1
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Blumenstiel JP. From the cauldron of conflict: Endogenous gene regulation by piRNA and other modes of adaptation enabled by selfish transposable elements. Semin Cell Dev Biol 2025; 164:1-12. [PMID: 38823219 DOI: 10.1016/j.semcdb.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 04/28/2024] [Accepted: 05/06/2024] [Indexed: 06/03/2024]
Abstract
Transposable elements (TEs) provide a prime example of genetic conflict because they can proliferate in genomes and populations even if they harm the host. However, numerous studies have shown that TEs, though typically harmful, can also provide fuel for adaptation. This is because they code functional sequences that can be useful for the host in which they reside. In this review, I summarize the "how" and "why" of adaptation enabled by the genetic conflict between TEs and hosts. In addition, focusing on mechanisms of TE control by small piwi-interacting RNAs (piRNAs), I highlight an indirect form of adaptation enabled by conflict. In this case, mechanisms of host defense that regulate TEs have been redeployed for endogenous gene regulation. I propose that the genetic conflict released by meiosis in early eukaryotes may have been important because, among other reasons, it spurred evolutionary innovation on multiple interwoven trajectories - on the part of hosts and also embedded genetic parasites. This form of evolution may function as a complexity generating engine that was a critical player in eukaryotic evolution.
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Affiliation(s)
- Justin P Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, United States.
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2
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Kantor B, O'Donovan B, Rittiner J, Hodgson D, Lindner N, Guerrero S, Dong W, Zhang A, Chiba-Falek O. The therapeutic implications of all-in-one AAV-delivered epigenome-editing platform in neurodegenerative disorders. Nat Commun 2024; 15:7259. [PMID: 39179542 PMCID: PMC11344155 DOI: 10.1038/s41467-024-50515-6] [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: 04/09/2023] [Accepted: 07/12/2024] [Indexed: 08/26/2024] Open
Abstract
Safely and efficiently controlling gene expression is a long-standing goal of biomedical research, and CRISPR/Cas system can be harnessed to create powerful tools for epigenetic editing. Adeno-associated-viruses (AAVs) represent the delivery vehicle of choice for therapeutic platform. However, their small packaging capacity isn't suitable for large constructs including most CRISPR/dCas9-effector vectors. Thus, AAV-based CRISPR/Cas systems have been delivered via two separate viral vectors. Here we develop a compact CRISPR/dCas9-based repressor system packaged in AAV as a single optimized vector. The system comprises the small Staphylococcus aureus (Sa)dCas9 and an engineered repressor molecule, a fusion of MeCP2's transcription repression domain (TRD) and KRAB. The dSaCas9-KRAB-MeCP2(TRD) vector platform repressed robustly and sustainably the expression of multiple genes-of-interest, in vitro and in vivo, including ApoE, the strongest genetic risk factor for late onset Alzheimer's disease (LOAD). Our platform broadens the CRISPR/dCas9 toolset available for transcriptional manipulation of gene expression in research and therapeutic settings.
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Affiliation(s)
- Boris Kantor
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA.
- Viral Vector Core, Duke University School of Medicine, Durham, NC, USA.
- Center for Advanced Genomic Technologies, Duke University School of Medicine, Durham, NC, USA.
| | - Bernadette O'Donovan
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
| | - Joseph Rittiner
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Viral Vector Core, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University School of Medicine, Durham, NC, USA
| | - Dellila Hodgson
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
| | - Nicholas Lindner
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Viral Vector Core, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University School of Medicine, Durham, NC, USA
| | - Sophia Guerrero
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Viral Vector Core, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University School of Medicine, Durham, NC, USA
| | - Wendy Dong
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Viral Vector Core, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University School of Medicine, Durham, NC, USA
| | - Austin Zhang
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Viral Vector Core, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University School of Medicine, Durham, NC, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA.
