annealing (SSA) is initiated when a double strand break (DSB) occurs between two flanking repeated sequences, resulting in a deletion that leaves a single copy of the repeat. We studied budding yeast strains carrying two 200-bp URA3 sequences separated by 2.6 kb of spacer DNA (phage lambda) in which a site-specific DSB can be created by HO or Cas9 endonucleases. Repeat-mediated deletion requires removal of long 3'-ended single-stranded tails (flaps) by Rad1-Rad10 with the assistance of Msh2-Msh3, Saw1 and Slx4. A natural 3% divergence of unequally spaced heterologies between these repeats (designated F and A) causes a significant reduction in the frequency of SSA repair. This decrease is caused by heteroduplex rejection in which mismatches (MMs) in the annealed intermediate are recognized by the MutS (Msh2 and Msh6) components of the MM repair (MMR) pathway coupled to unwinding of the duplex by the Sgs1-Rmi1-Top3 helicase. MutL homologs, Mlh1-Pms1 (MutL), are not required for rejection but play their expected role in mismatch correction. Remarkably, heteroduplex rejection is very low in strains where the divergent repeats were immediately adjacent (Tailless strains) and the DSB was induced by Cas9. These results suggest that the presence of nonhomologous tails strongly stimulates heteroduplex rejection in SSA. DNA sequencing analysis of SSA products from the FA Tailed strain showed a gradient of correction favoring the sequence opposite each 3' end of the annealed strand. Mismatches located in the center of the repair intermediate were corrected by Msh2-Msh6 mediated mismatch correction, while correction of MMs at the extremity of the SSA intermediate often appears to use a different mechanism, possibly by 3' nonhomologous tail removal that includes part of the homologous sequence. In contrast, in FA Tailless strains there was a uniform repair of the MMs across the repeat. A distinctive pattern of correction was found in the absence of MSH2, in both Tailed and Tailless strains, different from the spectrum seen in a msh3Δ msh6Δ double mutant. Previous work has shown that SSA is Rad51-independent but dependent on the strand annealing activity of Rad52. However Rad52 becomes dispensable in a Tailless construct where the DSB is induced by Cas9 or in transformation of a plasmid where SSA occurs in the absence of nonhomologous tails.
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Affiliation(s)
- Elena Sapède
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Neal Sugawara
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Randall G. Tyers
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Yuko Nakajima
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Mosammat Faria Afreen
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jesselin Romero Escobar
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - James E. Haber
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
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17
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Xu S, Neupane S, Wang H, Pham TP, Snyman M, Huynh TV, Wang L. Efficient CRISPR genome editing and integrative genomic analyses reveal the mosaicism of Cas-induced mutations and pleiotropic effects of scarlet gene in an emerging model system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577787. [PMID: 38352317 PMCID: PMC10862705 DOI: 10.1101/2024.01.29.577787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Despite the revolutionary impacts of CRISPR-Cas gene editing systems, the effective and widespread use of CRISPR technologies in emerging model organisms still faces significant challenges. These include the inefficiency in generating heritable mutations at the organismal level, limited knowledge about the genomic consequences of gene editing, and an inadequate understanding of the inheritance patterns of CRISPR-Cas-induced mutations. This study addresses these issues by 1) developing an efficient microinjection delivery method for CRISPR editing in the microcrustacean Daphnia pulex; 2) assessing the editing efficiency of Cas9 and Cas12a nucleases, examining mutation inheritance patterns, and analyzing the local and global mutation spectrum in the scarlet mutants; and 3) investigating the transcriptomes of scarlet mutants to understand the pleiotropic effects of scarlet underlying their swimming behavior changes. Our reengineered CRISPR microinjection method results in efficient biallelic editing with both nucleases. While indels are dominant in Cas-induced mutations, a few on-site large deletions (>1kb) are observed, most likely caused by microhomology-mediated end joining repair. Knock-in of a stop codon cassette to the scarlet locus was successful, despite complex induced mutations surrounding the target site. Moreover, extensive germline mosaicism exists in some mutants, which unexpectedly produce different phenotypes/genotypes in their asexual progenies. Lastly, our transcriptomic analyses unveil significant gene expression changes associated with scarlet knock-out and altered swimming behavior in mutants, including several genes (e.g., NMDA1, ABAT, CNTNAP2) involved in human neurodegenerative diseases. This study expands our understanding of the dynamics of gene editing in the tractable model organism Daphnia and highlights its promising potential as a neurological disease model.
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Affiliation(s)
- Sen Xu
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Swatantra Neupane
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Hongjun Wang
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Thinh Phu Pham
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Marelize Snyman
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Trung V. Huynh
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Li Wang
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
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18
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Khan AG, Rojas-Montero M, González-Delgado A, Lopez SC, Fang RF, Shipman SL. An experimental census of retrons for DNA production and genome editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577267. [PMID: 38328236 PMCID: PMC10849725 DOI: 10.1101/2024.01.25.577267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Retrons are bacterial immune systems that use reverse transcribed DNA as a detector of phage infection. They are also increasingly deployed as a component of biotechnology. For genome editing, for instance, retrons are modified so that the reverse transcribed DNA (RT-DNA) encodes an editing donor. Retrons are commonly found in bacterial genomes; thousands of unique retrons have now been predicted bioinformatically. However, only a small number have been characterized experimentally. Here, we add substantially to the corpus of experimentally studied retrons. We synthesized >100 previously untested retrons to identify the natural sequence of RT-DNA they produce, quantify their RT-DNA production, and test the relative efficacy of editing using retron-derived donors to edit bacterial genomes, phage genomes, and human genomes. We add 62 new empirically determined, natural RT-DNAs, which are not predictable from the retron sequence alone. We report a large diversity in RT-DNA production and editing rates across retrons, finding that top performing editors outperform those used in previous studies, and are drawn from a subset of the retron phylogeny.
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Affiliation(s)
- Asim G. Khan
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | | | | | - Santiago C. Lopez
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, CA, USA
| | - Rebecca F. Fang
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Neuroscience, University of California, San Francisco, CA, USA
| | - Seth L. Shipman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA
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19
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Jiang D, Zhang J. Ascertainment Bias in the Genomic Test of Positive Selection on Regulatory Sequences. Mol Biol Evol 2024; 41:msad284. [PMID: 38149460 PMCID: PMC10766478 DOI: 10.1093/molbev/msad284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/12/2023] [Accepted: 12/22/2023] [Indexed: 12/28/2023] Open
Abstract
Evolution of gene expression mediated by cis-regulatory changes is thought to be an important contributor to organismal adaptation, but identifying adaptive cis-regulatory changes is challenging due to the difficulty in knowing the expectation under no positive selection. A new approach for detecting positive selection on transcription factor binding sites (TFBSs) was recently developed, thanks to the application of machine learning in predicting transcription factor (TF) binding affinities of DNA sequences. Given a TFBS sequence from a focal species and the corresponding inferred ancestral sequence that differs from the former at n sites, one can predict the TF-binding affinities of many n-step mutational neighbors of the ancestral sequence and obtain a null distribution of the derived binding affinity, which allows testing whether the binding affinity of the real derived sequence deviates significantly from the null distribution. Applying this test genomically to all experimentally identified binding sites of 3 TFs in humans, a recent study reported positive selection for elevated binding affinities of TFBSs. Here, we show that this genomic test suffers from an ascertainment bias because, even in the absence of positive selection for strengthened binding, the binding affinities of known human TFBSs are more likely to have increased than decreased in evolution. We demonstrate by computer simulation that this bias inflates the false positive rate of the selection test. We propose several methods to mitigate the ascertainment bias and show that almost all previously reported positive selection signals disappear when these methods are applied.
