1
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Fujita T, Fujii H. iChIP-SILAC analysis identifies epigenetic regulators of CpG methylation of the p16 INK4A gene. FEBS Lett 2024; 598:1094-1109. [PMID: 38627195 DOI: 10.1002/1873-3468.14878] [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: 02/14/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 05/12/2024]
Abstract
Allele-specific epigenetic events regulate the expression of specific genes such as tumor suppressor genes. Methods to biochemically identify epigenetic regulators remain limited. Here, we used insertional chromatin immunoprecipitation (iChIP) to address this issue. iChIP combined with quantitative mass spectrometry identified DNA methyltransferase 1 (DNMT1) and epigenetic regulators as proteins that potentially interact with a region of the p16INK4A gene that is CpG-methylated in one allele in HCT116 cells. Some of the identified proteins are involved in the CpG methylation of this region, and of these, DEAD-box helicase 24 (DDX24) contributes to CpG methylation by regulating the protein levels of DNMT1. Thus, iChIP is a useful method to identify proteins which bind to a target locus of interest.
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Affiliation(s)
- Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Japan
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2
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MacKenzie TMG, Cisneros R, Maynard RD, Snyder MP. Reverse-ChIP Techniques for Identifying Locus-Specific Proteomes: A Key Tool in Unlocking the Cancer Regulome. Cells 2023; 12:1860. [PMID: 37508524 PMCID: PMC10377898 DOI: 10.3390/cells12141860] [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: 05/29/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
A phenotypic hallmark of cancer is aberrant transcriptional regulation. Transcriptional regulation is controlled by a complicated array of molecular factors, including the presence of transcription factors, the deposition of histone post-translational modifications, and long-range DNA interactions. Determining the molecular identity and function of these various factors is necessary to understand specific aspects of cancer biology and reveal potential therapeutic targets. Regulation of the genome by specific factors is typically studied using chromatin immunoprecipitation followed by sequencing (ChIP-Seq) that identifies genome-wide binding interactions through the use of factor-specific antibodies. A long-standing goal in many laboratories has been the development of a 'reverse-ChIP' approach to identify unknown binding partners at loci of interest. A variety of strategies have been employed to enable the selective biochemical purification of sequence-defined chromatin regions, including single-copy loci, and the subsequent analytical detection of associated proteins. This review covers mass spectrometry techniques that enable quantitative proteomics before providing a survey of approaches toward the development of strategies for the purification of sequence-specific chromatin as a 'reverse-ChIP' technique. A fully realized reverse-ChIP technique holds great potential for identifying cancer-specific targets and the development of personalized therapeutic regimens.
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Affiliation(s)
| | - Rocío Cisneros
- Sarafan ChEM-H/IMA Postbaccalaureate Fellow in Target Discovery, Stanford University, Stanford, CA 94305, USA
| | - Rajan D Maynard
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Genetics Department, Stanford University, Stanford, CA 94305, USA
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3
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Mondal S, Ramanathan M, Miao W, Meyers RM, Rao D, Lopez-Pajares V, Siprashvili Z, Reynolds DL, Porter DF, Ferguson I, Neela P, Zhao Y, Meservey LM, Guo M, Yang YY, Li L, Wang Y, Khavari PA. PROBER identifies proteins associated with programmable sequence-specific DNA in living cells. Nat Methods 2022; 19:959-968. [PMID: 35927480 PMCID: PMC10202087 DOI: 10.1038/s41592-022-01552-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/20/2022] [Indexed: 11/08/2022]
Abstract
DNA-protein interactions mediate physiologic gene regulation and may be altered by DNA variants linked to polygenic disease. To enhance the speed and signal-to-noise ratio (SNR) in the identification and quantification of proteins associated with specific DNA sequences in living cells, we developed proximal biotinylation by episomal recruitment (PROBER). PROBER uses high-copy episomes to amplify SNR, and proximity proteomics (BioID) to identify the transcription factors and additional gene regulators associated with short DNA sequences of interest. PROBER quantified both constitutive and inducible association of transcription factors and corresponding chromatin regulators to target DNA sequences and binding quantitative trait loci due to single-nucleotide variants. PROBER identified alterations in regulator associations due to cancer hotspot mutations in the hTERT promoter, indicating that these mutations increase promoter association with specific gene activators. PROBER provides an approach to rapidly identify proteins associated with specific DNA sequences and their variants in living cells.
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Affiliation(s)
- Smarajit Mondal
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | | | - Weili Miao
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | - Robin M Meyers
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | - Deepti Rao
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | | | - Zurab Siprashvili
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | - David L Reynolds
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | - Douglas F Porter
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | - Ian Ferguson
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | - Poornima Neela
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | - Yang Zhao
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
| | | | - Margaret Guo
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA
- Program in Biomedical Informatics, Stanford University, Stanford, CA, USA
| | - Yen-Yu Yang
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Lin Li
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Veterans Affairs, Palo Alto Healthcare System, Palo Alto, CA, USA.
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4
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Fujii H. pSIR-bsr, a self-inactivating retrovirus vector expressing the blasticidin S-resistance gene. Biol Methods Protoc 2021; 6:bpab022. [PMID: 34926829 PMCID: PMC8678448 DOI: 10.1093/biomethods/bpab022] [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: 10/16/2021] [Revised: 11/23/2021] [Accepted: 12/01/2021] [Indexed: 11/23/2022] Open
Abstract
Self-inactivating retrovirus vectors are useful tools for generating stable cell lines harbouring designed exogenous sequences but lacking the constitutive transcriptional activity of the long terminal repeats that are usually retained by non-self-inactivating retrovirus vectors. Thus, self-inactivating retrovirus vectors are ideal vehicles for integrated transgenes comprising transcriptional regulatory sequences, and for the genes expressed by these regulatory sequences. This article describes the development of a self-inactivating retrovirus vector retaining a blasticidin S-resistance (bsr) gene. The vector, named pSIR-bsr, would be useful for transducing multiple expression vectors with different selection markers.
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Affiliation(s)
- Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori 036-8562, Japan
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5
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Li J, Xu B, He M, Zong X, Cunningham T, Sha C, Fan Y, Cross R, Hanna JH, Feng Y. Control of Foxp3 induction and maintenance by sequential histone acetylation and DNA demethylation. Cell Rep 2021; 37:110124. [PMID: 34910919 PMCID: PMC8711072 DOI: 10.1016/j.celrep.2021.110124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 09/07/2021] [Accepted: 11/22/2021] [Indexed: 12/18/2022] Open
Abstract
Regulatory T (Treg) cells play crucial roles in suppressing deleterious immune response. Here, we investigate how Treg cells are mechanistically induced in vitro (iTreg) and stabilized via transcriptional regulation of Treg lineage-specifying factor Foxp3. We find that acetylation of histone tails at the Foxp3 promoter is required for inducing Foxp3 transcription. Upon induction, histone acetylation signals via bromodomain-containing proteins, particularly targets of inhibitor JQ1, and sustains Foxp3 transcription via a global or trans effect. Subsequently, Tet-mediated DNA demethylation of Foxp3 cis-regulatory elements, mainly enhancer CNS2, increases chromatin accessibility and protein binding, stabilizing Foxp3 transcription and obviating the need for the histone acetylation signal. These processes transform stochastic iTreg induction into a stable cell fate, with the former sensitive and the latter resistant to genetic and environmental perturbations. Thus, sequential histone acetylation and DNA demethylation in Foxp3 induction and maintenance reflect stepwise mechanical switches governing iTreg cell lineage specification.