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3
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Yun S, Noh M, Yu J, Kim HJ, Hui CC, Lee H, Son JE. Unlocking biological mechanisms with integrative functional genomics approaches. Mol Cells 2024; 47:100092. [PMID: 39019219 PMCID: PMC11345568 DOI: 10.1016/j.mocell.2024.100092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
Reverse genetics offers precise functional insights into genes through the targeted manipulation of gene expression followed by phenotypic assessment. While these approaches have proven effective in model organisms such as Saccharomyces cerevisiae, large-scale genetic manipulations in human cells were historically unfeasible due to methodological limitations. However, recent advancements in functional genomics, particularly clustered regularly interspaced short palindromic repeats (CRISPR)-based screening technologies and next-generation sequencing platforms, have enabled pooled screening technologies that allow massively parallel, unbiased assessments of biological phenomena in human cells. This review provides a comprehensive overview of cutting-edge functional genomic screening technologies applicable to human cells, ranging from short hairpin RNA screens to modern CRISPR screens. Additionally, we explore the integration of CRISPR platforms with single-cell approaches to monitor gene expression, chromatin accessibility, epigenetic regulation, and chromatin architecture following genetic perturbations at the omics level. By offering an in-depth understanding of these genomic screening methods, this review aims to provide insights into more targeted and effective strategies for genomic research and personalized medicine.
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Affiliation(s)
- Sehee Yun
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Minsoo Noh
- Department of Life Sciences, Korea University, Seoul 02841, Korea; Department of Internal Medicine and Laboratory of Genomics and Translational Medicine, Gachon University College of Medicine, Incheon 21565, Korea
| | - Jivin Yu
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Hyeon-Jai Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Chi-Chung Hui
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hunsang Lee
- Department of Life Sciences, Korea University, Seoul 02841, Korea.
| | - Joe Eun Son
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea.
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Oh Y, Gwon LW, Lee HK, Hur JK, Park KH, Kim KP, Lee SH. Highly efficient and specific regulation of gene expression using enhanced CRISPR-Cas12f system. Gene Ther 2024; 31:358-365. [PMID: 38918512 DOI: 10.1038/s41434-024-00458-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024]
Abstract
The recently developed CRISPR activator (CRISPRa) system uses a CRISPR-Cas effector-based transcriptional activator to effectively control the expression of target genes without causing DNA damage. However, existing CRISPRa systems based on Cas9/Cas12a necessitate improvement in terms of efficacy and accuracy due to limitations associated with the CRISPR-Cas module itself. To overcome these limitations and effectively and accurately regulate gene expression, we developed an efficient CRISPRa system based on the small CRISPR-Cas effector Candidatus Woesearchaeota Cas12f (CWCas12f). By engineering the CRISPR-Cas module, linking activation domains, and using various combinations of linkers and nuclear localization signal sequences, the optimized eCWCas12f-VPR system enabled effective and target-specific regulation of gene expression compared with that using the existing CRISPRa system. The eCWCas12f-VPR system developed in this study has substantial potential for controlling the transcription of endogenous genes in living organisms and serves as a foundation for future gene therapy and biological research.
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Affiliation(s)
- Yeounsun Oh
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Lee Wha Gwon
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Hyomin K Lee
- Major in Medical Genetics, Department of Medicine, Hanyang University, Seoul, 04763, Republic of Korea
| | - Junho K Hur
- Department of Genetics, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea
- Department of Medicine, HY Institute of Bioscience and Biotechnology, Hanyang University, Seoul, 04763, Republic of Korea
- Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Atlanta, GA, 30303, USA
| | - Kwang-Hyun Park
- KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
| | - Kee-Pyo Kim
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.