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Affiliation(s)
- Daohan Jiang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Present address: Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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20
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Bai W, Huang M, Li C, Li J. The biological principles and advanced applications of DSB repair in CRISPR-mediated yeast genome editing. Synth Syst Biotechnol 2023; 8:584-596. [PMID: 37711546 PMCID: PMC10497738 DOI: 10.1016/j.synbio.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/16/2023] Open
Abstract
To improve the performance of yeast cell factories for industrial production, extensive CRISPR-mediated genome editing systems have been applied by artificially creating double-strand breaks (DSBs) to introduce mutations with the assistance of intracellular DSB repair. Diverse strategies of DSB repair are required to meet various demands, including precise editing or random editing with customized gRNAs or a gRNA library. Although most yeasts remodeling techniques have shown rewarding performance in laboratory verification, industrial yeast strain manipulation relies only on very limited strategies. Here, we comprehensively reviewed the molecular mechanisms underlying recent industrial applications to provide new insights into DSB cleavage and repair pathways in both Saccharomyces cerevisiae and other unconventional yeast species. The discussion of DSB repair covers the most frequently used homologous recombination (HR) and nonhomologous end joining (NHEJ) strategies to the less well-studied illegitimate recombination (IR) pathways, such as single-strand annealing (SSA) and microhomology-mediated end joining (MMEJ). Various CRISPR-based genome editing tools and corresponding gene editing efficiencies are described. Finally, we summarize recently developed CRISPR-based strategies that use optimized DSB repair for genome-scale editing, providing a direction for further development of yeast genome editing.
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Affiliation(s)
- Wenxin Bai
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 100081, Beijing, PR China
- The BIT-QUB International Joint Laboratory in Synthetic Biology, Beijing, 100081, PR China
| | - Meilan Huang
- School of Chemistry and Chemical Engineering, David Keir Building, Queen's University Belfast, Stranmillis Road, Northern Ireland, BT9 5AG, Belfast, United Kingdom
- The BIT-QUB International Joint Laboratory in Synthetic Biology, Beijing, 100081, PR China
| | - Chun Li
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 100081, Beijing, PR China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China
| | - Jun Li
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 100081, Beijing, PR China
- The BIT-QUB International Joint Laboratory in Synthetic Biology, Beijing, 100081, PR China
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21
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Renganaath K, Albert FW. Trans -eQTL hotspots shape complex traits by modulating cellular states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567054. [PMID: 38014174 PMCID: PMC10680915 DOI: 10.1101/2023.11.14.567054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Regulatory genetic variation shapes gene expression, providing an important mechanism connecting DNA variation and complex traits. The causal relationships between gene expression and complex traits remain poorly understood. Here, we integrated transcriptomes and 46 genetically complex growth traits in a large cross between two strains of the yeast Saccharomyces cerevisiae . We discovered thousands of genetic correlations between gene expression and growth, suggesting functional connections. Local regulatory variation was a minor source of these genetic correlations. Instead, genetic correlations tended to arise from multiple independent trans -acting regulatory loci. Trans -acting hotspots that affect the expression of numerous genes accounted for particularly large fractions of genetic growth variation and of genetic correlations between gene expression and growth. Genes with genetic correlations were enriched for similar biological processes across traits, but with heterogeneous direction of effect. Our results reveal how trans -acting regulatory hotspots shape complex traits by altering cellular states.
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Jakobson CM, Aguilar-Rodríguez J, Jarosz DF. Hsp90 shapes adaptation by controlling the fitness consequences of regulatory variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564848. [PMID: 37961536 PMCID: PMC10634948 DOI: 10.1101/2023.10.30.564848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The essential stress-responsive chaperone Hsp90 impacts development and adaptation from microbes to humans. Yet despite evidence of its role in evolution, pathogenesis, and oncogenic transformation, the molecular mechanisms by which Hsp90 alters the consequences of mutations remain vigorously debated. Here we exploit the power of nucleotide-resolution genetic mapping in Saccharomyces cerevisiae to uncover more than 1,000 natural variant-to-phenotype associations governed by this molecular chaperone. Strikingly, Hsp90 more frequently modified the phenotypic effects of cis-regulatory variation than variants that altered protein sequence. Moreover, these interactions made the largest contribution to Hsp90-dependent heredity. Nearly all interacting variants-both regulatory and protein-coding-fell within clients of Hsp90 or targets of its direct binding partners. Hsp90 activity affected mutations in evolutionarily young genes, segmental deletions, and heterozygotes, highlighting its influence on variation central to evolutionary novelty. Reconciling the diverse epistatic effects of this chaperone, synthetic transcriptional regulation and reconstructions of natural alleles by genome editing revealed a central role for Hsp90 in regulating the fundamental relationship between activity and phenotype. Our findings establish that non-coding variation is a core driver of Hsp90's influence on heredity, offering a mechanistic explanation for the chaperone's strong effects on evolution and development across species.
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Affiliation(s)
- Christopher M. Jakobson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally
| | - José Aguilar-Rodríguez
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- These authors contributed equally
| | - Daniel F. Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
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Abstract
RNA-guided DNA writing enzymes offer promise for programmable gene insertion.
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Affiliation(s)
- Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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Liu H, Sun M, Zhang J. Genomic estimates of mutation and substitution rates contradict the evolutionary speed hypothesis of the latitudinal diversity gradient. Proc Biol Sci 2023; 290:20231787. [PMID: 37876195 PMCID: PMC10598419 DOI: 10.1098/rspb.2023.1787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
The latitudinal diversity gradient (LDG) refers to a decrease in biodiversity from the equator to the poles. The evolutionary speed hypothesis, backed by the metabolic theory of ecology, asserts that nucleotide mutation and substitution rates per site per year are higher and thereby speciation rates are higher at higher temperatures, generating the LDG. However, prior empirical investigations of the relationship between the temperature and mutation or substitution rate were based on a few genes and the results were mixed. We here revisit this relationship using genomic data. No significant correlation between the temperature and mutation rate is found in 13 prokaryotes or in 107 eukaryotes. An analysis of 234 diverse trios of bacterial taxa indicates that the synonymous substitution rate is not significantly associated with the growth temperature. The same data, however, reveal a significant negative association between the nonsynonymous substitution rate and temperature, which is explainable by a larger fraction of detrimental nonsynonymous mutations at higher temperatures due to a stronger demand for protein stability. We conclude that the evolutionary speed hypothesis of the LDG is unsupported by genomic data and advise that future mechanistic studies of the LDG should focus on other hypotheses.