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Affiliation(s)
- Jun Li
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Minghong He
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xinying Zong
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Trevor Cunningham
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cher Sha
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Richard Cross
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yongqiang Feng
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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6
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Javaid N, Choi S. CRISPR/Cas System and Factors Affecting Its Precision and Efficiency. Front Cell Dev Biol 2021; 9:761709. [PMID: 34901007 PMCID: PMC8652214 DOI: 10.3389/fcell.2021.761709] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/01/2021] [Indexed: 12/20/2022] Open
Abstract
The diverse applications of genetically modified cells and organisms require more precise and efficient genome-editing tool such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas). The CRISPR/Cas system was originally discovered in bacteria as a part of adaptive-immune system with multiple types. Its engineered versions involve multiple host DNA-repair pathways in order to perform genome editing in host cells. However, it is still challenging to get maximum genome-editing efficiency with fewer or no off-targets. Here, we focused on factors affecting the genome-editing efficiency and precision of CRISPR/Cas system along with its defense-mechanism, orthologues, and applications.
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Affiliation(s)
- Nasir Javaid
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- S&K Therapeutics, Ajou University Campus Plaza, Suwon, South Korea
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7
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Zhang H, Qin C, An C, Zheng X, Wen S, Chen W, Liu X, Lv Z, Yang P, Xu W, Gao W, Wu Y. Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer. Mol Cancer 2021; 20:126. [PMID: 34598686 PMCID: PMC8484294 DOI: 10.1186/s12943-021-01431-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/19/2021] [Indexed: 02/06/2023] Open
Abstract
The 2020 Nobel Prize in Chemistry was awarded to Emmanuelle Charpentier and Jennifer Doudna for the development of the Clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease9 (CRISPR/Cas9) gene editing technology that provided new tools for precise gene editing. It is possible to target any genomic locus virtually using only a complex nuclease protein with short RNA as a site-specific endonuclease. Since cancer is caused by genomic changes in tumor cells, CRISPR/Cas9 can be used in the field of cancer research to edit genomes for exploration of the mechanisms of tumorigenesis and development. In recent years, the CRISPR/Cas9 system has been increasingly used in cancer research and treatment and remarkable results have been achieved. In this review, we introduced the mechanism and development of the CRISPR/Cas9-based gene editing system. Furthermore, we summarized current applications of this technique for basic research, diagnosis and therapy of cancer. Moreover, the potential applications of CRISPR/Cas9 in new emerging hotspots of oncology research were discussed, and the challenges and future directions were highlighted.
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Affiliation(s)
- Huimin Zhang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Chunhong Qin
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.,Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Changming An
- Department of Head and Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiwang Zheng
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.,General Hospital, Clinical Medical Academy, Shenzhen University, Shenzhen, 518055, Guangdong, China
| | - Shuxin Wen
- Department of Otolaryngology Head & Neck Surgery, Shanxi Bethune Hospital, Taiyuan, 030032, Shanxi, China
| | - Wenjie Chen
- Department of Otolaryngology Head & Neck Surgery, Shanxi Bethune Hospital, Taiyuan, 030032, Shanxi, China
| | - Xianfang Liu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250022, Shandong, China
| | - Zhenghua Lv
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250022, Shandong, China
| | - Pingchang Yang
- Research Center of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, 518055, Guangdong, China.,Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen, 518055, Guangdong, China
| | - Wei Xu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250022, Shandong, China.
| | - Wei Gao
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China. .,General Hospital, Clinical Medical Academy, Shenzhen University, Shenzhen, 518055, Guangdong, China. .,Department of Cell biology and Genetics, Basic Medical School of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
| | - Yongyan Wu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China. .,Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China. .,General Hospital, Clinical Medical Academy, Shenzhen University, Shenzhen, 518055, Guangdong, China.
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8
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Yuno M, Nagata S, Fujita T, Fujii H. MSCV-based retroviral plasmids expressing 3xFLAG-Sp-dCas9 for enChIP analysis. Biol Methods Protoc 2021; 6:bpab013. [PMID: 34409168 PMCID: PMC8365529 DOI: 10.1093/biomethods/bpab013] [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: 03/05/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/17/2022] Open
Abstract
Engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) is a technology for purifying specific genomic regions to facilitate identification of their associated molecules, including proteins, RNAs, and other genomic regions. In enChIP, the target genomic region is tagged with engineered DNA-binding molecules, for example, a variant of the clustered regularly interspaced short palindromic repeats (CRISPR) system consisting of a guide RNA (gRNA) and a catalytically inactive form of Cas9 (dCas9). In this study, to increase the flexibility of enChIP and expand the range of target cells, we generated murine stem cell virus (MSCV)-based retroviral plasmids for expressing dCas9. We constructed MSCV-based retroviral plasmids expressing Streptococcus pyogenes dCas9 fused to a 3xFLAG-tag (3xFLAG-Sp-dCas9) and various drug resistance genes. We showed that by using these plasmids, it is feasible to purify target genomic regions with yields comparable to those reported using other systems. These systems might give enChIP users greater flexibility in choosing optimal systems for drug selection of transduced cells.
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Affiliation(s)
- Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shoko Nagata
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
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9
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Saifaldeen M, Al-Ansari DE, Ramotar D, Aouida M. Dead Cas9-sgRNA Complex Shelters Vulnerable DNA Restriction Enzyme Sites from Cleavage for Cloning Applications. CRISPR J 2021; 4:275-289. [PMID: 33876957 DOI: 10.1089/crispr.2020.0134] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The creation of the nuclease-dead Cas protein (dCas9) offers a new platform for a plethora of new discoveries. Diverse dCas9 tools have been developed for transcription regulation, epigenetic engineering, base editing, genome imaging, genetic screens, and chromatin immunoprecipitation. Here, we show that dCas9 and single-guide RNA preassembled to form ribonucleoprotein dCas9-sgRNA (referred to as dRNP) is capable of specifically and reversibly blocking the activity of DNA cleavage by restriction enzymes (REs). We show that the inhibition of RE activities occurs when the recognition or the cleavage site of the DNA is overlapped by the sgRNA or the protospacer adjacent motif sequence. Furthermore, we show that multiple dRNPs can be used simultaneously to inhibit more than one RE sites. As such, we exploited this novel finding as a method to demonstrate that inserts can be ligated into vectors, and vice versa, whereby selective RE sites are temporarily sheltered to allow the desired cloning.
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Affiliation(s)
- Maryam Saifaldeen
- College of Health and Life Sciences, Division of Biological and Biomedical Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Dana E Al-Ansari
- College of Health and Life Sciences, Division of Biological and Biomedical Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Dindial Ramotar
- College of Health and Life Sciences, Division of Biological and Biomedical Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Mustapha Aouida
- College of Health and Life Sciences, Division of Biological and Biomedical Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
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10
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Fujita H, Fujita T, Fujii H. Locus-Specific Genomic DNA Purification Using the CRISPR System: Methods and Applications. CRISPR J 2021; 4:290-300. [PMID: 33876963 DOI: 10.1089/crispr.2020.0038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A multitude of molecular interactions with chromatin governs various chromosomal functions in cells. Insights into the molecular compositions at specific genomic regions are pivotal to deepen our understanding of regulatory mechanisms and the pathogenesis of disorders caused by the abnormal regulation of genes. The locus-specific purification of genomic DNA using the clustered regularly interspaced short palindromic repeats (CRISPR) system enables the isolation of target genomic regions for identification of bound interacting molecules. This CRISPR-based DNA purification method has many applications. In this study, we present an overview of the CRISPR-based DNA purification methodologies as well as recent applications.