| | - Seung Hwan Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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Kang YK, Eom J, Min B, Park JS. SETDB1 deletion causes DNA demethylation and upregulation of multiple zinc-finger genes. Mol Biol Rep 2024; 51:778. [PMID: 38904842 PMCID: PMC11192681 DOI: 10.1007/s11033-024-09703-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/04/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND SETDB1 (SET domain bifurcated-1) is a histone H3-lysine 9 (H3K9)-specific methyltransferase that mediates heterochromatin formation and repression of target genes. Despite the assumed functional link between DNA methylation and SETDB1-mediated H3K9 trimethylations, several studies have shown that SETDB1 operates autonomously of DNA methylation in a region- and cell-specific manner. This study analyzes SETDB1-null HAP1 cells through a linked methylome and transcriptome analysis, intending to explore genes controlled by SETDB1-involved DNA methylation. METHODS AND RESULTS We investigated SETDB1-mediated regulation of DNA methylation and gene transcription in human HAP1 cells using reduced-representation bisulfite sequencing (RRBS) and RNA sequencing. While two-thirds of differentially methylated CpGs (DMCs) in genic regions were hypomethylated in SETDB1-null cells, we detected a plethora of C2H2-type zinc-finger protein genes (C2H2-ZFP, 223 of 749) among the DMC-associated genes. Most C2H2-ZFPs with DMCs in their promoters were found hypomethylated in SETDB1-KO cells, while other non-ZFP genes with promoter DMCs were not. These C2H2-ZFPs with DMCs in their promoters were significantly upregulated in SETDB1-KO cells. Similarly, C2H2-ZFP genes were upregulated in SETDB1-null 293T cells, suggesting that SETDB1's function in ZFP gene repression is widespread. There are several C2H2-ZFP gene clusters on chromosome 19, which were selectively hypomethylated in SETDB1-KO cells. CONCLUSIONS SETDB1 collectively and specifically represses a substantial fraction of the C2H2-ZFP gene family. Through the en-bloc silencing of a set of ZFP genes, SETDB1 may help establish a panel of ZFP proteins that are expressed cell-type specifically and thereby can serve as signature proteins for cellular identity.
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Affiliation(s)
- Yong-Kook Kang
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea.
- Department of Functional Genomics, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea.
| | - Jaemin Eom
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
- Department of Functional Genomics, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea
| | - Byungkuk Min
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Jung Sun Park
- Development and Differentiation Research Center, Aging Convergence Research Center (ACRC), Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
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6
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He J, Huo X, Pei G, Jia Z, Yan Y, Yu J, Qu H, Xie Y, Yuan J, Zheng Y, Hu Y, Shi M, You K, Li T, Ma T, Zhang MQ, Ding S, Li P, Li Y. Dual-role transcription factors stabilize intermediate expression levels. Cell 2024; 187:2746-2766.e25. [PMID: 38631355 DOI: 10.1016/j.cell.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/08/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
Precise control of gene expression levels is essential for normal cell functions, yet how they are defined and tightly maintained, particularly at intermediate levels, remains elusive. Here, using a series of newly developed sequencing, imaging, and functional assays, we uncover a class of transcription factors with dual roles as activators and repressors, referred to as condensate-forming level-regulating dual-action transcription factors (TFs). They reduce high expression but increase low expression to achieve stable intermediate levels. Dual-action TFs directly exert activating and repressing functions via condensate-forming domains that compartmentalize core transcriptional unit selectively. Clinically relevant mutations in these domains, which are linked to a range of developmental disorders, impair condensate selectivity and dual-action TF activity. These results collectively address a fundamental question in expression regulation and demonstrate the potential of level-regulating dual-action TFs as powerful effectors for engineering controlled expression levels.
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Affiliation(s)
- Jinnan He
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiangru Huo
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Gaofeng Pei
- State Key Laboratory of Membrane Biology, Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Zeran Jia
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yiming Yan
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Jiawei Yu
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Haozhi Qu
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yunxin Xie
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Junsong Yuan
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yuan Zheng
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yanyan Hu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Minglei Shi
- Bioinformatics Division, National Research Center for Information Science and Technology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kaiqiang You
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tianhua Ma
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Michael Q Zhang
- Bioinformatics Division, National Research Center for Information Science and Technology, School of Medicine, Tsinghua University, Beijing 100084, China; Department of Biological Sciences, Center for Systems Biology, The University of Texas, Dallas, TX 75080-3021, USA
| | - Sheng Ding
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Pilong Li
- State Key Laboratory of Membrane Biology, Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China.