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Affiliation(s)
- Haoxuan Liu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Evolutionary & Organismal Biology and the Fourth Affiliated Hospital of Zhejiang University, Zhejiang University School of Medicine, Hangzhou 310058, People's Republic of China
| | - Mengyi Sun
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Cachera P, Olsson H, Coumou H, Jensen ML, Sánchez B, Strucko T, van den Broek M, Daran JM, Jensen M, Sonnenschein N, Lisby M, Mortensen U. CRI-SPA: a high-throughput method for systematic genetic editing of yeast libraries. Nucleic Acids Res 2023; 51:e91. [PMID: 37572348 PMCID: PMC10516668 DOI: 10.1093/nar/gkad656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 07/07/2023] [Accepted: 08/10/2023] [Indexed: 08/14/2023] Open
Abstract
Biological functions are orchestrated by intricate networks of interacting genetic elements. Predicting the interaction landscape remains a challenge for systems biology and new research tools allowing simple and rapid mapping of sequence to function are desirable. Here, we describe CRI-SPA, a method allowing the transfer of chromosomal genetic features from a CRI-SPA Donor strain to arrayed strains in large libraries of Saccharomyces cerevisiae. CRI-SPA is based on mating, CRISPR-Cas9-induced gene conversion, and Selective Ploidy Ablation. CRI-SPA can be massively parallelized with automation and can be executed within a week. We demonstrate the power of CRI-SPA by transferring four genes that enable betaxanthin production into each strain of the yeast knockout collection (≈4800 strains). Using this setup, we show that CRI-SPA is highly efficient and reproducible, and even allows marker-free transfer of genetic features. Moreover, we validate a set of CRI-SPA hits by showing that their phenotypes correlate strongly with the phenotypes of the corresponding mutant strains recreated by reverse genetic engineering. Hence, our results provide a genome-wide overview of the genetic requirements for betaxanthin production. We envision that the simplicity, speed, and reliability offered by CRI-SPA will make it a versatile tool to forward systems-level understanding of biological processes.
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Affiliation(s)
- Paul Cachera
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Helén Olsson
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Hilde Coumou
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
| | - Mads L Jensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
| | - Benjamín J Sánchez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
| | - Tomas Strucko
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Michael K Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Uffe H Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
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da Silva JF, Tou CJ, King EM, Eller ML, Ma L, Rufino-Ramos D, Kleinstiver BP. Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557440. [PMID: 37745481 PMCID: PMC10515857 DOI: 10.1101/2023.09.12.557440] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Genome editing technologies that install diverse edits can widely enable genetic studies and new therapeutics. Here we develop click editing, a genome writing platform that couples the advantageous properties of DNA-dependent DNA polymerases with RNA-programmable nickases (e.g. CRISPR-Cas) to permit the installation of a range of edits including substitutions, insertions, and deletions. Click editors (CEs) leverage the "click"-like bioconjugation ability of HUH endonucleases (HUHes) with single stranded DNA substrates to covalently tether "click DNA" (clkDNA) templates encoding user-specifiable edits at targeted genomic loci. Through iterative optimization of the modular components of CEs (DNA polymerase and HUHe orthologs, architectural modifications, etc.) and their clkDNAs (template configurations, repair evading substitutions, etc.), we demonstrate the ability to install precise genome edits with minimal indels and no unwanted byproduct insertions. Since clkDNAs can be ordered as simple DNA oligonucleotides for cents per base, it is possible to screen many different clkDNA parameters rapidly and inexpensively to maximize edit efficiency. Together, click editing is a precise and highly versatile platform for modifying genomes with a simple workflow and broad utility across diverse biological applications.
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Affiliation(s)
- Joana Ferreira da Silva
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - Connor J. Tou
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Biological Engineering Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Emily M. King
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, 02115, USA
| | - Madeline L. Eller
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Linyuan Ma
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - David Rufino-Ramos
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
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Quan N, Eguchi Y, Geiler-Samerotte K. Intra- FCY1: a novel system to identify mutations that cause protein misfolding. Front Genet 2023; 14:1198203. [PMID: 37745845 PMCID: PMC10512024 DOI: 10.3389/fgene.2023.1198203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
Protein misfolding is a common intracellular occurrence. Most mutations to coding sequences increase the propensity of the encoded protein to misfold. These misfolded molecules can have devastating effects on cells. Despite the importance of protein misfolding in human disease and protein evolution, there are fundamental questions that remain unanswered, such as, which mutations cause the most misfolding? These questions are difficult to answer partially because we lack high-throughput methods to compare the destabilizing effects of different mutations. Commonly used systems to assess the stability of mutant proteins in vivo often rely upon essential proteins as sensors, but misfolded proteins can disrupt the function of the essential protein enough to kill the cell. This makes it difficult to identify and compare mutations that cause protein misfolding using these systems. Here, we present a novel in vivo system named Intra-FCY1 that we use to identify mutations that cause misfolding of a model protein [yellow fluorescent protein (YFP)] in Saccharomyces cerevisiae. The Intra-FCY1 system utilizes two complementary fragments of the yeast cytosine deaminase Fcy1, a toxic protein, into which YFP is inserted. When YFP folds, the Fcy1 fragments associate together to reconstitute their function, conferring toxicity in media containing 5-fluorocytosine and hindering growth. But mutations that make YFP misfold abrogate Fcy1 toxicity, thus strains possessing misfolded YFP variants rise to high frequency in growth competition experiments. This makes such strains easier to study. The Intra-FCY1 system cancels localization of the protein of interest, thus can be applied to study the relative stability of mutant versions of diverse cellular proteins. Here, we confirm this method can identify novel mutations that cause misfolding, highlighting the potential for Intra-FCY1 to illuminate the relationship between protein sequence and stability.
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Affiliation(s)
- N. Quan
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Y. Eguchi
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, United States
| | - K. Geiler-Samerotte
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, United States
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
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Jiang D, Zhang J. Ascertainment bias in the genomic test of positive selection on regulatory sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.20.554030. [PMID: 37662307 PMCID: PMC10473660 DOI: 10.1101/2023.08.20.554030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Evolution of gene expression mediated by cis-regulatory changes is thought to be an important contributor to organismal adaptation, but identifying adaptive cis-regulatory changes is challenging due to the difficulty in knowing the expectation under no positive selection. A new approach for detecting positive selection on transcription factor binding sites (TFBSs) was recently developed, thanks to the application of machine learning in predicting transcription factor (TF) binding affinities of DNA sequences. Given a TFBS sequence from a focal species and the corresponding inferred ancestral sequence that differs from the former at n sites, one can predict the TF binding affinities of many n-step mutational neighbors of the ancestral sequence and obtain a null distribution of the derived binding affinity, which allows testing whether the binding affinity of the real derived sequence deviates significantly from the null distribution. Applying this test genomically to all experimentally identified binding sites of three TFs in humans, a recent study reported positive selection for elevated binding affinities of TFBSs. Here we show that this genomic test suffers from an ascertainment bias because, even in the absence of positive selection for strengthened binding, the binding affinities of known human TFBSs are more likely to have increased than decreased in evolution. We demonstrate by computer simulation that this bias inflates the false positive rate of the selection test. We propose several methods to mitigate the ascertainment bias and show that almost all previously reported positive selection signals disappear when these methods are applied.