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Affiliation(s)
- Hirotaka Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | - Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Aomori, Japan
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11
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Hu M, Cherkaoui I, Misra S, Rutter GA. Functional Genomics in Pancreatic β Cells: Recent Advances in Gene Deletion and Genome Editing Technologies for Diabetes Research. Front Endocrinol (Lausanne) 2020; 11:576632. [PMID: 33162936 PMCID: PMC7580382 DOI: 10.3389/fendo.2020.576632] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
The inheritance of variants that lead to coding changes in, or the mis-expression of, genes critical to pancreatic beta cell function can lead to alterations in insulin secretion and increase the risk of both type 1 and type 2 diabetes. Recently developed clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) gene editing tools provide a powerful means of understanding the impact of identified variants on cell function, growth, and survival and might ultimately provide a means, most likely after the transplantation of genetically "corrected" cells, of treating the disease. Here, we review some of the disease-associated genes and variants whose roles have been probed up to now. Next, we survey recent exciting developments in CRISPR/Cas9 technology and their possible exploitation for β cell functional genomics. Finally, we will provide a perspective as to how CRISPR/Cas9 technology may find clinical application in patients with diabetes.
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Affiliation(s)
- Ming Hu
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Ines Cherkaoui
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Shivani Misra
- Metabolic Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
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12
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Loo CS, Gatchalian J, Liang Y, Leblanc M, Xie M, Ho J, Venkatraghavan B, Hargreaves DC, Zheng Y. A Genome-wide CRISPR Screen Reveals a Role for the Non-canonical Nucleosome-Remodeling BAF Complex in Foxp3 Expression and Regulatory T Cell Function. Immunity 2020; 53:143-157.e8. [PMID: 32640256 PMCID: PMC7341821 DOI: 10.1016/j.immuni.2020.06.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/20/2020] [Accepted: 06/12/2020] [Indexed: 12/21/2022]
Abstract
Regulatory T (Treg) cells play a pivotal role in suppressing auto-reactive T cells and maintaining immune homeostasis. Treg cell development and function are dependent on the transcription factor Foxp3. Here, we performed a genome-wide CRISPR loss-of-function screen to identify Foxp3 regulators in mouse primary Treg cells. Foxp3 regulators were enriched in genes encoding subunits of the SWI/SNF nucleosome-remodeling and SAGA chromatin-modifying complexes. Among the three SWI/SNF-related complexes, the Brd9-containing non-canonical (nc) BAF complex promoted Foxp3 expression, whereas the PBAF complex was repressive. Chemical-induced degradation of Brd9 led to reduced Foxp3 expression and reduced Treg cell function in vitro. Brd9 ablation compromised Treg cell function in inflammatory disease and tumor immunity in vivo. Furthermore, Brd9 promoted Foxp3 binding and expression of a subset of Foxp3 target genes. Our findings provide an unbiased analysis of the genetic networks regulating Foxp3 and reveal ncBAF as a target for therapeutic manipulation of Treg cell function.
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Affiliation(s)
- Chin-San Loo
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jovylyn Gatchalian
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yuqiong Liang
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mathias Leblanc
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mingjun Xie
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Josephine Ho
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bhargav Venkatraghavan
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Diana C Hargreaves
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Ye Zheng
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA.
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13
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Huang Y, Xiang Y, Xie Z, Cai Y, Yang Q, Huang H, Chen Z, Xiao Z, He Q. Mass spectrometry-based proteomic capture of proteins bound to the MACC1 promoter in colon cancer. Clin Exp Metastasis 2020; 37:477-487. [PMID: 32613480 DOI: 10.1007/s10585-020-10045-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/07/2020] [Indexed: 12/20/2022]
Abstract
MACC1 (metastasis associated in colon cancer 1) is a key driver that induces metastasis in colon cancer. However, the mechanisms by which MACC1 expression is transcriptionally regulated and the factors enriched at the MACC1 promoter remain largely unknown. The binding of proteins to specific DNA sites in the genome is a major determinant of genomic maintenance and the regulation of specific genes. The study herein utilized two methods to study the binding proteins of the MACC1 promoter region in colon cancer. Specifically, we adopted CRISPR-based chromatin affinity purification with mass spectrometry (CRISPR-ChAP-MS) and a biotin-streptavidin pulldown assay coupled with MS to identify the specific proteome bound to the MACC1 promoter in two colon cell lines with different metastatic potential. A total of 24 proteins were identified by CRISPR-ChAP-MS as binding to the MACC1 promoter, among which c-JUN was validated by ChIP-PCR. A total of 739 binding protein candidates were identified by biotin-streptavidin pulldown assays coupled with MS, of which HNF4G and PAX6 were validated and compared for their binding to the same promoter sites in the two cell lines. Our studies suggest distinctive proteomic factors associated with the MACC1 promoter in colon cells with different metastatic potential. The dynamic regulatory factors accumulated at the promoter of MACC1 may provide novel insights into the regulatory mechanisms of MACC1 transcription.
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Affiliation(s)
- Yahui Huang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China.,Department of Pathology, Xuchang Central Hospital, Henan University of Science and Technology, Xuchang, Henan, People's Republic of China
| | - Yi Xiang
- School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Zhongpeng Xie
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China.,Department of Pathology, Hainan General Hospital, Haikou, Hainan, People's Republic of China
| | - Yuxiang Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Qiongzhi Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Huichao Huang
- NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Zhuchu Chen
- NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Zhefeng Xiao
- NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.
| | - Qiongqiong He
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China. .,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China.
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14
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Shamsi F, Xue R, Huang TL, Lundh M, Liu Y, Leiria LO, Lynes MD, Kempf E, Wang CH, Sugimoto S, Nigro P, Landgraf K, Schulz T, Li Y, Emanuelli B, Kothakota S, Williams LT, Jessen N, Pedersen SB, Böttcher Y, Blüher M, Körner A, Goodyear LJ, Mohammadi M, Kahn CR, Tseng YH. FGF6 and FGF9 regulate UCP1 expression independent of brown adipogenesis. Nat Commun 2020; 11:1421. [PMID: 32184391 PMCID: PMC7078224 DOI: 10.1038/s41467-020-15055-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/10/2020] [Indexed: 12/21/2022] Open
Abstract
Uncoupling protein-1 (UCP1) plays a central role in energy dissipation in brown adipose tissue (BAT). Using high-throughput library screening of secreted peptides, we identify two fibroblast growth factors (FGF), FGF6 and FGF9, as potent inducers of UCP1 expression in adipocytes and preadipocytes. Surprisingly, this occurs through a mechanism independent of adipogenesis and involves FGF receptor-3 (FGFR3), prostaglandin-E2 and interaction between estrogen receptor-related alpha, flightless-1 (FLII) and leucine-rich-repeat-(in FLII)-interacting-protein-1 as a regulatory complex for UCP1 transcription. Physiologically, FGF6/9 expression in adipose is upregulated by exercise and cold in mice, and FGF9/FGFR3 expression in human neck fat is significantly associated with UCP1 expression. Loss of FGF9 impairs BAT thermogenesis. In vivo administration of FGF9 increases UCP1 expression and thermogenic capacity. Thus, FGF6 and FGF9 are adipokines that can regulate UCP1 through a transcriptional network that is dissociated from brown adipogenesis, and act to modulate systemic energy metabolism.
