1
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Arakawa H, Miura H, Quadros RM, Ohtsuka M, Gurumurthy C. Cross-contamination of CRISPR guides and other unrelated nucleotide sequences among commercial oligonucleotides. Nucleic Acids Res 2024; 52:3137-3145. [PMID: 38324466 PMCID: PMC11014326 DOI: 10.1093/nar/gkae068] [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: 09/26/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024] Open
Abstract
Custom oligonucleotides (oligos) are widely used reagents in biomedical research. Some common applications of oligos include polymerase chain reaction (PCR), sequencing, hybridization, microarray, and library construction. The reliability of oligos in such applications depends on their purity and specificity. Here, we report that commercially available oligos are frequently contaminated with nonspecific sequences (i.e. other unrelated oligonucleotides). Most of the oligos that we designed to amplify clustered regularly interspersed palindromic repeats (CRISPR) guide sequences contained nonspecific CRISPR guides. These contaminants were detected in research-grade oligos procured from eight commercial oligo-suppliers located in three different geographic regions of the world. Deep sequencing of some of the oligos revealed a variety of contaminants. Given the wide range of applications of oligos, the impact of oligo cross-contamination varies greatly depending on the field and the experimental method. Incorporating appropriate control experiments in research design can help ensure that the quality of oligo reagents meets the intended purpose. This can also minimize risk depending on the purposes for which the oligos are used.
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Affiliation(s)
- Hiroshi Arakawa
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Hiromi Miura
- Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Kanagawa Japan
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, University of Nebraska Medical Center, Omaha, NE, USA
| | - Masato Ohtsuka
- Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Kanagawa Japan
- The Institute of Medical Sciences, Tokai University, Kanagawa, Japan
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2
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Prusty A, Panchal A, Singh RK, Prasad M. Major transcription factor families at the nexus of regulating abiotic stress response in millets: a comprehensive review. PLANTA 2024; 259:118. [PMID: 38592589 DOI: 10.1007/s00425-024-04394-2] [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: 12/30/2023] [Accepted: 03/17/2024] [Indexed: 04/10/2024]
Abstract
Millets stand out as a sustainable crop with the potential to address the issues of food insecurity and malnutrition. These small-seeded, drought-resistant cereals have adapted to survive a broad spectrum of abiotic stresses. Researchers are keen on unravelling the regulatory mechanisms that empower millets to withstand environmental adversities. The aim is to leverage these identified genetic determinants from millets for enhancing the stress tolerance of major cereal crops through genetic engineering or breeding. This review sheds light on transcription factors (TFs) that govern diverse abiotic stress responses and play role in conferring tolerance to various abiotic stresses in millets. Specifically, the molecular functions and expression patterns of investigated TFs from various families, including bHLH, bZIP, DREB, HSF, MYB, NAC, NF-Y and WRKY, are comprehensively discussed. It also explores the potential of TFs in developing stress-tolerant crops, presenting a comprehensive discussion on diverse strategies for their integration.
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Affiliation(s)
- Ankita Prusty
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Panchal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Roshan Kumar Singh
- Department of Botany, Mahishadal Raj College, Purba Medinipur, Garh Kamalpur, West Bengal, 721628, India
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Department of Genetics, University of Delhi, South Campus, Benito-Juarez Road, New Delhi, 110021, India.