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Affiliation(s)
- Daohan Jiang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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29
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Shi L, Su J, Cho MJ, Song H, Dong X, Liang Y, Zhang Z. Promoter editing for the genetic improvement of crops. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4349-4366. [PMID: 37204916 DOI: 10.1093/jxb/erad175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/06/2023] [Indexed: 05/21/2023]
Abstract
Gene expression plays a fundamental role in the regulation of agronomically important traits in crop plants. The genetic manipulation of plant promoters through genome editing has emerged as an effective strategy to create favorable traits in crops by altering the expression pattern of the pertinent genes. Promoter editing can be applied in a directed manner, where nucleotide sequences associated with favorable traits are precisely generated. Alternatively, promoter editing can also be exploited as a random mutagenic approach to generate novel genetic variations within a designated promoter, from which elite alleles are selected based on their phenotypic effects. Pioneering studies have demonstrated the potential of promoter editing in engineering agronomically important traits as well as in mining novel promoter alleles valuable for plant breeding. In this review, we provide an update on the application of promoter editing in crops for increased yield, enhanced tolerance to biotic and abiotic stresses, and improved quality. We also discuss several remaining technical bottlenecks and how this strategy may be better employed for the genetic improvement of crops in the future.
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Affiliation(s)
- Lu Shi
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jing Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, CA 94704, USA
| | - Hao Song
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoou Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing 210095, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, Jiangsu 210014, China
| | - Ying Liang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhiyong Zhang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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30
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Zhang Z, Bao X, Lin CP. Progress and Prospects of Gene Editing in Pluripotent Stem Cells. Biomedicines 2023; 11:2168. [PMID: 37626665 PMCID: PMC10452926 DOI: 10.3390/biomedicines11082168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 08/27/2023] Open
Abstract
Applying programmable nucleases in gene editing has greatly shaped current research in basic biology and clinical translation. Gene editing in human pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), is highly relevant to clinical cell therapy and thus should be examined with particular caution. First, since all mutations in PSCs will be carried to all their progenies, off-target edits of editors will be amplified. Second, due to the hypersensitivity of PSCs to DNA damage, double-strand breaks (DSBs) made by gene editing could lead to low editing efficiency and the enrichment of cell populations with defective genomic safeguards. In this regard, DSB-independent gene editing tools, such as base editors and prime editors, are favored due to their nature to avoid these consequences. With more understanding of the microbial world, new systems, such as Cas-related nucleases, transposons, and recombinases, are also expanding the toolbox for gene editing. In this review, we discuss current applications of programmable nucleases in PSCs for gene editing, the efforts researchers have made to optimize these systems, as well as new tools that can be potentially employed for differentiation modeling and therapeutic applications.
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Affiliation(s)
| | | | - Chao-Po Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (Z.Z.); (X.B.)
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González-Delgado A, Lopez SC, Rojas-Montero M, Fishman CB, Shipman SL. Simultaneous multi-site editing of individual genomes using retron arrays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549397. [PMID: 37503029 PMCID: PMC10370050 DOI: 10.1101/2023.07.17.549397] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Our understanding of genomics is limited by the scale of our genomic technologies. While libraries of genomic manipulations scaffolded on CRISPR gRNAs have been transformative, these existing approaches are typically multiplexed across genomes. Yet much of the complexity of real genomes is encoded within a genome across sites. Unfortunately, building cells with multiple, non-adjacent precise mutations remains a laborious cycle of editing, isolating an edited cell, and editing again. Here, we describe a technology for precisely modifying multiple sites on a single genome simultaneously. This technology - termed a multitron - is built from a heavily modified retron, in which multiple donor-encoding msds are produced from a single transcript. The multitron architecture is compatible with both recombineering in prokaryotic cells and CRISPR editing in eukaryotic cells. We demonstrate applications for this approach in molecular recording, genetic element minimization, and metabolic engineering.
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Affiliation(s)
| | - Santiago C. Lopez
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, CA, USA
| | | | - Chloe B. Fishman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Seth L. Shipman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA
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Fichter KM, Setayesh T, Malik P. Strategies for precise gene edits in mammalian cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:536-552. [PMID: 37215153 PMCID: PMC10192336 DOI: 10.1016/j.omtn.2023.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
CRISPR-Cas technologies have the potential to revolutionize genetic medicine. However, work is still needed to make this technology clinically efficient for gene correction. A barrier to making precise genetic edits in the human genome is controlling how CRISPR-Cas-induced DNA breaks are repaired by the cell. Since error-prone non-homologous end-joining is often the preferred cellular repair pathway, CRISPR-Cas-induced breaks often result in gene disruption. Homology-directed repair (HDR) makes precise genetic changes and is the clinically desired pathway, but this repair pathway requires a homology donor template and cycling cells. Newer editing strategies, such as base and prime editing, can affect precise repair for relatively small edits without requiring HDR and circumvent cell cycle dependence. However, these technologies have limitations in the extent of genetic editing and require the delivery of bulky cargo. Here, we discuss the pros and cons of precise gene correction using CRISPR-Cas-induced HDR, as well as base and prime editing for repairing small mutations. Finally, we consider emerging new technologies, such as recombination and transposases, which can circumvent both cell cycle and cellular DNA repair dependence for editing the genome.
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Affiliation(s)
- Katye M. Fichter
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Tahereh Setayesh
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Punam Malik
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Hematology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
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Zimmermann A, Prieto-Vivas JE, Cautereels C, Gorkovskiy A, Steensels J, Van de Peer Y, Verstrepen KJ. A Cas3-base editing tool for targetable in vivo mutagenesis. Nat Commun 2023; 14:3389. [PMID: 37296137 PMCID: PMC10256805 DOI: 10.1038/s41467-023-39087-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
The generation of genetic diversity via mutagenesis is routinely used for protein engineering and pathway optimization. Current technologies for random mutagenesis often target either the whole genome or relatively narrow windows. To bridge this gap, we developed CoMuTER (Confined Mutagenesis using a Type I-E CRISPR-Cas system), a tool that allows inducible and targetable, in vivo mutagenesis of genomic loci of up to 55 kilobases. CoMuTER employs the targetable helicase Cas3, signature enzyme of the class 1 type I-E CRISPR-Cas system, fused to a cytidine deaminase to unwind and mutate large stretches of DNA at once, including complete metabolic pathways. The tool increases the number of mutations in the target region 350-fold compared to the rest of the genome, with an average of 0.3 mutations per kilobase. We demonstrate the suitability of CoMuTER for pathway optimization by doubling the production of lycopene in Saccharomyces cerevisiae after a single round of mutagenesis.
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Affiliation(s)
- Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Julian E Prieto-Vivas
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Charlotte Cautereels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Anton Gorkovskiy
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium.
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium.