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Affiliation(s)
- Farnaz Shamsi
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Ruidan Xue
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
- Division of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tian Lian Huang
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Morten Lundh
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Yang Liu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Luiz O Leiria
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
- Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- Center of Research of Inflammatory Diseases, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Matthew D Lynes
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Elena Kempf
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
- Center for Pediatric Research Leipzig, University Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
| | - Chih-Hao Wang
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Satoru Sugimoto
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Pasquale Nigro
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Kathrin Landgraf
- Center for Pediatric Research Leipzig, University Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
| | - Tim Schulz
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
- German Institute of Human Nutrition, Potsdam-Rehbrücke, Germany
| | - Yiming Li
- Division of Endocrinology and Metabolism, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Brice Emanuelli
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Niels Jessen
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8200, Aarhus N, Denmark
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Steen Bønløkke Pedersen
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8200, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, 8200, Aarhus N, Denmark
| | - Yvonne Böttcher
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology, Akershus Universitetssykehus, Lørenskog, Norway
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Matthias Blüher
- Department of Internal Medicine (Endocrinology and Nephrology), University of Leipzig, Leipzig, Germany
| | - Antje Körner
- Center for Pediatric Research Leipzig, University Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
| | - Laurie J Goodyear
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Moosa Mohammadi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - C Ronald Kahn
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Yu-Hua Tseng
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138, USA.
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15
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Abstract
The prokaryote-derived CRISPR-Cas genome editing systems have transformed our ability to manipulate, detect, image and annotate specific DNA and RNA sequences in living cells of diverse species. The ease of use and robustness of this technology have revolutionized genome editing for research ranging from fundamental science to translational medicine. Initial successes have inspired efforts to discover new systems for targeting and manipulating nucleic acids, including those from Cas9, Cas12, Cascade and Cas13 orthologues. Genome editing by CRISPR-Cas can utilize non-homologous end joining and homology-directed repair for DNA repair, as well as single-base editing enzymes. In addition to targeting DNA, CRISPR-Cas-based RNA-targeting tools are being developed for research, medicine and diagnostics. Nuclease-inactive and RNA-targeting Cas proteins have been fused to a plethora of effector proteins to regulate gene expression, epigenetic modifications and chromatin interactions. Collectively, the new advances are considerably improving our understanding of biological processes and are propelling CRISPR-Cas-based tools towards clinical use in gene and cell therapies.
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Affiliation(s)
- Adrian Pickar-Oliver
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
- Department of Surgery, Duke University Medical Center, Durham, NC, USA.
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16
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Fujita T, Fujii H. Purification of specific DNA species using the CRISPR system. Biol Methods Protoc 2019; 4:bpz008. [PMID: 32395626 PMCID: PMC7200925 DOI: 10.1093/biomethods/bpz008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/02/2019] [Accepted: 06/07/2019] [Indexed: 11/30/2022] Open
Abstract
In 2013, we developed a new method of engineered DNA-binding molecule-mediated chromatin immunoprecipitation that incorporates the clustered regularly interspaced short palindromic repeats (CRISPR) system to purify specific DNA species. This CRISPR-mediated purification can be performed in-cell or in vitro; CRISPR complexes can be expressed to tag target DNA sequences in the cells to be analyzed, or a CRISPR ribonucleoprotein complex consisting of recombinant nuclease-dead Cas9 (dCas9) and synthetic guide RNA can be used to tag target DNA sequences in vitro. Both methods enable purification of specific DNA sequences in chromatin structures for subsequent identification of molecules (proteins, RNAs, and other genomic regions) associated with the target sequences. The in vitro method also enables enrichment of purified DNA sequences from a pool of heterogeneous sequences for next-generation sequencing or other applications. In this review, we outline the principle of CRISPR-mediated purification of specific DNA species and discuss recent advances in the technology.
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Affiliation(s)
- Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Zaifu-cho 5, Hirosaki, Aomori, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Zaifu-cho 5, Hirosaki, Aomori, Japan
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17
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Xu X, Qi LS. A CRISPR–dCas Toolbox for Genetic Engineering and Synthetic Biology. J Mol Biol 2019; 431:34-47. [DOI: 10.1016/j.jmb.2018.06.037] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/20/2018] [Accepted: 06/20/2018] [Indexed: 12/21/2022]
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18
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Lavender P, Kelly A, Hendy E, McErlean P. CRISPR-based reagents to study the influence of the epigenome on gene expression. Clin Exp Immunol 2018; 194:9-16. [PMID: 30030848 PMCID: PMC6156815 DOI: 10.1111/cei.13190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2018] [Indexed: 12/22/2022] Open
Abstract
The use of epigenome editing is set to expand our knowledge of how epigenetic landscapes facilitate gene expression capacity within a given cell. As epigenetic landscape profiling in health and disease becomes more commonplace, so does the requirement to assess the functional impact that particular regulatory domains and DNA methylation profiles have upon gene expression capacity. That functional assessment is particularly pertinent when analysing epigenomes in disease states where the reversible nature of histone and DNA modification might yield plausible therapeutic targets. In this review we discuss first the nature of the epigenetic landscape, secondly the types of factors that deposit and erase the various modifications, consider how modifications transduce their signals, and lastly address current tools for experimental epigenome editing with particular emphasis on the immune system.
