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Mehryar MM, Shi X, Li J, Wu Q. DNA polymerases in precise and predictable CRISPR/Cas9-mediated chromosomal rearrangements. BMC Biol 2023; 21:288. [PMID: 38066536 PMCID: PMC10709867 DOI: 10.1186/s12915-023-01784-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Recent studies have shown that, owning to its cohesive cleavage, Cas9-mediated CRISPR gene editing outcomes at junctions of chromosomal rearrangements or DNA-fragment editing are precise and predictable; however, the underlying mechanisms are poorly understood due to lack of suitable assay system and analysis tool. RESULTS Here we developed a customized computer program to take account of staggered or cohesive Cas9 cleavage and to rapidly process large volumes of junctional sequencing reads from chromosomal rearrangements or DNA-fragment editing, including DNA-fragment inversions, duplications, and deletions. We also established a sensitive assay system using HPRT1 and DCK as reporters for cell growth during DNA-fragment editing by Cas9 with dual sgRNAs and found prominent large resections or long deletions at junctions of chromosomal rearrangements. In addition, we found that knockdown of PolQ (encoding Polθ polymerase), which has a prominent role in theta-mediated end joining (TMEJ) or microhomology-mediated end joining (MMEJ), results in increased large resections but decreased small deletions. We also found that the mechanisms for generating small deletions of 1bp and >1bp during DNA-fragment editing are different with regard to their opposite dependencies on Polθ and Polλ (encoded by the PolL gene). Specifically, Polθ suppresses 1bp deletions but promotes >1bp deletions, whereas Polλ promotes 1bp deletions but suppresses >1bp deletions. Finally, we found that Polλ is the main DNA polymerase responsible for fill-in of the 5' overhangs of staggered Cas9 cleavage ends. CONCLUSIONS These findings contribute to our understanding of the molecular mechanisms of CRISPR/Cas9-mediated DNA-fragment editing and have important implications for controllable, precise, and predictable gene editing.
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Affiliation(s)
- Mohammadreza M Mehryar
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Xin Shi
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Jingwei Li
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- WLA Laboratories, Shanghai, 201203, China.
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2
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Feng C, Wang J, Chu X. Large-scale data-driven and physics-based models offer insights into the relationships among the structures, dynamics, and functions of chromosomes. J Mol Cell Biol 2023; 15:mjad042. [PMID: 37365687 PMCID: PMC10782906 DOI: 10.1093/jmcb/mjad042] [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: 01/06/2023] [Revised: 03/22/2023] [Accepted: 06/25/2023] [Indexed: 06/28/2023] Open
Abstract
The organized three-dimensional chromosome architecture in the cell nucleus provides scaffolding for precise regulation of gene expression. When the cell changes its identity in the cell-fate decision-making process, extensive rearrangements of chromosome structures occur accompanied by large-scale adaptations of gene expression, underscoring the importance of chromosome dynamics in shaping genome function. Over the last two decades, rapid development of experimental methods has provided unprecedented data to characterize the hierarchical structures and dynamic properties of chromosomes. In parallel, these enormous data offer valuable opportunities for developing quantitative computational models. Here, we review a variety of large-scale polymer models developed to investigate the structures and dynamics of chromosomes. Different from the underlying modeling strategies, these approaches can be classified into data-driven ('top-down') and physics-based ('bottom-up') categories. We discuss their contributions to offering valuable insights into the relationships among the structures, dynamics, and functions of chromosomes and propose the perspective of developing data integration approaches from different experimental technologies and multidisciplinary theoretical/simulation methods combined with different modeling strategies.