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Lear SK, Lopez SC, González-Delgado A, Bhattarai-Kline S, Shipman SL. Temporally resolved transcriptional recording in E. coli DNA using a Retro-Cascorder. Nat Protoc 2023; 18:1866-1892. [PMID: 37059915 PMCID: PMC10631475 DOI: 10.1038/s41596-023-00819-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/09/2023] [Indexed: 04/16/2023]
Abstract
Biological signals occur over time in living cells. Yet most current approaches to interrogate biology, particularly gene expression, use destructive techniques that quantify signals only at a single point in time. A recent technological advance, termed the Retro-Cascorder, overcomes this limitation by molecularly logging a record of gene expression events in a temporally organized genomic ledger. The Retro-Cascorder works by converting a transcriptional event into a DNA barcode using a retron reverse transcriptase and then storing that event in a unidirectionally expanding clustered regularly interspaced short palindromic repeats (CRISPR) array via acquisition by CRISPR-Cas integrases. This CRISPR array-based ledger of gene expression can be retrieved at a later point in time by sequencing. Here we describe an implementation of the Retro-Cascorder in which the relative timing of transcriptional events from multiple promoters of interest is recorded chronologically in Escherichia coli populations over multiple days. We detail the molecular components required for this technology, provide a step-by-step guide to generate the recording and retrieve the data by Illumina sequencing, and give instructions for how to use custom software to infer the relative transcriptional timing from the sequencing data. The example recording is generated in 2 d, preparation of sequencing libraries and sequencing can be accomplished in 2-3 d, and analysis of data takes up to several hours. This protocol can be implemented by someone familiar with basic bacterial culture, molecular biology and bioinformatics. Analysis can be minimally run on a personal computer.
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Affiliation(s)
- Sierra K Lear
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- UCSF-UCB Graduate Program in Bioengineering, University of California, Berkeley, CA, USA
| | - Santiago C Lopez
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- UCSF-UCB Graduate Program in Bioengineering, University of California, Berkeley, CA, USA
| | | | - Santi Bhattarai-Kline
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Seth L Shipman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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35
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Kinsler G, Schmidlin K, Newell D, Eder R, Apodaca S, Lam G, Petrov D, Geiler-Samerotte K. Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch. J Mol Evol 2023; 91:293-310. [PMID: 37237236 PMCID: PMC10276131 DOI: 10.1007/s00239-023-10114-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/30/2023] [Indexed: 05/28/2023]
Abstract
The phrase "survival of the fittest" has become an iconic descriptor of how natural selection works. And yet, precisely measuring fitness, even for single-celled microbial populations growing in controlled laboratory conditions, remains a challenge. While numerous methods exist to perform these measurements, including recently developed methods utilizing DNA barcodes, all methods are limited in their precision to differentiate strains with small fitness differences. In this study, we rule out some major sources of imprecision, but still find that fitness measurements vary substantially from replicate to replicate. Our data suggest that very subtle and difficult to avoid environmental differences between replicates create systematic variation across fitness measurements. We conclude by discussing how fitness measurements should be interpreted given their extreme environment dependence. This work was inspired by the scientific community who followed us and gave us tips as we live tweeted a high-replicate fitness measurement experiment at #1BigBatch.
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Affiliation(s)
| | - Kara Schmidlin
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
| | - Daphne Newell
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
- School of Life Sciences, Arizona State University, Tempe, USA
| | - Rachel Eder
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
- School of Life Sciences, Arizona State University, Tempe, USA
| | - Sam Apodaca
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA
- School of Life Sciences, Arizona State University, Tempe, USA
| | | | | | - Kerry Geiler-Samerotte
- Center for Mechanisms of Evolution, Arizona State University, Tempe, USA.
- School of Life Sciences, Arizona State University, Tempe, USA.
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36
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Martínez AA, Lang GI. Identifying Targets of Selection in Laboratory Evolution Experiments. J Mol Evol 2023; 91:345-355. [PMID: 36810618 PMCID: PMC11197053 DOI: 10.1007/s00239-023-10096-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023]
Abstract
Adaptive evolution navigates a balance between chance and determinism. The stochastic processes of mutation and drift generate phenotypic variation; however, once mutations reach an appreciable frequency in the population, their fate is governed by the deterministic action of selection, enriching for favorable genotypes and purging the less-favorable ones. The net result is that replicate populations will traverse similar-but not identical-pathways to higher fitness. This parallelism in evolutionary outcomes can be leveraged to identify the genes and pathways under selection. However, distinguishing between beneficial and neutral mutations is challenging because many beneficial mutations will be lost due to drift and clonal interference, and many neutral (and even deleterious) mutations will fix by hitchhiking. Here, we review the best practices that our laboratory uses to identify genetic targets of selection from next-generation sequencing data of evolved yeast populations. The general principles for identifying the mutations driving adaptation will apply more broadly.
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Affiliation(s)
| | - Gregory I Lang
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
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37
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Jia HJ, Jia PP, Yin S, Bu LK, Yang G, Pei DS. Engineering bacteriophages for enhanced host range and efficacy: insights from bacteriophage-bacteria interactions. Front Microbiol 2023; 14:1172635. [PMID: 37323893 PMCID: PMC10264812 DOI: 10.3389/fmicb.2023.1172635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/10/2023] [Indexed: 06/17/2023] Open
Abstract
Bacteriophages, the most abundant organisms on earth, have the potential to address the rise of multidrug-resistant bacteria resulting from the overuse of antibiotics. However, their high specificity and limited host range can hinder their effectiveness. Phage engineering, through the use of gene editing techniques, offers a means to enhance the host range of bacteria, improve phage efficacy, and facilitate efficient cell-free production of phage drugs. To engineer phages effectively, it is necessary to understand the interaction between phages and host bacteria. Understanding the interaction between the receptor recognition protein of bacteriophages and host receptors can serve as a valuable guide for modifying or replacing these proteins, thereby altering the receptor range of the bacteriophage. Research and development focused on the CRISPR-Cas bacterial immune system against bacteriophage nucleic acids can provide the necessary tools to promote recombination and counter-selection in engineered bacteriophage programs. Additionally, studying the transcription and assembly functions of bacteriophages in host bacteria can facilitate the engineered assembly of bacteriophage genomes in non-host environments. This review highlights a comprehensive summary of phage engineering methods, including in-host and out-of-host engineering, and the use of high-throughput methods to understand their role. The main aim of these techniques is to harness the intricate interactions between bacteriophages and hosts to inform and guide the engineering of bacteriophages, particularly in the context of studying and manipulating the host range of bacteriophages. By employing advanced high-throughput methods to identify specific bacteriophage receptor recognition genes, and subsequently introducing modifications or performing gene swapping through in-host recombination or out-of-host synthesis, it becomes possible to strategically alter the host range of bacteriophages. This capability holds immense significance for leveraging bacteriophages as a promising therapeutic approach against antibiotic-resistant bacteria.