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3
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Wang D, Xiu J, Zhao J, Luo J. miR‐AB, a miRNA‐based shRNA viral toolkit for multicolor‐barcoded multiplex RNAi at a single‐cell level. EMBO Rep 2022; 23:e53691. [PMID: 35201651 PMCID: PMC8982575 DOI: 10.15252/embr.202153691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 01/21/2022] [Accepted: 01/30/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Dapeng Wang
- Department of Immunology Binzhou Medical University Shandong China
| | - Jianbo Xiu
- State Key Laboratory of Medical Molecular Biology Institute of Basic Medical Sciences Chinese Academy of Medical Sciences Beijing China
| | - Jiangyue Zhao
- Department of Ophthalmology The 4th Affiliated Hospital of China Medical University Shenyang China
| | - Junli Luo
- Department of Molecular Medicine The Scripps Research Institute Jupiter FL USA
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4
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Yates JD, Russell RC, Barton NJ, Yost HJ, Hill J. A simple and rapid method for enzymatic synthesis of CRISPR-Cas9 sgRNA libraries. Nucleic Acids Res 2021; 49:e131. [PMID: 34554233 PMCID: PMC8682767 DOI: 10.1093/nar/gkab838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 11/14/2022] Open
Abstract
CRISPR-Cas9 sgRNA libraries have transformed functional genetic screening and have enabled several innovative methods that rely on simultaneously targeting numerous genetic loci. Such libraries could be used in a vast number of biological systems and in the development of new technologies, but library generation is hindered by the cost, time, and sequence data required for sgRNA library synthesis. Here, we describe a rapid enzymatic method for generating robust, variant-matched libraries from any source of cDNA in under 3 h. This method, which we have named SLALOM, utilizes a custom sgRNA scaffold sequence and a novel method for detaching oligonucleotides from solid supports by a strand displacing polymerase. With this method, we constructed libraries targeting the E. coli genome and the transcriptome of developing zebrafish hearts, demonstrating its ability to expand the reach of CRISPR technology and facilitate methods requiring custom libraries.
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Affiliation(s)
- Joshua D Yates
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - Robert C Russell
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - Nathaniel J Barton
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - H Joseph Yost
- Molecular Medicine Program and Department of Neurobiology, University of Utah, Salt Lake City, UT, USA
| | - Jonathon T Hill
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
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5
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Abstract
The CRISPR/Cas9 genome editing system has been one of the greatest scientific discoveries in the last decade. The highly efficient and precise editing ability of this technology is of great therapeutic value and benefits the basic sciences as an advantageous research tool. In recent years, forward genetic screens using CRISPR technology have been widely adopted, with genome-wide or pathway-focused screens leading to important and novel discoveries. CRISPR screens have been used primarily in cancer biology, virology, and basic cell biology, but they have rarely been applied to diabetes research. A potential reason for this is that diabetes-related research can be more complicated, often involving cross talk between multiple organs or cell types. Nevertheless, many questions can still be reduced to the study of a single cell type if assays are carefully designed. Here we review the application of CRISPR screen technology and provide perspective on how it can be used in diabetes research.
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Affiliation(s)
- Peng Yi
- Section for Islet Cell and Regenerative Biology, and CRISPR Screen Core Laboratory, Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Noelle Morrow
- Section for Islet Cell and Regenerative Biology, and CRISPR Screen Core Laboratory, Joslin Diabetes Center, Harvard Medical School, Boston, MA
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6
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Iyer VS, Jiang L, Shen Y, Boddul SV, Panda SK, Kasza Z, Schmierer B, Wermeling F. Designing custom CRISPR libraries for hypothesis-driven drug target discovery. Comput Struct Biotechnol J 2020; 18:2237-2246. [PMID: 32952937 PMCID: PMC7479249 DOI: 10.1016/j.csbj.2020.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/24/2020] [Accepted: 08/09/2020] [Indexed: 12/20/2022] Open
Abstract
Over the last decade Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) has been developed into a potent molecular biology tool used to rapidly modify genes or their expression in a multitude of ways. In parallel, CRISPR-based screening approaches have been developed as powerful discovery platforms for dissecting the genetic basis of cellular behavior, as well as for drug target discovery. CRISPR screens can be designed in numerous ways. Here, we give a brief background to CRISPR screens and discuss the pros and cons of different design approaches, including unbiased genome-wide screens that target all known genes, as well as hypothesis-driven custom screens in which selected subsets of genes are targeted (Fig. 1). We provide several suggestions for how a custom screen can be designed, which could broadly serve as inspiration for any experiment that includes candidate gene selection. Finally, we discuss how results from CRISPR screens could be translated into drug development, as well as future trends we foresee in the rapidly evolving CRISPR screen field.