| | - Yinqing Li
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
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7
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Laurent M, Geoffroy M, Pavani G, Guiraud S. CRISPR-Based Gene Therapies: From Preclinical to Clinical Treatments. Cells 2024; 13:800. [PMID: 38786024 PMCID: PMC11119143 DOI: 10.3390/cells13100800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/03/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024] Open
Abstract
In recent years, clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) protein have emerged as a revolutionary gene editing tool to treat inherited disorders affecting different organ systems, such as blood and muscles. Both hematological and neuromuscular genetic disorders benefit from genome editing approaches but face different challenges in their clinical translation. The ability of CRISPR/Cas9 technologies to modify hematopoietic stem cells ex vivo has greatly accelerated the development of genetic therapies for blood disorders. In the last decade, many clinical trials were initiated and are now delivering encouraging results. The recent FDA approval of Casgevy, the first CRISPR/Cas9-based drug for severe sickle cell disease and transfusion-dependent β-thalassemia, represents a significant milestone in the field and highlights the great potential of this technology. Similar preclinical efforts are currently expanding CRISPR therapies to other hematologic disorders such as primary immunodeficiencies. In the neuromuscular field, the versatility of CRISPR/Cas9 has been instrumental for the generation of new cellular and animal models of Duchenne muscular dystrophy (DMD), offering innovative platforms to speed up preclinical development of therapeutic solutions. Several corrective interventions have been proposed to genetically restore dystrophin production using the CRISPR toolbox and have demonstrated promising results in different DMD animal models. Although these advances represent a significant step forward to the clinical translation of CRISPR/Cas9 therapies to DMD, there are still many hurdles to overcome, such as in vivo delivery methods associated with high viral vector doses, together with safety and immunological concerns. Collectively, the results obtained in the hematological and neuromuscular fields emphasize the transformative impact of CRISPR/Cas9 for patients affected by these debilitating conditions. As each field suffers from different and specific challenges, the clinical translation of CRISPR therapies may progress differentially depending on the genetic disorder. Ongoing investigations and clinical trials will address risks and limitations of these therapies, including long-term efficacy, potential genotoxicity, and adverse immune reactions. This review provides insights into the diverse applications of CRISPR-based technologies in both preclinical and clinical settings for monogenic blood disorders and muscular dystrophy and compare advances in both fields while highlighting current trends, difficulties, and challenges to overcome.
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Affiliation(s)
- Marine Laurent
- INTEGRARE, UMR_S951, Genethon, Inserm, Univ Evry, Université Paris-Saclay, 91190 Evry, France
| | | | - Giulia Pavani
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Simon Guiraud
- SQY Therapeutics, 78180 Montigny-le-Bretonneux, France
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Mohamad Zamberi NN, Abuhamad AY, Low TY, Mohtar MA, Syafruddin SE. dCas9 Tells Tales: Probing Gene Function and Transcription Regulation in Cancer. CRISPR J 2024; 7:73-87. [PMID: 38635328 DOI: 10.1089/crispr.2023.0078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing is evolving into an essential tool in the field of biological and medical research. Notably, the development of catalytically deactivated Cas9 (dCas9) enzyme has substantially broadened its traditional boundaries in gene editing or perturbation. The conjugation of dCas9 with various molecular effectors allows precise control over transcriptional processes, epigenetic modifications, visualization of chromosomal dynamics, and several other applications. This expanded repertoire of CRISPR-Cas9 applications has emerged as an invaluable molecular tool kit that empowers researchers to comprehensively interrogate and gain insights into health and diseases. This review delves into the advancements in Cas9 protein engineering, specifically on the generation of various dCas9 tools that have significantly enhanced the CRISPR-based technology capability and versatility. We subsequently discuss the multifaceted applications of dCas9, especially in interrogating the regulation and function of genes that involve in supporting cancer pathogenesis. In addition, we also delineate the designing and utilization of dCas9-based tools as well as highlighting its current constraints and transformative potentials in cancer research.