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Affiliation(s)
- P. Lavender
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial ScienceMRC and Asthma UK Centre in Allergic Mechanisms of Asthma, King’s College LondonLondonUK
| | - A. Kelly
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial ScienceMRC and Asthma UK Centre in Allergic Mechanisms of Asthma, King’s College LondonLondonUK
| | - E. Hendy
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial ScienceMRC and Asthma UK Centre in Allergic Mechanisms of Asthma, King’s College LondonLondonUK
| | - P. McErlean
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial ScienceMRC and Asthma UK Centre in Allergic Mechanisms of Asthma, King’s College LondonLondonUK
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19
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Liu X, Zhang Y, Chen Y, Li M, Shao Z, Zhang MQ, Xu J. CAPTURE: In Situ Analysis of Chromatin Composition of Endogenous Genomic Loci by Biotinylated dCas9. ACTA ACUST UNITED AC 2018; 123:e64. [PMID: 29927077 DOI: 10.1002/cpmb.64] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cis-regulatory elements (CREs) play a pivotal role in spatiotemporal control of tissue-specific gene expression, yet the molecular composition of the vast majority of CREs in native chromatin remains unknown. In this article, we describe the clustered regularly interspaced short palindromic repeats (CRISPR) affinity purification in situ of regulatory elements (CAPTURE) approach to simultaneously identify locus-specific chromatin-regulating protein complexes and long-range DNA interactions. Using an in vivo biotinylated nuclease-deficient Cas9 (dCas9) protein and programmable single guide RNAs (sgRNAs), this approach allows for high-resolution and locus-specific isolation of protein complexes and long-range chromatin looping associated with single copy CREs in mammalian cells. Unbiased analysis of the compositional structure of developmentally regulated or disease-associated CREs identifies new features of transcriptional regulation. Hence, CAPTURE provides a versatile platform to study genomic locus-regulating chromatin composition in a mammalian genome. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Xin Liu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yong Chen
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, Texas
| | - Mushan Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhen Shao
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Michael Q Zhang
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, Texas
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
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20
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Hamidian A, Vaapil M, von Stedingk K, Fujita T, Persson CU, Eriksson P, Veerla S, De Preter K, Speleman F, Fujii H, Påhlman S, Mohlin S. Promoter-associated proteins of EPAS1 identified by enChIP-MS - A putative role of HDX as a negative regulator. Biochem Biophys Res Commun 2018; 499:291-298. [PMID: 29577908 DOI: 10.1016/j.bbrc.2018.03.150] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 03/20/2018] [Indexed: 11/21/2022]
Abstract
Presence of perivascular neuroblastoma cells with high expression of hypoxia inducible factor (HIF)-2α correlates with distant metastasis and aggressive disease. Regulation of HIFs are traditionally considered to occur post-translationally, but we have recently shown that HIF-2α is unconventionally regulated also at the transcriptional level in neuroblastoma cells. Regulatory factors binding directly to EPAS1 (encoding HIF-2α) to promote transcription are yet to be defined. Here, we employ the novel CRISPR/Cas9-based engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) - mass spectrometry (MS) methodology to, in an unbiased fashion, identify proteins that associate with the EPAS1 promoter under normoxic and hypoxic conditions. Our enChIP analysis resulted in 27 proteins binding to the EPAS1 promoter in neuroblastoma cells. In agreement with a general hypoxia-driven downregulation of gene transcription, the majority (24 out of 27) of proteins dissociate from the promoter at hypoxia. Among them were several nucleosome-associated proteins suggesting a general opening of chromatin as one explanation to induced EPAS1 transcription at hypoxia. Of particular interest from the list of released factors at hypoxia was the highly divergent homeobox (HDX) transcription factor, that we show inversely correlates with HIF-2α in neuroblastoma cells. We propose a putative model where HDX negatively regulates EPAS1 expression through a release-of-inhibition mechanism.
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Affiliation(s)
- Arash Hamidian
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | - Marica Vaapil
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | | | - Toshitsugu Fujita
- Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita City, Osaka, 565-0871, Japan; Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Zaifu-cho 5, Hirosaki, Aomori Prefecture, 036-8562, Japan
| | - Camilla U Persson
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | - Pontus Eriksson
- Department of Oncology and Pathology, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Srinivas Veerla
- Department of Oncology and Pathology, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University, Ghent, B-9000, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, B-9000, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, B-9000, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, B-9000, Ghent, Belgium
| | - Hodaka Fujii
- Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita City, Osaka, 565-0871, Japan; Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Zaifu-cho 5, Hirosaki, Aomori Prefecture, 036-8562, Japan
| | - Sven Påhlman
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | - Sofie Mohlin
- Department of Pediatrics, Clinical Sciences, Lund University, Lund, Sweden.
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21
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Fujita T, Yuno M, Fujii H. enChIP systems using different CRISPR orthologues and epitope tags. BMC Res Notes 2018; 11:154. [PMID: 29482606 PMCID: PMC5828479 DOI: 10.1186/s13104-018-3262-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/17/2018] [Indexed: 12/15/2022] Open
Abstract
Objective Previously, we developed the engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) technology, which isolates specific genomic regions while preserving their molecular interactions. In enChIP, the locus of interest is tagged with engineered DNA-binding molecules such as the clustered regularly interspaced short palindromic repeats (CRISPR) system, consisting of a catalytically inactive form of Cas9 (dCas9) and guide RNA, followed by affinity purification of the tagged locus to allow identification of associated molecules. In our previous studies, we used a 3xFLAG-tagged CRISPR system from Streptococcus pyogenes (S. pyogenes). In this study, to increase the flexibility of enChIP, we used the CRISPR system from Staphylococcus aureus (S. aureus) along with different epitope tags. Results We generated a plasmid expressing S. aureus dCas9 (Sa-dCas9) fused to a nuclear localization signal (NLS) and a 3xFLAG-tag (Sa-dCas9-3xFLAG). The yields of enChIP using Sa-dCas9-3xFLAG were comparable to those using S. pyogenes dCas9 fused with an NLS and a 3xFLAG-tag (3xFLAG-Sp-dCas9). We also generated another enChIP system using Sp-dCas9 fused with an NLS and a 2xAM-tag (Sp-dCas9-2xAM). We obtained high enChIP yields using this system as well. Our findings indicate that these tools will increase the flexibility of enChIP analysis.
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Affiliation(s)
- Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan.,Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan. .,Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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22
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Han B, Zhou B, Qu Y, Gao B, Xu Y, Chung S, Tanaka H, Yang W, Giuliano AE, Cui X. FOXC1-induced non-canonical WNT5A-MMP7 signaling regulates invasiveness in triple-negative breast cancer. Oncogene 2017; 37:1399-1408. [PMID: 29249801 PMCID: PMC5844802 DOI: 10.1038/s41388-017-0021-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/13/2017] [Accepted: 10/19/2017] [Indexed: 12/12/2022]
Abstract
Triple-negative breast cancer (TNBC) has high rates of local recurrence and distant metastasis, partially due to its high invasiveness. The Forkhead box C1 (FOXC1) transcription factor has been shown to be specifically overexpressed in TNBC and associated with poor clinical outcome. How TNBC’s high invasiveness is driven by FOXC1 and its downstream targets remains poorly understood. In the present study, pathway-specific PCR array assays revealed that WNT5A and matrix metalloproteinase-7 (MMP7) were upregulated by FOXC1 in TNBC cells. Interestingly, WNT5A mediates the upregulation of MMP7 by FOXC1 and the WNT5A-MMP7 axis is essential for FOXC1-induced invasiveness of TNBC cells in vitro. Xenograft models showed that the lung extravasation and metastasis of FOXC1-overexpressing TNBC cells were attenuated by knocking out WNT5A, but could be restored by MMP7 overexpression. Mechanistically, FOXC1 can bind directly to the WNT5A promoter region to activate its expression. Engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP), coupled with mass spectrometry, identified FOXC1-interacting proteins including a group of heterogeneous nuclear ribonucleoproteins involved in WNT5A transcription induction. Finally, we found that WNT5A activates NF-κB signaling to induce MMP7 expression. Collectively, these data demonstrate a FOXC1-elicited non-canonical WNT5A signaling mechanism comprising NF-κB and MMP7 that is essential for TNBC cell invasiveness, thereby providing implications toward developing an effective therapy for TNBC.