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Affiliation(s)
- Vaishnavi Srinivasan Iyer
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Long Jiang
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Yunbing Shen
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Sanjaykumar V Boddul
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Sudeepta Kumar Panda
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Zsolt Kasza
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Bernhard Schmierer
- High Throughput Genome Engineering, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Fredrik Wermeling
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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7
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Development of a DNA double-strand break-free base editing tool in Corynebacterium glutamicum for genome editing and metabolic engineering. Metab Eng Commun 2020; 11:e00135. [PMID: 32577397 PMCID: PMC7300154 DOI: 10.1016/j.mec.2020.e00135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/15/2020] [Accepted: 05/24/2020] [Indexed: 12/26/2022] Open
Abstract
As a traditional amino acid producing bacterium, Corynebacterium glutamicum is a platform strain for production of various fine chemicals. Based on the CRISPR (Clustered regularly interspaced short palindromic repeats)-Cas9 system, gene editing tools that enable base conversion in the genome of C. glutamicum have been developed. However, some problems such as genomic instability caused by DNA double-strand break (DSB) and off-target effects need to be solved. In this study, a DSB-free single nucleotide genome editing system was developed by construction of a bi-directional base conversion tool TadA-dCas9-AID. This system includes cytosine base editors (CBEs): activation-induced cytidine deaminase (AID) and adenine deaminase (ABEs): tRNA adenosine deaminase (TadA), which can specifically target the gene through a 20-nt single guide RNA (sgRNA) and achieve the base conversion of C-T, C-G and A-G in the 28-bp editing window upstream of protospacer adjacent motif. Finally, as a proof-of-concept demonstration, the system was used to construct a mutant library of zwf gene in C. glutamicum S9114 genome to improve the production of a typical nutraceutical N-acetylglucosamine (GlcNAc). The GlcNAc titer of the mutant strain K293R was increased by 31.9% to 9.1 g/L in shake flask. Here, the developed bases conversion tool TadA-dCas9-AID does not need DNA double-strand break and homologous template, and is effective for genome editing and metabolic engineering in C. glutamicum. A DNA double-strand break-free base editing tool was developed in Corynebacterium glutamicum S9114, which can produce diverse single base mutations. The base editing tool can be used for base mutations on genome and metabolic engineering of C. glutamicum S9114. High efficiency 20N target sequence linking strategy was developed. The base editing tool is used to increase the titer of GlcNAc.
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8
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Wegner M, Husnjak K, Kaulich M. Unbiased and Tailored CRISPR/Cas gRNA Libraries by SynthesizingCovalently-closed-circular (3Cs) DNA. Bio Protoc 2020; 10:e3472. [PMID: 33654707 DOI: 10.21769/bioprotoc.3472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 01/01/2023] Open
Abstract
Simplicity, efficiency and versatility of the CRISPR/Cas system greatly contributed to its rapid use in a broad range of fields. Applications of unbiased CRISPR/Cas screenings are increasing and thus there is a growing need for unbiased and tailored CRISPR/Cas gRNA libraries. Conventional methods for gRNA library generation apply PCR and cloning techniques, thus coupling library diversity with distribution. Here, we provide additional technical expertise to apply our covalently-closed-circular synthesized (3Cs) gRNA library generation technology for the generation of high-quality CRISPR/Cas gRNA libraries. F1-origin of replication-containing plasmid DNA is transformed into CJ236 bacteria for single colony outgrow followed by M13KO7 bacteriophage superinfection for the production and preparation of circular dU-containing ssDNA. dU-ssDNA is annealed with homology- and gRNA-encoding DNA oligonucleotides for their T7 DNA polymerase-mediated extension to form hetero-duplexed CCC-dsDNA (3Cs-dsDNA). 3Cs-dsDNA is electroporated for the selected amplification of the newly synthesized, gRNA-containing strand. To remove wild-type plasmid remnants, the purified plasmid DNA is digested with restriction enzymes targeting the gRNA-placeholder sequence in the template DNA. Undigested plasmid is electroporated for the extraction of the final 3Cs gRNA library. Due to the absence of PCR amplification and conventional cloning steps, the 3Cs technology uncouples sequence diversity from sequence distribution, thereby generating gRNA libraries with near-uniform distribution in diversities being only limited by electroporation efficiencies.