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Affiliation(s)
- Huang-Jie Jia
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Pan-Pan Jia
- School of Public Health, Chongqing Medical University, Chongqing, China
| | - Supei Yin
- Urinary Nephropathy Center, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ling-Kang Bu
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Guan Yang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, China
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38
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Zhang J, Yu H, Li J. De novo domestication: retrace the history of agriculture to design future crops. Curr Opin Biotechnol 2023; 81:102946. [PMID: 37080109 DOI: 10.1016/j.copbio.2023.102946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023]
Abstract
Certain crops were domesticated from their wild progenitors and have served as the major staple food since then, but now suffered from the limited genetic diversity in breeding. Enormous wild species possess unique advantages such as stress tolerance, polyploidy, perennial habit, and natural nutrition. However, it remains a big challenge to utilize wild species in conventional breeding. With recent advances in biotechnologies, one new breeding strategy, de novo domestication, has emerged and been demonstrated by pioneer work. Here, we review the emergence and milestone progress of de novo domestication and discuss how wild relatives could be exploited into new types of crops. With the understanding of the genetic basis of crop domestication and the development of biotechnologies, various elite wild germplasms will be designed and practiced to fulfill particular breeding goals and create new types of crops. De novo domestication is paving a new way for breeding the future.
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Affiliation(s)
- Jingkun Zhang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, China; University of Chinese Academy of Sciences, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, China; University of Chinese Academy of Sciences, China.
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, China; University of Chinese Academy of Sciences, China; Hainan Yazhou Bay Seed Laboratory, China.
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39
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Chen SAA, Kern AF, Ang RML, Xie Y, Fraser HB. Gene-by-environment interactions are pervasive among natural genetic variants. CELL GENOMICS 2023; 3:100273. [PMID: 37082145 PMCID: PMC10112290 DOI: 10.1016/j.xgen.2023.100273] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 10/09/2022] [Accepted: 01/31/2023] [Indexed: 04/22/2023]
Abstract
Gene-by-environment (GxE) interactions, in which a genetic variant's phenotypic effect is condition specific, are fundamental for understanding fitness landscapes and evolution but have been difficult to identify at the single-nucleotide level. Although many condition-specific quantitative trait loci (QTLs) have been mapped, these typically contain numerous inconsequential variants in linkage, precluding understanding of the causal GxE variants. Here, we introduce BARcoded Cas9 retron precise parallel editing via homology (CRISPEY-BAR), a high-throughput precision genome editing strategy, and use it to map GxE interactions of naturally occurring genetic polymorphisms impacting yeast growth. We identified hundreds of GxE variants within condition-specific QTLs, revealing unexpected genetic complexity. Moreover, we found that 93.7% of non-neutral natural variants within ergosterol biosynthesis pathway genes showed GxE interactions, including many impacting antifungal drug resistance through diverse molecular mechanisms. In sum, our results suggest an extremely complex, context-dependent fitness landscape characterized by pervasive GxE interactions while also demonstrating massively parallel genome editing as an effective means for investigating this complexity.
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Affiliation(s)
- Shi-An A. Chen
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Alexander F. Kern
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roy Moh Lik Ang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yihua Xie
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Hunter B. Fraser
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Corresponding author
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40
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Ang RML, Chen SAA, Kern AF, Xie Y, Fraser HB. Widespread epistasis among beneficial genetic variants revealed by high-throughput genome editing. CELL GENOMICS 2023; 3:100260. [PMID: 37082144 PMCID: PMC10112194 DOI: 10.1016/j.xgen.2023.100260] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/27/2022] [Accepted: 01/06/2023] [Indexed: 04/22/2023]
Abstract
The phenotypic effect of any genetic variant can be altered by variation at other genomic loci. Known as epistasis, these genetic interactions shape the genotype-phenotype map of every species, yet their origins remain poorly understood. To investigate this, we employed high-throughput genome editing to measure the fitness effects of 1,826 naturally polymorphic variants in four strains of Saccharomyces cerevisiae. About 31% of variants affect fitness, of which 24% have strain-specific fitness effects indicative of epistasis. We found that beneficial variants are more likely to exhibit genetic interactions and that these interactions can be mediated by specific traits such as flocculation ability. This work suggests that adaptive evolution will often involve trade-offs where a variant is only beneficial in some genetic backgrounds, potentially explaining why many beneficial variants remain polymorphic. In sum, we provide a framework to understand the factors influencing epistasis with single-nucleotide resolution, revealing widespread epistasis among beneficial variants.
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Affiliation(s)
- Roy Moh Lik Ang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Shi-An A. Chen
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Alexander F. Kern
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Yihua Xie
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Hunter B. Fraser
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Corresponding author
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41
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Lear SK, Shipman SL. Molecular recording: transcriptional data collection into the genome. Curr Opin Biotechnol 2023; 79:102855. [PMID: 36481341 PMCID: PMC10547096 DOI: 10.1016/j.copbio.2022.102855] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Advances in regenerative medicine depend upon understanding the complex transcriptional choreography that guides cellular development. Transcriptional molecular recorders, tools that record different transcriptional events into the genome of cells, hold promise to elucidate both the intensity and timing of transcriptional activity at single-cell resolution without requiring destructive multitime point assays. These technologies are dependent on DNA writers, which translate transcriptional signals into stable genomic mutations that encode the duration, intensity, and order of transcriptional events. In this review, we highlight recent progress toward more informative and multiplexable transcriptional recording through the use of three different types of DNA writing - recombineering, Cas1-Cas2 acquisition, and prime editing - and the architecture of the genomic data generated.
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Affiliation(s)
- Sierra K Lear
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA; Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, CA, USA
| | - Seth L Shipman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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42
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Wei H, Li X. Deep mutational scanning: A versatile tool in systematically mapping genotypes to phenotypes. Front Genet 2023; 14:1087267. [PMID: 36713072 PMCID: PMC9878224 DOI: 10.3389/fgene.2023.1087267] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Unveiling how genetic variations lead to phenotypic variations is one of the key questions in evolutionary biology, genetics, and biomedical research. Deep mutational scanning (DMS) technology has allowed the mapping of tens of thousands of genetic variations to phenotypic variations efficiently and economically. Since its first systematic introduction about a decade ago, we have witnessed the use of deep mutational scanning in many research areas leading to scientific breakthroughs. Also, the methods in each step of deep mutational scanning have become much more versatile thanks to the oligo-synthesizing technology, high-throughput phenotyping methods and deep sequencing technology. However, each specific possible step of deep mutational scanning has its pros and cons, and some limitations still await further technological development. Here, we discuss recent scientific accomplishments achieved through the deep mutational scanning and describe widely used methods in each step of deep mutational scanning. We also compare these different methods and analyze their advantages and disadvantages, providing insight into how to design a deep mutational scanning study that best suits the aims of the readers' projects.