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Affiliation(s)
- Cibo Feng
- Advanced Materials Thrust, Function Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou 511400, China
- Green e Materials Laboratory, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou 511400, China
- College of Physics, Jilin University, Changchun 130012, China
| | - Jin Wang
- Department of Chemistry and Physics, The State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Xiakun Chu
- Advanced Materials Thrust, Function Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou 511400, China
- Green e Materials Laboratory, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou 511400, China
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR 999077, China
- Guangzhou Municipal Key Laboratory of Materials Informatics, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou 511400, China
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3
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Inhibition of Carotenoid Biosynthesis by CRISPR/Cas9 Triggers Cell Wall Remodelling in Carrot. Int J Mol Sci 2021; 22:ijms22126516. [PMID: 34204559 PMCID: PMC8234013 DOI: 10.3390/ijms22126516] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 12/03/2022] Open
Abstract
Recent data indicate that modifications to carotenoid biosynthesis pathway in plants alter the expression of genes affecting chemical composition of the cell wall. Phytoene synthase (PSY) is a rate limiting factor of carotenoid biosynthesis and it may exhibit species-specific and organ-specific roles determined by the presence of psy paralogous genes, the importance of which often remains unrevealed. Thus, the aim of this work was to elaborate the roles of two psy paralogs in a model system and to reveal biochemical changes in the cell wall of psy knockout mutants. For this purpose, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated (Cas9) proteins (CRISPR/Cas9) vectors were introduced to carotenoid-rich carrot (Daucus carota) callus cells in order to induce mutations in the psy1 and psy2 genes. Gene sequencing, expression analysis, and carotenoid content analysis revealed that the psy2 gene is critical for carotenoid biosynthesis in this model and its knockout blocks carotenogenesis. The psy2 knockout also decreased the expression of the psy1 paralog. Immunohistochemical staining of the psy2 mutant cells showed altered composition of arabinogalactan proteins, pectins, and extensins in the mutant cell walls. In particular, low-methylesterified pectins were abundantly present in the cell walls of carotenoid-rich callus in contrast to the carotenoid-free psy2 mutant. Transmission electron microscopy revealed altered plastid transition to amyloplasts instead of chromoplasts. The results demonstrate for the first time that the inhibited biosynthesis of carotenoids triggers the cell wall remodelling.
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4
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Wu Q, Shou J. Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering. J Mol Cell Biol 2021; 12:828-856. [PMID: 33125070 PMCID: PMC7883824 DOI: 10.1093/jmcb/mjaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s, the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development. In particular, the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of 3D genomes. CRISPR gene-editing outcomes result from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break repair machineries. Recent studies revealed, however, that the CRISPR genome-editing system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA. Here, we synthesize the current understanding of CRISPR DNA fragment-editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes. Specifically, we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering. We then summarize different types of chromosomal rearrangements by DNA fragment editing. Finally, we review significant progress from precise 1D gene editing toward predictable 3D genome engineering and synthetic biology. The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.
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Affiliation(s)
- Qiang Wu
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jia Shou
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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5
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Wu Q, Liu P, Wang L. Many facades of CTCF unified by its coding for three-dimensional genome architecture. J Genet Genomics 2020; 47:407-424. [PMID: 33187878 DOI: 10.1016/j.jgg.2020.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/15/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023]
Abstract
CCCTC-binding factor (CTCF) is a multifunctional zinc finger protein that is conserved in metazoan species. CTCF is consistently found to play an important role in many diverse biological processes. CTCF/cohesin-mediated active chromatin 'loop extrusion' architects three-dimensional (3D) genome folding. The 3D architectural role of CTCF underlies its multifarious functions, including developmental regulation of gene expression, protocadherin (Pcdh) promoter choice in the nervous system, immunoglobulin (Ig) and T-cell receptor (Tcr) V(D)J recombination in the immune system, homeobox (Hox) gene control during limb development, as well as many other aspects of biology. Here, we review the pleiotropic functions of CTCF from the perspective of its essential role in 3D genome architecture and topological promoter/enhancer selection. We envision the 3D genome as an enormous complex architecture, with tens of thousands of CTCF sites as connecting nodes and CTCF proteins as mysterious bonds that glue together genomic building parts with distinct articulation joints. In particular, we focus on the internal mechanisms by which CTCF controls higher order chromatin structures that manifest its many façades of physiological and pathological functions. We also discuss the dichotomic role of CTCF sites as intriguing 3D genome nodes for seemingly contradictory 'looping bridges' and 'topological insulators' to frame a beautiful magnificent house for a cell's nuclear home.