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Affiliation(s)
- Martin Wegner
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt/Main, Germany
| | - Koraljka Husnjak
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt/Main, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt/Main, Germany.,Frankfurt Cancer Institute, Frankfurt/Main, Germany.,Cardio-Pulmonary Institute, Frankfurt/Main, Germany
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9
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Wegner M, Diehl V, Bittl V, de Bruyn R, Wiechmann S, Matthess Y, Hebel M, Hayes MGB, Schaubeck S, Benner C, Heinz S, Bremm A, Dikic I, Ernst A, Kaulich M. Circular synthesized CRISPR/Cas gRNAs for functional interrogations in the coding and noncoding genome. eLife 2019; 8:e42549. [PMID: 30838976 PMCID: PMC6424562 DOI: 10.7554/elife.42549] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 02/25/2019] [Indexed: 02/06/2023] Open
Abstract
Current technologies used to generate CRISPR/Cas gene perturbation reagents are labor intense and require multiple ligation and cloning steps. Furthermore, increasing gRNA sequence diversity negatively affects gRNA distribution, leading to libraries of heterogeneous quality. Here, we present a rapid and cloning-free mutagenesis technology that can efficiently generate covalently-closed-circular-synthesized (3Cs) CRISPR/Cas gRNA reagents and that uncouples sequence diversity from sequence distribution. We demonstrate the fidelity and performance of 3Cs reagents by tailored targeting of all human deubiquitinating enzymes (DUBs) and identify their essentiality for cell fitness. To explore high-content screening, we aimed to generate the largest up-to-date gRNA library that can be used to interrogate the coding and noncoding human genome and simultaneously to identify genes, predicted promoter flanking regions, transcription factors and CTCF binding sites that are linked to doxorubicin resistance. Our 3Cs technology enables fast and robust generation of bias-free gene perturbation libraries with yet unmatched diversities and should be considered an alternative to established technologies.
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Affiliation(s)
- Martin Wegner
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Valentina Diehl
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Verena Bittl
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Buchmann Institute for Molecular Life SciencesGoethe UniversityFrankfurtGermany
| | - Rahel de Bruyn
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Svenja Wiechmann
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Project Group Translational Medicine & Pharmacology TMPFraunhofer Institute for Molecular Biology and Applied Ecology IMEFrankfurtGermany
| | - Yves Matthess
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Marie Hebel
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Michael GB Hayes
- Department of MedicineUniversity of California, San DiegoSan DiegoUnited States
| | - Simone Schaubeck
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
| | - Christopher Benner
- Department of MedicineUniversity of California, San DiegoSan DiegoUnited States
| | - Sven Heinz
- Department of MedicineUniversity of California, San DiegoSan DiegoUnited States
| | - Anja Bremm
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Buchmann Institute for Molecular Life SciencesGoethe UniversityFrankfurtGermany
| | - Ivan Dikic
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Buchmann Institute for Molecular Life SciencesGoethe UniversityFrankfurtGermany
- Frankfurt Cancer InstituteFrankfurt am MainGermany
- Cardio-Pulmonary InstituteFrankfurt am MainGermany
| | - Andreas Ernst
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Project Group Translational Medicine & Pharmacology TMPFraunhofer Institute for Molecular Biology and Applied Ecology IMEFrankfurtGermany
| | - Manuel Kaulich
- Institute of Biochemistry IIGoethe University Frankfurt - Medical Faculty, University HospitalFrankfurtGermany
- Frankfurt Cancer InstituteFrankfurt am MainGermany
- Cardio-Pulmonary InstituteFrankfurt am MainGermany
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10
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Kawasumi R, Abe T, Arakawa H, Garre M, Hirota K, Branzei D. ESCO1/2's roles in chromosome structure and interphase chromatin organization. Genes Dev 2017; 31:2136-2150. [PMID: 29196537 PMCID: PMC5749162 DOI: 10.1101/gad.306084.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/09/2017] [Indexed: 11/24/2022]
Abstract