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Affiliation(s)
- Nurul Nadia Mohamad Zamberi
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Asmaa Y Abuhamad
- Bionanotechnology Research Group, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Saiful Effendi Syafruddin
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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9
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Yahsi B, Palaz F, Dincer P. Applications of CRISPR Epigenome Editors in Tumor Immunology and Autoimmunity. ACS Synth Biol 2024; 13:413-427. [PMID: 38298016 DOI: 10.1021/acssynbio.3c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Over the past decade, CRISPR-Cas systems have become indispensable tools for genetic engineering and have been used in clinical trials for various diseases. Beyond genome editing, CRISPR-Cas systems can also be used for performing programmable epigenetic modifications. Recent efforts in enhancing CRISPR-based epigenome modifiers have yielded potent tools enabling targeted DNA methylation/demethylation capable of sustaining epigenetic memory through numerous cell divisions. Moreover, it has been understood that during chronic inflammatory states, including cancer, T cells encounter a state called T cell exhaustion that involves elevated inhibitory receptors (e.g., LAG-3, TIM3, PD-1, CD39) and reduced effector T cell-related protein levels (IFN-γ, granzyme B, and perforin). Importantly, epigenetic dysregulation has been identified as one of the key drivers of T cell exhaustion, and it remains one of the biggest obstacles in the field of immunotherapy and decreases the efficiency of chimeric antigen receptor T (CAR-T) cell therapy. Similarly, autoimmune diseases exhibit epigenetically dysfunctional regulatory T (Treg) cells. For instance, FOXP3 intronic regions, known as conserved noncoding sequences, display hypomethylation in healthy states but hypermethylation in pathological contexts. Therefore, the reversal of epigenetic dysregulation in cancer and autoimmune diseases using CRISPR-based epigenome modifiers has important therapeutic implications. In this review, we outline the progressive refinement of CRISPR-based epigenome modifiers and explore their potential therapeutic applications in tumor immunology and autoimmunity.
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Affiliation(s)
- Berkay Yahsi
- Hacettepe University School of Medicine, Ankara 06100, Turkey
| | - Fahreddin Palaz
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | - Pervin Dincer
- Department of Medical Biology, Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
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10
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Hannon Bozorgmehr J. Four classic "de novo" genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences. Mol Genet Genomics 2024; 299:6. [PMID: 38315248 DOI: 10.1007/s00438-023-02090-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 10/15/2023] [Indexed: 02/07/2024]
Abstract
Despite being previously regarded as extremely unlikely, the idea that entirely novel protein-coding genes can emerge from non-coding sequences has gradually become accepted over the past two decades. Examples of "de novo origination", resulting in lineage-specific "orphan" genes, lacking coding orthologs, are now produced every year. However, many are likely cases of duplicates that are difficult to recognize. Here, I re-examine the claims and show that four very well-known examples of genes alleged to have emerged completely "from scratch"- FLJ33706 in humans, Goddard in fruit flies, BSC4 in baker's yeast and AFGP2 in codfish-may have plausible evolutionary ancestors in pre-existing genes. The first two are likely highly diverged retrogenes coding for regulatory proteins that have been misidentified as orphans. The antifreeze glycoprotein, moreover, may not have evolved from repetitive non-genic sequences but, as in several other related cases, from an apolipoprotein that could have become pseudogenized before later being reactivated. These findings detract from various claims made about de novo gene birth and show there has been a tendency not to invest the necessary effort in searching for homologs outside of a very limited syntenic or phylostratigraphic methodology. A robust approach is used for improving detection that draws upon similarities, not just in terms of statistical sequence analysis, but also relating to biochemistry and function, to obviate notable failures to identify homologs.
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11
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Teixeira AP, Fussenegger M. Synthetic Gene Circuits for Regulation of Next-Generation Cell-Based Therapeutics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309088. [PMID: 38126677 PMCID: PMC10885662 DOI: 10.1002/advs.202309088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Indexed: 12/23/2023]
Abstract
Arming human cells with synthetic gene circuits enables to expand their capacity to execute superior sensing and response actions, offering tremendous potential for innovative cellular therapeutics. This can be achieved by assembling components from an ever-expanding molecular toolkit, incorporating switches based on transcriptional, translational, or post-translational control mechanisms. This review provides examples from the three classes of switches, and discusses their advantages and limitations to regulate the activity of therapeutic cells in vivo. Genetic switches designed to recognize internal disease-associated signals often encode intricate actuation programs that orchestrate a reduction in the sensed signal, establishing a closed-loop architecture. Conversely, switches engineered to detect external molecular or physical cues operate in an open-loop fashion, switching on or off upon signal exposure. The integration of such synthetic gene circuits into the next generation of chimeric antigen receptor T-cells is already enabling precise calibration of immune responses in terms of magnitude and timing, thereby improving the potency and safety of therapeutic cells. Furthermore, pre-clinical engineered cells targeting other chronic diseases are gathering increasing attention, and this review discusses the path forward for achieving clinical success. With synthetic biology at the forefront, cellular therapeutics holds great promise for groundbreaking treatments.