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Affiliation(s)
- Huijin Wei
- Zhejiang University—University of Edinburgh Institute, Zhejiang University, Haining, Zhejiang, China
| | - Xianghua Li
- Zhejiang University—University of Edinburgh Institute, Zhejiang University, Haining, Zhejiang, China,Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom,The Second Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China,Biomedical and Health Translational Centre of Zhejiang Province, Haining, Zhejiang, China,*Correspondence: Xianghua Li,
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43
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Žun G, Doberšek K, Petrovič U. Construction and evaluation of gRNA arrays for multiplex CRISPR-Cas9. Yeast 2023; 40:32-41. [PMID: 36536407 PMCID: PMC10107897 DOI: 10.1002/yea.3833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 11/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Endonuclease system CRISPR-Cas9 represents a powerful toolbox for the budding yeast's Saccharomyces cerevisiae genome perturbation. The resulting double-strand breaks are preferentially repaired via highly efficient homologous recombination, which subsequently leads to marker-free genome editing. The goal of this study was to evaluate precise targeting of multiple loci simultaneously. To construct an array of independently expressing guide RNAs (gRNAs), the genes encoding them were assembled through a BioBrick construction procedure. We designed a multiplex CRISPR-Cas9 system for targeting 6 marker genes, whereby the gRNA array was expressed from a single plasmid. To evaluate the performance of the gRNA array, the activity of the designed system was assessed by the success rate of the introduction of perturbations within the target loci: successful gRNA expression, followed by target DNA double-strand breaks formation and their repair by homologous recombination led to premature termination of the coding sequence of the marker genes, resulting in the prevention of growth of the transformants on the corresponding selection media. In conclusion, we successfully introduced up to five simultaneous perturbations within single cells of yeast S. cerevisiae using the multiplex CRISPR-Cas9 system. While this has been done before, we here present an alternative sequential BioBrick assembly with the capability to accommodate many highly similar gRNA-expression cassettes, and an exhaustive evaluation of their performance.
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Affiliation(s)
- Gašper Žun
- Department of Molecular and Biomedical SciencesJožef Stefan InstituteLjubljanaSlovenia
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Katja Doberšek
- Department of Molecular and Biomedical SciencesJožef Stefan InstituteLjubljanaSlovenia
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaLjubljanaSlovenia
| | - Uroš Petrovič
- Department of Molecular and Biomedical SciencesJožef Stefan InstituteLjubljanaSlovenia
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
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Abdrabou A, Duong BTV, Chen K, Atwal RS, Labib M, Lin S, Angers S, Kelley SO. nuPRISM: Microfluidic Genome-Wide Phenotypic Screening Platform for Cellular Nuclei. ACS CENTRAL SCIENCE 2022; 8:1618-1626. [PMID: 36589880 PMCID: PMC9801500 DOI: 10.1021/acscentsci.2c00836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Indexed: 06/17/2023]
Abstract
Genome-wide loss-of-function screens are critical tools to identify novel genetic regulators of intracellular proteins. However, studying the changes in the organelle-specific expression profile of intracellular proteins can be challenging due to protein localization differences across the whole cell, hindering context-dependent protein expression and activity analyses. Here, we describe nuPRISM, a microfluidics chip specifically designed for large-scale isolated nuclei sorting. The new device enables rapid genome-wide loss-of-function phenotypic CRISPR-Cas9 screens directed at intranuclear targets. We deployed this technology to identify novel genetic regulators of β-catenin nuclear accumulation, a phenotypic hallmark of APC-mutated colorectal cancer. nuPRISM expands our ability to capture aberrant nuclear morphological and functional traits associated with distinctive signal transduction and subcellular localization-driven functional processes with substantial resolution and high throughput.
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Affiliation(s)
- Abdalla
M. Abdrabou
- Department
of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
| | - Bill T. V. Duong
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Kangfu Chen
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Randy Singh Atwal
- Department
of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
| | - Mahmoud Labib
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60611, United States
| | - Sichun Lin
- Terrence
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Stephane Angers
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Department
of Biochemistry, Faculty of Medicine, University
of Toronto, Toronto, Ontario M5S 1A8, Canada
- Terrence
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Shana O. Kelley
- Department
of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60611, United States
- Department
of Biomedical Engineering, Northwestern
University, Evanston, Illinois 60611, United States
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
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45
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Mechanisms of regulatory evolution in yeast. Curr Opin Genet Dev 2022; 77:101998. [PMID: 36220001 PMCID: PMC10117219 DOI: 10.1016/j.gde.2022.101998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 02/06/2023]
Abstract
Studies of regulatory variation in yeast - at the level of new mutations, polymorphisms within a species, and divergence between species - have provided great insight into the molecular and evolutionary processes responsible for the evolution of gene expression in eukaryotes. The increasing ease with which yeast genomes can be manipulated and expression quantified in a high-throughput manner has recently accelerated mechanistic studies of cis- and trans-regulatory variation at multiple evolutionary timescales. These studies have, for example, identified differences in the properties of cis- and trans-acting mutations that affect their evolutionary fate, experimentally characterized the molecular mechanisms through which cis- and trans-regulatory variants act, and illustrated how regulatory networks can diverge between species with or without changes in gene expression.
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46
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Biederstädt A, Manzar GS, Daher M. Multiplexed engineering and precision gene editing in cellular immunotherapy. Front Immunol 2022; 13:1063303. [PMID: 36483551 PMCID: PMC9723254 DOI: 10.3389/fimmu.2022.1063303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022] Open
Abstract
The advent of cellular immunotherapy in the clinic has entirely redrawn the treatment landscape for a growing number of human cancers. Genetically reprogrammed immune cells, including chimeric antigen receptor (CAR)-modified immune effector cells as well as T cell receptor (TCR) therapy, have demonstrated remarkable responses across different hard-to-treat patient populations. While these novel treatment options have had tremendous success in providing long-term remissions for a considerable fraction of treated patients, a number of challenges remain. Limited in vivo persistence and functional exhaustion of infused immune cells as well as tumor immune escape and on-target off-tumor toxicities are just some examples of the challenges which restrain the potency of today's genetically engineered cell products. Multiple engineering strategies are being explored to tackle these challenges.The advent of multiplexed precision genome editing has in recent years provided a flexible and highly modular toolkit to specifically address some of these challenges by targeted genetic interventions. This class of next-generation cellular therapeutics aims to endow engineered immune cells with enhanced functionality and shield them from immunosuppressive cues arising from intrinsic immune checkpoints as well as the hostile tumor microenvironment (TME). Previous efforts to introduce additional genetic modifications into immune cells have in large parts focused on nuclease-based tools like the CRISPR/Cas9 system or TALEN. However, nuclease-inactive platforms including base and prime editors have recently emerged and promise a potentially safer route to rewriting genetic sequences and introducing large segments of transgenic DNA without inducing double-strand breaks (DSBs). In this review, we discuss how these two exciting and emerging fields-cellular immunotherapy and precision genome editing-have co-evolved to enable a dramatic expansion in the possibilities to engineer personalized anti-cancer treatments. We will lay out how various engineering strategies in addition to nuclease-dependent and nuclease-inactive precision genome editing toolkits are increasingly being applied to overcome today's limitations to build more potent cellular therapeutics. We will reflect on how novel information-rich unbiased discovery approaches are continuously deepening our understanding of fundamental mechanisms governing tumor biology. We will conclude with a perspective of how multiplexed-engineered and gene edited cell products may upend today's treatment paradigms as they evolve into the next generation of more potent cellular immunotherapies.