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Affiliation(s)
- Qiang Wu
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China.
| | - Peifeng Liu
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Leyang Wang
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
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6
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Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus. SCIENCE CHINA-LIFE SCIENCES 2020; 63:835-844. [PMID: 32249388 DOI: 10.1007/s11427-019-1598-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/04/2019] [Indexed: 01/04/2023]
Abstract
During development, gene expression is spatiotemporally regulated by long-distance chromatin interactions between distal enhancers and target promoters. However, how specificity of the interactions between enhancers and promoters is achieved remains largely unknown. As there are far more enhancers than promoters in mammalian genomes, the complexities of enhancer choice during gene regulation remain obscure. CTCF, the CCCTC-binding factor that directionally binds to a vast range of genomic sites known as CBSs (CTCF-binding sites), mediates oriented chromatin looping between a substantial set of distal enhancers and target promoters. To investigate mechanisms by which CTCF engages in enhancer choice, we used CRISPR/Cas9-based DNA-fragment editing to duplicate CBS-containing enhancers and promoters in the native genomic locus of the clustered Pcdhα genes. We found that the promoter is regulated by the proximal one among duplicated enhancers and that this choice is dependent on CTCF-mediated directional enhancer-promoter looping. In addition, gene expression is unaltered upon the switch of enhancers. Moreover, after promoter duplication, only the proximal promoter is chosen by CTCF-mediated directional chromatin looping to contact with the distal enhancer. Finally, we demonstrated that both enhancer activation and chromatin looping with the promoter are essential for gene expression. These findings have important implications regarding the role of CTCF in specific interactions between enhancers and promoters as well as developmental regulation of gene expression by enhancer switching.
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7
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Lu Y, Shou J, Jia Z, Wu Y, Li J, Guo Y, Wu Q. Genetic evidence for asymmetric blocking of higher-order chromatin structure by CTCF/cohesin. Protein Cell 2019; 10:914-920. [PMID: 31559572 PMCID: PMC6881428 DOI: 10.1007/s13238-019-00656-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Yujia Lu
- MOE Key Lab of Systems Biomedicine, Center for Comparative Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jia Shou
- MOE Key Lab of Systems Biomedicine, Center for Comparative Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhilian Jia
- MOE Key Lab of Systems Biomedicine, Center for Comparative Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yonghu Wu
- MOE Key Lab of Systems Biomedicine, Center for Comparative Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinhuan Li
- MOE Key Lab of Systems Biomedicine, Center for Comparative Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, 200240, China
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong, China
| | - Ya Guo
- MOE Key Lab of Systems Biomedicine, Center for Comparative Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, 200240, China
- MRC London Institute of Medical Sciences, Imperial College London, London, W12 0NN, UK
| | - Qiang Wu
- MOE Key Lab of Systems Biomedicine, Center for Comparative Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, 200240, China.
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8
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Shi X, Shou J, Mehryar MM, Li J, Wang L, Zhang M, Huang H, Sun X, Wu Q. Cas9 has no exonuclease activity resulting in staggered cleavage with overhangs and predictable di- and tri-nucleotide CRISPR insertions without template donor. Cell Discov 2019; 5:53. [PMID: 31636963 PMCID: PMC6796948 DOI: 10.1038/s41421-019-0120-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/06/2019] [Indexed: 11/25/2022] Open
Affiliation(s)
- Xin Shi
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jia Shou
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Mohammadreza M. Mehryar
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jingwei Li
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Leyang Wang
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Mo Zhang
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Haiyan Huang
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaofang Sun
- The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiang Wu
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Joint International Research Laboratory of Metabolic & Developmental Sciences, Institute of Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai, China
- The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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9
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Qian M, Cheng Y, Wang X. The methodology study of three-dimensional (3D) genome research. Semin Cell Dev Biol 2019; 90:12-18. [DOI: 10.1016/j.semcdb.2018.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 12/12/2022]
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10
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The advances in CRISPR technology and 3D genome. Semin Cell Dev Biol 2018; 90:54-61. [PMID: 30004018 DOI: 10.1016/j.semcdb.2018.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 07/08/2018] [Indexed: 12/26/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system is a prokaryotic immune system that used to resist foreign genetic factors. It rapidly becomes the hot technology in life sciences and is applies for genome editing to solve the problem of genome-derived diseases. Using CRISPR/Cas technique, the biological DNA sequence can be repaired, cut, replaced, or added. It can effectively change the human stem cells and is expected to achieve results in the treatment. Compared with ZFN and TALEN genome editing techniques, CRISPR is more effective, accurate, and convenient. The application of CRISPR technique in three dimensional (3D) genome structure makes us understand the relationship between linear DNA sequence and 3D chromatin structure. Utilizing CRISPR/Cas9 genome editing to reverse or delete CTCF binding sites, to recognize changes of topological isomerism of the genome and interactions between chromatin loops. The purpose of this review is to introduce the characteristics and classification of the current CRISPR/Cas system, multiple functions, and potential therapeutic uses, as well as to outline the effect of the technique on chromatin loops by changing CTCF sites in 3D genomes. We will also briefly describe the importance of ethical dilemmas to be faced in CRISPR applications and provide a perspective for potential CRISPR considerations.