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Affiliation(s)
- Ana P. Teixeira
- Department of Biosystems Science and EngineeringETH ZurichKlingelbergstrasse 48BaselCH‐4056Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichKlingelbergstrasse 48BaselCH‐4056Switzerland
- Faculty of ScienceUniversity of BaselKlingelbergstrasse 48BaselCH‐4056Switzerland
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12
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DeJulius CR, Walton BL, Colazo JM, d'Arcy R, Francini N, Brunger JM, Duvall CL. Engineering approaches for RNA-based and cell-based osteoarthritis therapies. Nat Rev Rheumatol 2024; 20:81-100. [PMID: 38253889 PMCID: PMC11129836 DOI: 10.1038/s41584-023-01067-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2023] [Indexed: 01/24/2024]
Abstract
Osteoarthritis (OA) is a chronic, debilitating disease that substantially impairs the quality of life of affected individuals. The underlying mechanisms of OA are diverse and are becoming increasingly understood at the systemic, tissue, cellular and gene levels. However, the pharmacological therapies available remain limited, owing to drug delivery barriers, and consist mainly of broadly immunosuppressive regimens, such as corticosteroids, that provide only short-term palliative benefits and do not alter disease progression. Engineered RNA-based and cell-based therapies developed with synthetic chemistry and biology tools provide promise for future OA treatments with durable, efficacious mechanisms of action that can specifically target the underlying drivers of pathology. This Review highlights emerging classes of RNA-based technologies that hold potential for OA therapies, including small interfering RNA for gene silencing, microRNA and anti-microRNA for multi-gene regulation, mRNA for gene supplementation, and RNA-guided gene-editing platforms such as CRISPR-Cas9. Various cell-engineering strategies are also examined that potentiate disease-dependent, spatiotemporally regulated production of therapeutic molecules, and a conceptual framework is presented for their application as OA treatments. In summary, this Review highlights modern genetic medicines that have been clinically approved for other diseases, in addition to emerging genome and cellular engineering approaches, with the goal of emphasizing their potential as transformative OA treatments.
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Affiliation(s)
- Carlisle R DeJulius
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Bonnie L Walton
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Juan M Colazo
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Richard d'Arcy
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Nora Francini
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Jonathan M Brunger
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
| | - Craig L Duvall
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
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13
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Godneeva B, Ninova M, Fejes-Toth K, Aravin A. SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes. eLife 2023; 12:RP89493. [PMID: 37999956 PMCID: PMC10672805 DOI: 10.7554/elife.89493] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023] Open
Abstract
The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. Unlike mammals that have four TIF1 members, Drosophila only encodes one member of the family, Bonus. Bonus has been implicated in embryonic development and organogenesis and shown to regulate several signaling pathways, however, its targets and mechanism of action remained poorly understood. We found that knockdown of Bonus in early oogenesis results in severe defects in ovarian development and in ectopic expression of genes that are normally repressed in the germline, demonstrating its essential function in the ovary. Recruitment of Bonus to chromatin leads to silencing associated with accumulation of the repressive H3K9me3 mark. We show that Bonus associates with the histone methyltransferase SetDB1 and the chromatin remodeler NuRD and depletion of either component releases Bonus-induced repression. We further established that Bonus is SUMOylated at a single site at its N-terminus that is conserved among insects and this modification is indispensable for Bonus's repressive activity. SUMOylation influences Bonus's subnuclear localization, its association with chromatin and interaction with SetDB1. Finally, we showed that Bonus SUMOylation is mediated by the SUMO E3-ligase Su(var)2-10, revealing that although SUMOylation of TIF1 proteins is conserved between insects and mammals, both the mechanism and specific site of modification is different in the two taxa. Together, our work identified Bonus as a regulator of tissue-specific gene expression and revealed the importance of SUMOylation as a regulator of complex formation in the context of transcriptional repression.