In this study, Kawasumi et al. researched how ESCO1/2 acetyltransferases mediating SMC3 acetylation and sister chromatid cohesion (SCC) interact and contribute to chromosome structure and proliferation. Using chicken DT40 cell lines with mutations in ESCO1/2, SMC3 acetylation, and the cohesin remover WAPL, they show that cohesion establishment by vertebrate ESCO1/2 is linked to interphase chromatin architecture formation. ESCO1/2 acetyltransferases mediating SMC3 acetylation and sister chromatid cohesion (SCC) are differentially required for genome integrity and development. Here we established chicken DT40 cell lines with mutations in ESCO1/2, SMC3 acetylation, and the cohesin remover WAPL. Both ESCO1 and ESCO2 promoted SCC, while ESCO2 was additionally and specifically required for proliferation and centromere integrity. ESCO1 overexpression fully suppressed the slow proliferation and centromeric separation phenotypes of esco2 cells but only partly suppressed its chromosome arm SCC defects. Concomitant inactivation of ESCO1 and ESCO2 caused lethality owing to compromised mitotic chromosome segregation. Neither wapl nor acetyl-mimicking smc3-QQ mutations rescued esco1 esco2 lethality. Notably, esco1 esco2 wapl conditional mutants showed very severe proliferation defects associated with catastrophic mitoses and also abnormal interphase chromatin organization patterns. The results indicate that cohesion establishment by vertebrate ESCO1/2 is linked to interphase chromatin architecture formation, a newly identified function of cohesin acetyltransferases that is both fundamentally and medically relevant.
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Affiliation(s)
- Ryotaro Kawasumi
- The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy
| | - Takuya Abe
- The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy.,Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Hiroshi Arakawa
- The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy
| | - Massimiliano Garre
- The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Dana Branzei
- The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology (IFOM), 20139 Milan, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 27100 Pavia, Italy
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11
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D'Agostino Y, D'Aniello S. Molecular basis, applications and challenges of CRISPR/Cas9: a continuously evolving tool for genome editing. Brief Funct Genomics 2017; 16:211-216. [PMID: 28057617 DOI: 10.1093/bfgp/elw038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) system is a recently discovered tool for genome editing that has quickly revolutionized the ability to generate site-specific mutations in a wide range of animal models, including nonhuman primates. Indeed, a significant number of scientific reports describing single or multiplex guide RNA microinjection, double-nicking strategies, site-specific knock-in and conditional knock-out have been published in less than three years. However, despite the great potential of this new technology, there are some limitations because of the presence of off-target genomic sites, which must be taken into consideration. To address this issue, various research teams have tried to improve the efficiency of the system through enzymatic modifications of the Cas9 protein or by the introduction of alternative strategies. Although several review articles are available that singly describe the molecular mechanism(s), applications and challenges of each of these strategies, a concise compilation of approaches is lacking. In the current review, we describe and evaluate most CRISPR/Cas9 approaches available at present, describing both mechanism of action, in addition to advantages or disadvantages. The primary goal of this work is to serve as a guide for not skilled researchers, facilitating the selection of the best strategy to target their gene of interest and allowing optimization of particular applications to the specific aims of the study. The present article also offers a unique perspective, focusing on the fact that CRISPR technology is opening a new genomic era, providing the means to manipulate specific genes in a targeted manner in all animal models, an endeavor previously considered to be difficult.
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12
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Cheng J, Pan W, Lu J. Dense sgRNA Library Construction Using a Molecular Chipper Approach. Bio Protoc 2017; 7:e2373. [PMID: 28835906 DOI: 10.21769/bioprotoc.2373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Genetic screens using single-guide-RNA (sgRNA) libraries and CRISPR technology have been powerful to identify genetic regulators for both coding and noncoding regions of the genome. Interrogating functional elements in noncoding regions requires sgRNA libraries that are densely covering, and ideally inexpensive, easy to implement and flexible for customization. We present a Molecular Chipper protocol for generating dense sgRNA libraries from genomic regions of interest. This approach utilizes a combination of random fragmentation and a Type III restriction enzyme to derive a dense coverage of sgRNA library from input DNA.