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Affiliation(s)
- Bingchen Han
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bo Zhou
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ying Qu
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bowen Gao
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yali Xu
- Department of Breast Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Stacey Chung
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hisashi Tanaka
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Wei Yang
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Armando E Giuliano
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xiaojiang Cui
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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23
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Fujita T, Kitaura F, Yuno M, Suzuki Y, Sugano S, Fujii H. Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in a chicken B cell line. DNA Res 2017; 24:537-548. [PMID: 28586432 PMCID: PMC5737561 DOI: 10.1093/dnares/dsx023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/04/2017] [Indexed: 12/05/2022] Open
Abstract
Chromosomal interactions regulate genome functions, such as transcription, via dynamic chromosomal organization in the nucleus. In this study, we attempted to identify genomic regions that physically bind to the promoter region of the Pax5 gene, which encodes a master regulator for B cell lineage commitment, in a chicken B cell line, DT40, with the goal of obtaining mechanistic insight into transcriptional regulation through chromosomal interaction. We found that the Pax5 promoter bound to multiple genomic regions using locus-specific chromatin immunoprecipitation (locus-specific ChIP), a method for locus-specific isolation of target genomic regions, in combination with next-generation sequencing (NGS). Comparing chromosomal interactions in wild-type DT40 with those in a macrophage-like counterpart, we found that some of the identified chromosomal interactions were organized in a B cell-specific manner. In addition, deletion of a B cell-specific interacting genomic region in chromosome 11, which was marked by active enhancer histone modifications, resulted in moderate but significant down-regulation of Pax5 transcription. Together, these results suggested that Pax5 transcription in DT40 is regulated by B cell-specific inter-chromosomal interactions. Moreover, these analyses showed that locus-specific ChIP combined with NGS analysis is useful for non-biased identification of functional genomic regions that physically interact with a locus of interest.
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Affiliation(s)
- Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori 036-8562, Japan.,Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Fusako Kitaura
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.,Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.,Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori 036-8562, Japan.,Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
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24
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Powell SK, Gregory J, Akbarian S, Brennand KJ. Application of CRISPR/Cas9 to the study of brain development and neuropsychiatric disease. Mol Cell Neurosci 2017; 82:157-166. [PMID: 28549865 DOI: 10.1016/j.mcn.2017.05.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/22/2017] [Indexed: 12/18/2022] Open
Abstract
CRISPR/Cas9 technology has transformed our ability to manipulate the genome and epigenome, from efficient genomic editing to targeted localization of effectors to specific loci. Through the manipulation of DNA- and histone-modifying enzyme activities, activation or repression of gene expression, and targeting of transcriptional regulators, the role of gene-regulatory and epigenetic pathways in basic biology and disease processes can be directly queried. Here, we discuss emerging CRISPR-based methodologies, with specific consideration of neurobiological applications of human induced pluripotent stem cell (hiPSC)-based models.
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Affiliation(s)
- S K Powell
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - J Gregory
- Instructional Technology Group, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - S Akbarian
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - K J Brennand
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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25
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Fujita T, Yuno M, Suzuki Y, Sugano S, Fujii H. Identification of physical interactions between genomic regions by enChIP-Seq. Genes Cells 2017; 22:506-520. [PMID: 28474362 DOI: 10.1111/gtc.12492] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/22/2017] [Indexed: 01/23/2023]
Abstract
Physical interactions between genomic regions play critical roles in the regulation of genome functions, including gene expression. Here, we show the feasibility of using engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) in combination with next-generation sequencing (NGS) (enChIP-Seq) to detect such interactions. In enChIP-Seq, the target genomic region is captured by an engineered DNA-binding complex, such as a clustered regularly interspaced short palindromic repeats (CRISPR) system consisting of a catalytically inactive form of Cas9 and a single guide RNA. Subsequently, the genomic regions that physically interact with the target genomic region in the captured complex are sequenced by NGS. Using enChIP-Seq, we found that the 5'HS5 locus, which is involved in the regulation of globin genes expression at the β-globin locus, interacts with multiple genomic regions upon erythroid differentiation in the human erythroleukemia cell line K562. Genes near the genomic regions inducibly associated with the 5'HS5 locus were transcriptionally up-regulated in the differentiated state, suggesting the existence of a coordinated transcription mechanism mediated by physical interactions between these loci. Thus, enChIP-Seq might be a potentially useful tool for detecting physical interactions between genomic regions in a nonbiased manner, which would facilitate elucidation of the molecular mechanisms underlying regulation of genome functions.
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Affiliation(s)
- Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.,Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.,Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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26
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Abstract
Prokaryotes use diverse strategies to improve fitness in the face of different environmental threats and stresses, including those posed by mobile genetic elements (e.g., bacteriophages and plasmids). To defend against these elements, many bacteria and archaea use elegant, RNA-directed, nucleic acid-targeting adaptive restriction machineries called CRISPR -: Cas (CRISPR-associated) systems. While providing an effective defense against foreign genetic elements, these systems have also been observed to play critical roles in regulating bacterial physiology during environmental stress. Increasingly, CRISPR-Cas systems, in particular the Type II systems containing the Cas9 endonuclease, have been exploited for their ability to bind desired nucleic acid sequences, as well as direct sequence-specific cleavage of their targets. Cas9-mediated genome engineering is transcending biological research as a versatile and portable platform for manipulating genetic content in myriad systems. Here, we present a systematic overview of CRISPR-Cas history and biology, highlighting the revolutionary tools derived from these systems, which greatly expand the molecular biologists' toolkit.
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Affiliation(s)
- Hannah K Ratner
- Department of Microbiology and Immunology, Microbiology and Molecular Genetics Program, Emory University, Atlanta, Georgia 30329
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30329
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329
| | - Timothy R Sampson
- Department of Microbiology and Immunology, Microbiology and Molecular Genetics Program, Emory University, Atlanta, Georgia 30329
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30329
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329
| | - David S Weiss
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30329
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30329
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27
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Fujita T, Yuno M, Fujii H. Allele-specific locus binding and genome editing by CRISPR at the p16INK4a locus. Sci Rep 2016; 6:30485. [PMID: 27465215 PMCID: PMC4964623 DOI: 10.1038/srep30485] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 07/06/2016] [Indexed: 01/08/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system has been adopted for a wide range of biological applications including genome editing. In some cases, dissection of genome functions requires allele-specific genome editing, but the use of CRISPR for this purpose has not been studied in detail. In this study, using the p16INK4a gene in HCT116 as a model locus, we investigated whether chromatin states, such as CpG methylation, or a single-nucleotide gap form in a target site can be exploited for allele-specific locus binding and genome editing by CRISPR in vivo. First, we showed that allele-specific locus binding and genome editing could be achieved by targeting allele-specific CpG-methylated regions, which was successful for one, but not all guide RNAs. In this regard, molecular basis underlying the success remains elusive at this stage. Next, we demonstrated that an allele-specific single-nucleotide gap form could be employed for allele-specific locus binding and genome editing by CRISPR, although it was important to avoid CRISPR tolerance of a single nucleotide mismatch brought about by mismatched base skipping. Our results provide information that might be useful for applications of CRISPR in studies of allele-specific functions in the genomes.
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Affiliation(s)
- Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan
| | - Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan
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28
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Abstract
The Cas9 protein (CRISPR-associated protein 9), derived from type II CRISPR (clustered regularly interspaced short palindromic repeats) bacterial immune systems, is emerging as a powerful tool for engineering the genome in diverse organisms. As an RNA-guided DNA endonuclease, Cas9 can be easily programmed to target new sites by altering its guide RNA sequence, and its development as a tool has made sequence-specific gene editing several magnitudes easier. The nuclease-deactivated form of Cas9 further provides a versatile RNA-guided DNA-targeting platform for regulating and imaging the genome, as well as for rewriting the epigenetic status, all in a sequence-specific manner. With all of these advances, we have just begun to explore the possible applications of Cas9 in biomedical research and therapeutics. In this review, we describe the current models of Cas9 function and the structural and biochemical studies that support it. We focus on the applications of Cas9 for genome editing, regulation, and imaging, discuss other possible applications and some technical considerations, and highlight the many advantages that CRISPR/Cas9 technology offers.