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Affiliation(s)
- Baira Godneeva
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
- Institute of Gene Biology, Russian Academy of SciencesMoscowRussian Federation
| | - Maria Ninova
- University of California, RiversideRiversideUnited States
| | - Katalin Fejes-Toth
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
| | - Alexei Aravin
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
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14
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Müller-Dott S, Tsirvouli E, Vazquez M, Ramirez Flores R, Badia-i-Mompel P, Fallegger R, Türei D, Lægreid A, Saez-Rodriguez J. Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities. Nucleic Acids Res 2023; 51:10934-10949. [PMID: 37843125 PMCID: PMC10639077 DOI: 10.1093/nar/gkad841] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/08/2023] [Accepted: 09/22/2023] [Indexed: 10/17/2023] Open
Abstract
Gene regulation plays a critical role in the cellular processes that underlie human health and disease. The regulatory relationship between transcription factors (TFs), key regulators of gene expression, and their target genes, the so called TF regulons, can be coupled with computational algorithms to estimate the activity of TFs. However, to interpret these findings accurately, regulons of high reliability and coverage are needed. In this study, we present and evaluate a collection of regulons created using the CollecTRI meta-resource containing signed TF-gene interactions for 1186 TFs. In this context, we introduce a workflow to integrate information from multiple resources and assign the sign of regulation to TF-gene interactions that could be applied to other comprehensive knowledge bases. We find that the signed CollecTRI-derived regulons outperform other public collections of regulatory interactions in accurately inferring changes in TF activities in perturbation experiments. Furthermore, we showcase the value of the regulons by examining TF activity profiles in three different cancer types and exploring TF activities at the level of single-cells. Overall, the CollecTRI-derived TF regulons enable the accurate and comprehensive estimation of TF activities and thereby help to interpret transcriptomics data.
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Affiliation(s)
- Sophia Müller-Dott
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Eirini Tsirvouli
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Ricardo O Ramirez Flores
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Pau Badia-i-Mompel
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Robin Fallegger
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Dénes Türei
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Astrid Lægreid
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
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15
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Rosspopoff O, Trono D. Take a walk on the KRAB side. Trends Genet 2023; 39:844-857. [PMID: 37716846 DOI: 10.1016/j.tig.2023.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/18/2023]
Abstract
Canonical Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) act as major repressors of transposable elements (TEs) via the KRAB-mediated recruitment of the heterochromatin scaffold KRAB-associated protein (KAP)1. KZFP genes emerged some 420 million years ago in the last common ancestor of coelacanth, lungfish, and tetrapods, and dramatically expanded to give rise to lineage-specific repertoires in contemporary species paralleling their TE load and turnover. However, the KRAB domain displays sequence and function variations that reveal repeated diversions from a linear TE-KZFP trajectory. This Review summarizes current knowledge on the evolution of KZFPs and discusses how ancestral noncanonical KZFPs endowed with variant KRAB, SCAN or DUF3669 domains have been utilized to achieve KAP1-independent functions.
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Affiliation(s)
- Olga Rosspopoff
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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16
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Fujimori T, Rios-Martinez C, Thurm AR, Hinks MM, Doughty BR, Sinha J, Le D, Hafner A, Greenleaf WJ, Boettiger AN, Bintu L. Single-cell chromatin state transitions during epigenetic memory formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560616. [PMID: 37873344 PMCID: PMC10592931 DOI: 10.1101/2023.10.03.560616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Repressive chromatin modifications are thought to compact chromatin to silence transcription. However, it is unclear how chromatin structure changes during silencing and epigenetic memory formation. We measured gene expression and chromatin structure in single cells after recruitment and release of repressors at a reporter gene. Chromatin structure is heterogeneous, with open and compact conformations present in both active and silent states. Recruitment of repressors associated with epigenetic memory produces chromatin compaction across 10-20 kilobases, while reversible silencing does not cause compaction at this scale. Chromatin compaction is inherited, but changes molecularly over time from histone methylation (H3K9me3) to DNA methylation. The level of compaction at the end of silencing quantitatively predicts epigenetic memory weeks later. Similarly, chromatin compaction at the Nanog locus predicts the degree of stem-cell fate commitment. These findings suggest that the chromatin state across tens of kilobases, beyond the gene itself, is important for epigenetic memory formation.