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Affiliation(s)
- Alexander Biederstädt
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Medicine III, Hematology and Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Gohar Shahwar Manzar
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - May Daher
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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47
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Ozguc O, Vonesch S. Finding abundance regulators. eLife 2022; 11:e83907. [PMID: 36326804 PMCID: PMC9633062 DOI: 10.7554/elife.83907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A new pooled screening method in yeast allows scientists to probe how protein levels are regulated by mutating thousands of genes at once.
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Affiliation(s)
- Olivia Ozguc
- Center for Microbiology, VIB-KU LeuvenLeuvenBelgium
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU LeuvenLeuvenBelgium
| | - Sibylle Vonesch
- Center for Microbiology, VIB-KU LeuvenLeuvenBelgium
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU LeuvenLeuvenBelgium
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Jiang W, Sivakrishna Rao G, Aman R, Butt H, Kamel R, Sedeek K, Mahfouz MM. High-efficiency retron-mediated single-stranded DNA production in plants. Synth Biol (Oxf) 2022; 7:ysac025. [PMID: 36452068 PMCID: PMC9700382 DOI: 10.1093/synbio/ysac025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/20/2022] [Accepted: 10/30/2022] [Indexed: 07/29/2023] Open
Abstract
Retrons are a class of retroelements that produce multicopy single-stranded DNA (ssDNA) and participate in anti-phage defenses in bacteria. Retrons have been harnessed for the overproduction of ssDNA, genome engineering and directed evolution in bacteria, yeast and mammalian cells. Retron-mediated ssDNA production in plants could unlock their potential applications in plant biotechnology. For example, ssDNA can be used as a template for homology-directed repair (HDR) in several organisms. However, current gene editing technologies rely on the physical delivery of synthetic ssDNA, which limits their applications. Here, we demonstrated retron-mediated overproduction of ssDNA in Nicotiana benthamiana. Additionally, we tested different retron architectures for improved ssDNA production and identified a new retron architecture that resulted in greater ssDNA abundance. Furthermore, co-expression of the gene encoding the ssDNA-protecting protein VirE2 from Agrobacterium tumefaciens with the retron systems resulted in a 10.7-fold increase in ssDNA production in vivo. We also demonstrated clustered regularly interspaced short palindromic repeats-retron-coupled ssDNA overproduction and targeted HDR in N. benthamiana. Overall, we present an efficient approach for in vivo ssDNA production in plants, which can be harnessed for biotechnological applications. Graphical Abstract.
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Affiliation(s)
| | | | - Rashid Aman
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Radwa Kamel
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Khalid Sedeek
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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Hou G, Zhou T, Xu N, Yin Z, Zhu X, Zhang Y, Cui Y, Ma J, Tang Y, Cheng Z, Shen Y, Chen Y, Zou LH, Wang YF, Yin Z, Guo Y, Ding H, Ye Z, Shen N. Integrative Functional Genomics Identifies Systemic Lupus Erythematosus Causal Genetic Variant in the IRF5 Risk Locus. Arthritis Rheumatol 2022; 75:574-585. [PMID: 36245280 DOI: 10.1002/art.42390] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/14/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022]
Abstract
OBJECTIVE IRF5 plays a crucial role in the development of lupus. Genome-wide association studies have identified several systemic lupus erythematosus (SLE) risk single-nucleotide polymorphisms (SNPs) enriched in the IRF5 locus. However, no comprehensive genome editing-based functional analysis exists to establish a direct link between these variants and altered IRF5 expression, particularly for enhancer variants. This study was undertaken to dissect the regulatory function and mechanisms of SLE IRF5 enhancer risk variants and to explore the utilization of clustered regularly interspaced short palindromic repeat interference (CRISPRi) to regulate the expression of disease risk gene to intervene in the disease. METHODS Epigenomic profiles and expression quantitative trait locus analysis were applied to prioritize putative functional variants in the IRF5 locus. CRISPR-mediated deletion, activation, and interference were performed to investigate the genetic function of rs4728142. Allele-specific chromatin immunoprecipitation-quantitative polymerase chain reaction and allele-specific formaldehyde-assisted isolation of regulatory element-quantitative polymerase chain reaction were used to decipher the mechanism of alleles differentially regulating IRF5 expression. The CRISPRi approach was used to evaluate the intervention effect in monocytes from SLE patients. RESULTS SLE risk SNP rs4728142 was located in an enhancer region, indicating a disease-related regulatory function, and risk allele rs4728142-A was closely associated with increased IRF5 expression. We demonstrated that an rs4728142-containing region could act as an enhancer to regulate the expression of IRF5. Moreover, rs4728142 affected the binding affinity of zinc finger and BTB domain-containing protein 3 (ZBTB3), a transcription factor involved in regulation. Furthermore, in monocytes from SLE patients, CRISPR-based interference with the regulation of this enhancer attenuated the production of disease-associated cytokines. CONCLUSION These results demonstrate that the rs4728142-A allele increases the SLE risk by affecting ZBTB3 binding, chromatin status, and regulating IRF5 expression, establishing a biologic link between genetic variation and lupus pathogenesis.
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Affiliation(s)
- Guojun Hou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China, and State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tian Zhou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ning Xu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhihua Yin
- Shenzhen Futian Hospital for Rheumatic Diseases, and Joint Research Laboratory for Rheumatology of Shenzhen University Health Science Center and Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China
| | - Xinyi Zhu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yutong Zhang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yange Cui
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jianyang Ma
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaorui Cheng
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiwei Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yashuo Chen
- Shenzhen Futian Hospital for Rheumatic Diseases, and Joint Research Laboratory for Rheumatology of Shenzhen University Health Science Center and Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China
| | - Ling-Hua Zou
- Shenzhen Futian Hospital for Rheumatic Diseases, and Joint Research Laboratory for Rheumatology of Shenzhen University Health Science Center and Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China
| | - Yong-Fei Wang
- School of Life and Health Sciences, School of Medicine, and Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Zihang Yin
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ya Guo
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Huihua Ding
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhizhong Ye
- Shenzhen Futian Hospital for Rheumatic Diseases, and Joint Research Laboratory for Rheumatology of Shenzhen University Health Science Center and Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, and Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
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High-throughput approaches to functional characterization of genetic variation in yeast. Curr Opin Genet Dev 2022; 76:101979. [PMID: 36075138 DOI: 10.1016/j.gde.2022.101979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022]
Abstract
Expansion of sequencing efforts to include thousands of genomes is providing a fundamental resource for determining the genetic diversity that exists in a population. Now, high-throughput approaches are necessary to begin to understand the role these genotypic changes play in affecting phenotypic variation. Saccharomyces cerevisiae maintains its position as an excellent model system to determine the function of unknown variants with its exceptional genetic diversity, phenotypic diversity, and reliable genetic manipulation tools. Here, we review strategies and techniques developed in yeast that scale classic approaches of assessing variant function. These approaches improve our ability to better map quantitative trait loci at a higher resolution, even for rare variants, and are already providing greater insight into the role that different types of mutations play in phenotypic variation and evolution not just in yeast but across taxa.
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