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Affiliation(s)
- Haifeng Wang
- Department of Bioengineering, Stanford University, Stanford, California 94305; , ,
| | - Marie La Russa
- Department of Bioengineering, Stanford University, Stanford, California 94305; , ,
- Biomedical Sciences Graduate Program, University of California, San Francisco, California 94158
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, California 94305; , ,
- Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305
- Chemistry, Engineering and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305
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29
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Fujita T, Yuno M, Fujii H. Efficient sequence-specific isolation of DNA fragments and chromatin by in vitro enChIP technology using recombinant CRISPR ribonucleoproteins. Genes Cells 2016; 21:370-7. [PMID: 26848818 DOI: 10.1111/gtc.12341] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 12/18/2015] [Indexed: 01/08/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system is widely used for various biological applications, including genome editing. We developed engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR to isolate target genomic regions from cells for their biochemical characterization. In this study, we developed 'in vitro enChIP' using recombinant CRISPR ribonucleoproteins (RNPs) to isolate target genomic regions. in vitro enChIP has the great advantage over conventional enChIP of not requiring expression of CRISPR complexes in cells. We first showed that in vitro enChIP using recombinant CRISPR RNPs can be used to isolate target DNA from mixtures of purified DNA in a sequence-specific manner. In addition, we showed that this technology can be used to efficiently isolate target genomic regions, while retaining their intracellular molecular interactions, with negligible contamination from irrelevant genomic regions. Thus, in vitro enChIP technology is of potential use for sequence-specific isolation of DNA, as well as for identification of molecules interacting with genomic regions of interest in vivo in combination with downstream analysis.
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Affiliation(s)
- Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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30
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Fujita T, Fujii H. Isolation of Specific Genomic Regions and Identification of Associated Molecules by enChIP. J Vis Exp 2016:e53478. [PMID: 26862718 PMCID: PMC4781690 DOI: 10.3791/53478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The identification of molecules associated with specific genomic regions of interest is required to understand the mechanisms of regulation of the functions of these regions. To enable the non-biased identification of molecules interacting with a specific genomic region of interest, we recently developed the engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) technique. Here, we describe how to use enChIP to isolate specific genomic regions and identify the associated proteins and RNAs. First, a genomic region of interest is tagged with a transcription activator-like (TAL) protein or a clustered regularly interspaced short palindromic repeats (CRISPR) complex consisting of a catalytically inactive form of Cas9 and a guide RNA. Subsequently, the chromatin is crosslinked and fragmented by sonication. The tagged locus is then immunoprecipitated and the crosslinking is reversed. Finally, the proteins or RNAs that are associated with the isolated chromatin are subjected to mass spectrometric or RNA sequencing analyses, respectively. This approach allows the successful identification of proteins and RNAs associated with a genomic region of interest.
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Affiliation(s)
- Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University;
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31
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Fujita T, Fujii H. Biochemical Analysis of Genome Functions Using Locus-Specific Chromatin Immunoprecipitation Technologies. GENE REGULATION AND SYSTEMS BIOLOGY 2016; 10:1-9. [PMID: 26819551 PMCID: PMC4718151 DOI: 10.4137/grsb.s32520] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/08/2015] [Accepted: 10/18/2015] [Indexed: 01/07/2023]
Abstract
To isolate specific genomic regions that retain their molecular interactions, allowing direct identification of chromatin-bound molecules, we developed two locus-specific chromatin immunoprecipitation (locus-specific ChIP) technologies, insertional ChIP (iChIP) and engineered DNA-binding molecule-mediated ChIP (enChIP) using the clustered regularly interspaced short palindromic repeats (CRISPR) system or transcription activator-like (TAL) proteins. Essentially, a locus-specific ChIP consists of locus-tagging and affinity purification and can be combined with downstream analyses to identify molecules associated with the target genomic regions. In this review, we discuss the applications of locus-specific ChIP to analyze the genome functions, including transcription and epigenetic regulation.
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Affiliation(s)
- Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
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32
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Applications of Engineered DNA-Binding Molecules Such as TAL Proteins and the CRISPR/Cas System in Biology Research. Int J Mol Sci 2015; 16:23143-64. [PMID: 26404236 PMCID: PMC4632690 DOI: 10.3390/ijms161023143] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 08/31/2015] [Accepted: 09/14/2015] [Indexed: 11/16/2022] Open
Abstract
Engineered DNA-binding molecules such as transcription activator-like effector (TAL or TALE) proteins and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) (CRISPR/Cas) system have been used extensively for genome editing in cells of various types and species. The sequence-specific DNA-binding activities of these engineered DNA-binding molecules can also be utilized for other purposes, such as transcriptional activation, transcriptional repression, chromatin modification, visualization of genomic regions, and isolation of chromatin in a locus-specific manner. In this review, we describe applications of these engineered DNA-binding molecules for biological purposes other than genome editing.
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33
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Fujii H, Fujita T. Isolation of Specific Genomic Regions and Identification of Their Associated Molecules by Engineered DNA-Binding Molecule-Mediated Chromatin Immunoprecipitation (enChIP) Using the CRISPR System and TAL Proteins. Int J Mol Sci 2015; 16:21802-12. [PMID: 26370991 PMCID: PMC4613281 DOI: 10.3390/ijms160921802] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 08/24/2015] [Accepted: 08/29/2015] [Indexed: 01/06/2023] Open
Abstract
Comprehensive understanding of genome functions requires identification of molecules (proteins, RNAs, genomic regions, etc.) bound to specific genomic regions of interest in vivo. To perform biochemical and molecular biological analysis of specific genomic regions, we developed engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) to purify genomic regions of interest. In enChIP, specific genomic regions are tagged for biochemical purification using engineered DNA-binding molecules, such as transcription activator-like (TAL) proteins and a catalytically inactive form of the clustered regularly interspaced short palindromic repeats (CRISPR) system. enChIP is a comprehensive approach that emphasizes non-biased search using next-generation sequencing (NGS), microarrays, mass spectrometry (MS), and other methods. Moreover, this approach is not restricted to cultured cell lines and can be easily extended to organisms. In this review, we discuss applications of enChIP to elucidating the molecular mechanisms underlying genome functions.
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Affiliation(s)
- Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita City, Osaka 565-0871, Japan.
| | - Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita City, Osaka 565-0871, Japan.