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Shou J, Li J, Liu Y, Wu Q. Precise and Predictable CRISPR Chromosomal Rearrangements Reveal Principles of Cas9-Mediated Nucleotide Insertion. Mol Cell 2018; 71:498-509.e4. [PMID: 30033371 DOI: 10.1016/j.molcel.2018.06.021] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/22/2018] [Accepted: 06/13/2018] [Indexed: 01/21/2023]
Abstract
Chromosomal rearrangements including large DNA-fragment inversions, deletions, and duplications by Cas9 with paired sgRNAs are important to investigate genome structural variations and developmental gene regulation, but little is known about the underlying mechanisms. Here, we report that disrupting CtIP or FANCD2, which have roles in alternative non-homologous end joining, enhances precise DNA-fragment deletion. By analyzing the inserted nucleotides at the junctions of DNA-fragment editing of deletions, inversions, and duplications and characterizing the cleaved products, we find that Cas9 endonucleolytically cleaves the noncomplementary strand with a flexible scissile profile upstream of the -3 position of the PAM site in vivo and in vitro, generating double-strand break ends with 5' overhangs of 1-3 nucleotides. Moreover, we find that engineered Cas9 nucleases have distinct cleavage profiles. Finally, Cas9-mediated nucleotide insertions are nonrandom and are equal to the combined sequences upstream of both PAM sites with predicted frequencies. Thus, precise and predictable DNA-fragment editing could be achieved by perturbing DNA repair genes and using appropriate PAM configurations.
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Affiliation(s)
- Jia Shou
- Key Lab of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, SCSB, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, SJTU Medical School, Shanghai 200240, China; Shanghai Key Lab of Biliary Tract Research, Xinhua Hospital, SJTU Medical School, Shanghai 200240, China
| | - Jinhuan Li
- Key Lab of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, SCSB, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, SJTU Medical School, Shanghai 200240, China; Shanghai Key Lab of Biliary Tract Research, Xinhua Hospital, SJTU Medical School, Shanghai 200240, China
| | - Yingbin Liu
- Shanghai Key Lab of Biliary Tract Research, Xinhua Hospital, SJTU Medical School, Shanghai 200240, China
| | - Qiang Wu
- Key Lab of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, SCSB, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Lab of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, SJTU Medical School, Shanghai 200240, China; Shanghai Key Lab of Biliary Tract Research, Xinhua Hospital, SJTU Medical School, Shanghai 200240, China.
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12
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Fan L, Lu Y, Shen X, Shao H, Suo L, Wu Q. Alpha protocadherins and Pyk2 kinase regulate cortical neuron migration and cytoskeletal dynamics via Rac1 GTPase and WAVE complex in mice. eLife 2018; 7:e35242. [PMID: 29911975 PMCID: PMC6047886 DOI: 10.7554/elife.35242] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/11/2018] [Indexed: 02/06/2023] Open
Abstract
Diverse clustered protocadherins are thought to function in neurite morphogenesis and neuronal connectivity in the brain. Here, we report that the protocadherin alpha (Pcdha) gene cluster regulates neuronal migration during cortical development and cytoskeletal dynamics in primary cortical culture through the WAVE (Wiskott-Aldrich syndrome family verprolin homologous protein, also known as Wasf) complex. In addition, overexpression of proline-rich tyrosine kinase 2 (Pyk2, also known as Ptk2b, Cakβ, Raftk, Fak2, and Cadtk), a non-receptor cell-adhesion kinase and scaffold protein downstream of Pcdhα, impairs cortical neuron migration via inactivation of the small GTPase Rac1. Thus, we define a molecular Pcdhα/WAVE/Pyk2/Rac1 axis from protocadherin cell-surface receptors to actin cytoskeletal dynamics in cortical neuron migration and dendrite morphogenesis in mouse brain.