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Affiliation(s)
- Jijun Cheng
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Yale Stem Cell Center, Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Wen Pan
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Yale Stem Cell Center, Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jun Lu
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Yale Stem Cell Center, Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA.,Yale Cooperative Center of Excellence in Hematology, Yale University, New Haven, Connecticut, USA.,Yale Center for RNA Science and Medicine, Yale University, New Haven, Connecticut, USA
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13
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Arakawa H. A Method to Convert mRNA into a Guide RNA (gRNA) Library without Requiring Previous Bioinformatics Knowledge of the Organism. Bio Protoc 2017; 7:e2319. [PMID: 34541069 DOI: 10.21769/bioprotoc.2319] [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: 12/04/2016] [Revised: 01/13/2017] [Accepted: 05/05/2017] [Indexed: 11/02/2022] Open
Abstract
While the diversity of species represents a diversity of special biological abilities, many of the genes that encode those special abilities in a variety of species are untouched, leaving an untapped gold mine of genetic information; however, despite current advances in genome bioinformatics, annotation of that genetic information is incomplete in most species, except for well-established model organisms, such as human, mouse, or yeast. A guide RNA (gRNA) library using the clustered regularly interspersed palindromic repeats (CRISPR)/Cas9 (CRISPR-associated protein 9) system can be used for the phenotypic screening of uncharacterized genes by forward genetics. The construction of a gRNA library usually requires an abundance of chemically synthesized oligos designed from annotated genes; if one wants to convert mRNA into gRNA without prior knowledge of the target DNA sequences, the major challenges are finding the sequences flanking the protospacer adjacent motif (PAM) and cutting out the 20-bp fragment. Recently, I developed a molecular biology-based technique to convert mRNA into a gRNA library (Arakawa, 2016) (Figure 1). Here I describe the detailed protocol of how to construct a gRNA library from mRNA. Figure 1.A method to convert mRNA into a gRNA library construction ( Sanjana et al., 2014 ). The scheme of the method is summarized. Each step of D-O is described in detail in the Procedure. Bg, BglII; Xb, XbaI; Bs, BsmBI; Aa, AatII. PCR, polymerase chain reaction; lentiCRISPR v2, lentiCRISPR version 2.
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Affiliation(s)
- Hiroshi Arakawa
- IFOM-FIRC Institute of Molecular Oncology Foundation, Milano, Italy
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14
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Bastianello G, Arakawa H. A double-strand break can trigger immunoglobulin gene conversion. Nucleic Acids Res 2016; 45:231-243. [PMID: 27701075 PMCID: PMC5224512 DOI: 10.1093/nar/gkw887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 09/22/2016] [Accepted: 09/26/2016] [Indexed: 12/23/2022] Open
Abstract
All three B cell-specific activities of the immunoglobulin (Ig) gene re-modeling system—gene conversion, somatic hypermutation and class switch recombination—require activation-induced deaminase (AID). AID-induced DNA lesions must be further processed and dissected into different DNA recombination pathways. In order to characterize potential intermediates for Ig gene conversion, we inserted an I-SceI recognition site into the complementarity determining region 1 (CDR1) of the Ig light chain locus of the AID knockout DT40 cell line, and conditionally expressed I-SceI endonuclease. Here, we show that a double-strand break (DSB) in CDR1 is sufficient to trigger Ig gene conversion in the absence of AID. The pattern and pseudogene usage of DSB-induced gene conversion were comparable to those of AID-induced gene conversion; surprisingly, sometimes a single DSB induced multiple gene conversion events. These constitute direct evidence that a DSB in the V region can be an intermediate for gene conversion. The fate of the DNA lesion downstream of a DSB had more flexibility than that of AID, suggesting two alternative models: (i) DSBs during the physiological gene conversion are in the minority compared to single-strand breaks (SSBs), which are frequently generated following DNA deamination, or (ii) the physiological gene conversion is mediated by a tightly regulated DSB that is locally protected from non-homologous end joining (NHEJ) or other non-homologous DNA recombination machineries.
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Affiliation(s)
- Giulia Bastianello
- IFOM - FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139 Milan, Italy.,Università degli Studi di Milano, Dipartimento di Bioscienze, Via Celoria 26, 20133 Milan, Italy
| | - Hiroshi Arakawa
- IFOM - FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139 Milan, Italy
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