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Kotani H, Taimatsu K, Ohga R, Ota S, Kawahara A. Efficient Multiple Genome Modifications Induced by the crRNAs, tracrRNA and Cas9 Protein Complex in Zebrafish. PLoS One 2015; 10:e0128319. [PMID: 26010089 PMCID: PMC4444095 DOI: 10.1371/journal.pone.0128319] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/26/2015] [Indexed: 12/22/2022] Open
Abstract
The type II clustered regularly interspaced short palindromic repeats (CRISPR) associated with Cas9 endonuclease (CRISPR/Cas9) has become a powerful genetic tool for understanding the function of a gene of interest. In zebrafish, the injection of Cas9 mRNA and guide-RNA (gRNA), which are prepared using an in vitro transcription system, efficiently induce DNA double-strand breaks (DSBs) at the targeted genomic locus. Because gRNA was originally constructed by fusing two short RNAs CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA), we examined the effect of synthetic crRNAs and tracrRNA with Cas9 mRNA or Cas9 protein on the genome editing activity. We previously reported that the disruption of tyrosinase (tyr) by tyr-gRNA/Cas9 mRNA causes a retinal pigment defect, whereas the disruption of spns2 by spns2-gRNA1/Cas9 mRNA leads to a cardiac progenitor migration defect in zebrafish. Here, we found that the injection of spns2-crRNA1, tyr-crRNA and tracrRNA with Cas9 mRNA or Cas9 protein simultaneously caused a migration defect in cardiac progenitors and a pigment defect in retinal epithelial cells. A time course analysis demonstrated that the injection of crRNAs and tracrRNA with Cas9 protein rapidly induced genome modifications compared with the injection of crRNAs and tracrRNA with Cas9 mRNA. We further show that the crRNA-tracrRNA-Cas9 protein complex is functional for the visualization of endogenous gene expression; therefore, this is a very powerful, ready-to-use system in zebrafish.
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Affiliation(s)
- Hirohito Kotani
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, Shimokato 1110, Chuo, Yamanashi, Japan
| | - Kiyohito Taimatsu
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, Shimokato 1110, Chuo, Yamanashi, Japan
| | - Rie Ohga
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, Shimokato 1110, Chuo, Yamanashi, Japan
| | - Satoshi Ota
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, Shimokato 1110, Chuo, Yamanashi, Japan
| | - Atsuo Kawahara
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, Shimokato 1110, Chuo, Yamanashi, Japan
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35
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Fujita T, Yuno M, Okuzaki D, Ohki R, Fujii H. Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing. PLoS One 2015; 10:e0123387. [PMID: 25874893 PMCID: PMC4395285 DOI: 10.1371/journal.pone.0123387] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/18/2015] [Indexed: 01/02/2023] Open
Abstract
Accumulating evidence suggests that RNAs interacting with genomic regions play important roles in the regulation of genome functions, including X chromosome inactivation and gene expression. However, to our knowledge, no non-biased methods of identifying RNAs that interact with a specific genomic region have been reported. Here, we used enChIP-RNA-Seq, a combination of engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) and RNA sequencing (RNA-Seq), to perform a non-biased search for RNAs interacting with telomeres. In enChIP-RNA-Seq, the target genomic regions are captured using an engineered DNA-binding molecule such as a transcription activator-like protein. Subsequently, RNAs that interact with the target genomic regions are purified and sequenced. The RNAs detected by enChIP-RNA-Seq contained known telomere-binding RNAs, including the telomerase RNA component (Terc), the RNA component of mitochondrial RNA processing endoribonuclease (Rmrp), and Cajal body-specific RNAs. In addition, a number of novel telomere-binding non-coding RNAs were also identified. Binding of two candidate non-coding RNAs to telomeres was confirmed by immunofluorescence microscopy and RNA fluorescence in situ hybridization (RNA-FISH) analyses. The novel telomere-binding non-coding RNAs identified here may play important roles in telomere functions. To our knowledge, this study is the first non-biased identification of RNAs associated with specific genomic regions. The results presented here suggest that enChIP-RNA-Seq analyses are useful for the identification of RNAs interacting with specific genomic regions, and may help to contribute to current understanding of the regulation of genome functions.
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Affiliation(s)
- Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Daisuke Okuzaki
- DNA-chip Development Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Rieko Ohki
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- * E-mail:
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36
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Fujita T, Kitaura F, Fujii H. A critical role of the Thy28-MYH9 axis in B cell-specific expression of the Pax5 gene in chicken B cells. PLoS One 2015; 10:e0116579. [PMID: 25607658 PMCID: PMC4301804 DOI: 10.1371/journal.pone.0116579] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/11/2014] [Indexed: 11/18/2022] Open
Abstract
Accumulating evidence suggests that Pax5 plays essential roles in B cell lineage commitment. However, molecular mechanisms of B cell-specific expression of Pax5 are not fully understood. Here, we applied insertional chromatin immunoprecipitation (iChIP) combined with stable isotope labeling using amino acids in cell culture (SILAC) (iChIP-SILAC) to direct identification of proteins interacting with the promoter region of the endogenous single-copy chicken Pax5 gene. By comparing B cells with macrophage-like cells trans-differentiated by ectopic expression of C/EBPβ, iChIP-SILAC detected B cell-specific interaction of a nuclear protein, Thy28/Thyn1, with the Pax5 1A promoter. Trans-differentiation of B cells into macrophage-like cells caused down-regulation of Thy28 expression. Loss-of-function of Thy28 induced decrease in Pax5 expression and recruitment of myosin-9 (MYH9), one of Thy28-interacting proteins, to the Pax5 1A promoter. Loss-of-function of MYH9 also induced decrease in Pax5 expression. Thus, our analysis revealed that Thy28 is functionally required for B cell-specific expression of Pax5 via recruitment of MYH9 to the Pax5 locus in chicken B cells.
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Affiliation(s)
- Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Fusako Kitaura
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- * E-mail:
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Fujita T, Fujii H. Efficient isolation of specific genomic regions retaining molecular interactions by the iChIP system using recombinant exogenous DNA-binding proteins. BMC Mol Biol 2014; 15:26. [PMID: 25428274 PMCID: PMC4253623 DOI: 10.1186/s12867-014-0026-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 11/12/2014] [Indexed: 01/02/2023] Open
Abstract
Background Comprehensive understanding of mechanisms of genome functions requires identification of molecules interacting with genomic regions of interest in vivo. We previously developed the insertional chromatin immunoprecipitation (iChIP) technology to isolate specific genomic regions retaining molecular interactions and identify their associated molecules. iChIP consists of locus-tagging and affinity purification. The recognition sequences of an exogenous DNA-binding protein such as LexA are inserted into a genomic region of interest in the cell to be analyzed. The exogenous DNA-binding protein fused with a tag(s) is expressed in the cell and the target genomic region is purified with antibody against the tag(s). In this study, we developed the iChIP system using recombinant DNA-binding proteins to make iChIP more straightforward than the conventional iChIP system using expression of the exogenous DNA-binding proteins in the cells to be analyzed. Results In this system, recombinant 3xFNLDD-D (r3xFNLDD-D) consisting of the 3xFLAG-tag, a nuclear localization signal (NLS), the DNA-binding domain plus the dimerization domain of the LexA protein, and the Dock-tag is used for isolation of specific genomic regions. r3xFNLDD-D was expressed using a silkworm-baculovirus expression system and purified by affinity purification. iChIP using r3xFNLDD-D could efficiently isolate the single-copy chicken Pax5 (cPax5) locus, in which LexA binding elements were inserted, with negligible contamination of other genomic regions. In addition, we could detect RNA associated with the cPax5 locus using this form of the iChIP system combined with RT-PCR. Conclusions The iChIP system using r3xFNLDD-D can isolate specific genomic regions retaining molecular interactions without expression of the exogenous DNA-binding protein in the cell to be analyzed. iChIP using r3xFNLDD-D would be more straightforward and useful for analysis of specific genomic regions to elucidate their functions as compared to the previously published iChIP protocol. Electronic supplementary material The online version of this article (doi:10.1186/s12867-014-0026-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan.
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan.
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