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Affiliation(s)
- Li Fan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer InstituteRenji Hospital affiliated to Shanghai Jiao Tong University Medical SchoolShanghaiChina
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yichao Lu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer InstituteRenji Hospital affiliated to Shanghai Jiao Tong University Medical SchoolShanghaiChina
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xiulian Shen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer InstituteRenji Hospital affiliated to Shanghai Jiao Tong University Medical SchoolShanghaiChina
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Hong Shao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer InstituteRenji Hospital affiliated to Shanghai Jiao Tong University Medical SchoolShanghaiChina
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Lun Suo
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
- Department of Assisted ReproductionShanghai Jiao Tong University Medical SchoolShanghaiChina
| | - Qiang Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Comparative Biomedicine, Institute of Systems Biomedicine, Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer InstituteRenji Hospital affiliated to Shanghai Jiao Tong University Medical SchoolShanghaiChina
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
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13
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Li R, Liu Y, Hou Y, Gan J, Wu P, Li C. 3D genome and its disorganization in diseases. Cell Biol Toxicol 2018; 34:351-365. [DOI: 10.1007/s10565-018-9430-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/26/2018] [Indexed: 01/25/2023]
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Abstract
Although the application of CRISPR/Cas9 genome engineering approaches was first reported in apicomplexan parasites only 3 years ago, this technology has rapidly become an essential component of research on apicomplexan parasites. This review briefly describes the history of CRISPR/Cas9 and the principles behind its use along with documenting its implementation in apicomplexan parasites, especially Plasmodium spp. and Toxoplasma gondii. We also discuss the recent use of CRISPR/Cas9 for whole genome screening of gene knockout mutants in T. gondii and highlight its use for seminal genetic manipulations of Cryptosporidium spp. Finally, we consider new variations of CRISPR/Cas9 that have yet to be implemented in apicomplexans. Whereas CRISPR/Cas9 has already accelerated rapid interrogation of gene function in apicomplexans, the full potential of this technology is yet to be realized as new variations and innovations are integrated into the field.
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15
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Yin M, Wang J, Wang M, Li X, Zhang M, Wu Q, Wang Y. Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites. Cell Res 2017; 27:1365-1377. [PMID: 29076501 DOI: 10.1038/cr.2017.131] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/09/2017] [Accepted: 09/11/2017] [Indexed: 12/14/2022] Open
Abstract
CTCF, a conserved 3D genome architecture protein, determines proper genome-wide chromatin looping interactions through directional binding to specific sequence elements of four modules within numerous CTCF-binding sites (CBSs) by its 11 zinc fingers (ZFs). Here, we report four crystal structures of human CTCF in complex with CBSs of the protocadherin (Pcdh) clusters. We show that directional CTCF binding to cognate CBSs of the Pcdh enhancers and promoters is achieved through inserting its ZF3, ZFs 4-7, and ZFs 9-11 into the major groove along CBSs, resulting in a sequence-specific recognition of module 4, modules 3 and 2, and module 1, respectively; and ZF8 serves as a spacer element for variable distances between modules 1 and 2. In addition, the base contact with the asymmetric "A" in the central position of modules 2-3, is essential for directional recognition of the CBSs with symmetric core sequences but lacking module 1. Furthermore, CTCF tolerates base changes at specific positions within the degenerated CBS sequences, permitting genome-wide CTCF binding to a diverse range of CBSs. Together, these complex structures provide important insights into the molecular mechanisms for the directionality, diversity, flexibility, dynamics, and conservation of multivalent CTCF binding to its cognate sites across the entire human genome.
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Affiliation(s)
- Maolu Yin
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiuyu Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinmei Li
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mo Zhang
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovative Center of Systems Biomedicine, SCSB, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China.,State Key Laboratory of Oncogenes and Related Genes, SJTU Medical School, Shanghai 200240, China.,School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China
| | - Qiang Wu
- Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovative Center of Systems Biomedicine, SCSB, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China.,State Key Laboratory of Oncogenes and Related Genes, SJTU Medical School, Shanghai 200240, China.,School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China
| | - Yanli Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China
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