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Affiliation(s)
- Taihei Fujimori
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Abby R. Thurm
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Michaela M. Hinks
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Joydeb Sinha
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA, USA
| | - Derek Le
- Department of Dermatology, Program in Epithelial Biology, Stanford University, Stanford, CA, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Antonina Hafner
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Current address: Department of Discovery Oncology, Genentech, CA, USA
| | - William J. Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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17
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Cai R, Lv R, Shi X, Yang G, Jin J. CRISPR/dCas9 Tools: Epigenetic Mechanism and Application in Gene Transcriptional Regulation. Int J Mol Sci 2023; 24:14865. [PMID: 37834313 PMCID: PMC10573330 DOI: 10.3390/ijms241914865] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
CRISPR/Cas9-mediated cleavage of DNA, which depends on the endonuclease activity of Cas9, has been widely used for gene editing due to its excellent programmability and specificity. However, the changes to the DNA sequence that are mediated by CRISPR/Cas9 affect the structures and stability of the genome, which may affect the accuracy of results. Mutations in the RuvC and HNH regions of the Cas9 protein lead to the inactivation of Cas9 into dCas9 with no endonuclease activity. Despite the loss of endonuclease activity, dCas9 can still bind the DNA strand using guide RNA. Recently, proteins with active/inhibitory effects have been linked to the end of the dCas9 protein to form fusion proteins with transcriptional active/inhibitory effects, named CRISPRa and CRISPRi, respectively. These CRISPR tools mediate the transcription activity of protein-coding and non-coding genes by regulating the chromosomal modification states of target gene promoters, enhancers, and other functional elements. Here, we highlight the epigenetic mechanisms and applications of the common CRISPR/dCas9 tools, by which we hope to provide a reference for future related gene regulation, gene function, high-throughput target gene screening, and disease treatment.
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Affiliation(s)
- Ruijie Cai
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Runyu Lv
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xin'e Shi
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Gongshe Yang
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jianjun Jin
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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18
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Czarnek M, Kochan J, Wawro M, Myrczek R, Bereta J. Construction of a Set of Novel Transposon Vectors for Efficient Silencing of Protein and lncRNA Genes via CRISPR Interference. Mol Biotechnol 2023; 65:1598-1607. [PMID: 36707469 PMCID: PMC10471651 DOI: 10.1007/s12033-023-00675-5] [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: 09/11/2022] [Accepted: 01/16/2023] [Indexed: 01/29/2023]
Abstract
In recent years, CRISPR interference (CRISPRi) technology of gene silencing has emerged as a promising alternative to RNA interference (RNAi) surpassing the latter in terms of efficiency and accuracy. Here, we describe the construction of a set of transposon vectors suitable for constitutive or tetracycline (doxycycline)-inducible silencing of genes of interest via CRISPRi method and conferring three different antibiotic resistances, using vectors available via Addgene repository. We have analyzed the performance of the new vectors in the silencing of mouse Adam10 and human lncRNA, NORAD. The empty vector variants can be used to efficiently silence any genes of interest.
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Affiliation(s)
- Maria Czarnek
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387, Kraków, Poland
| | - Jakub Kochan
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387, Kraków, Poland
| | - Mateusz Wawro
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387, Kraków, Poland
| | - Rafał Myrczek
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387, Kraków, Poland
| | - Joanna Bereta
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387, Kraków, Poland.
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19
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Godneeva B, Ninova M, Fejes Tóth K, Aravin AA. SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.14.536936. [PMID: 37645991 PMCID: PMC10461926 DOI: 10.1101/2023.04.14.536936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. Unlike mammals that have four TIF1 members, Drosophila only encodes one member of the family, Bonus. Bonus has been implicated in embryonic development and organogenesis and shown to regulate several signaling pathways, however, its targets and mechanism of action remained poorly understood. We found that knockdown of Bonus in early oogenesis results in severe defects in ovarian development and in ectopic expression of genes that are normally repressed in the germline, demonstrating its essential function in the ovary. Recruitment of Bonus to chromatin leads to silencing associated with accumulation of the repressive H3K9me3 mark. We show that Bonus associates with the histone methyltransferase SetDB1 and the chromatin remodeler NuRD and depletion of either component releases Bonus-induced repression. We further established that Bonus is SUMOylated at a single site at its N-terminus that is conserved among insects and this modification is indispensable for Bonus's repressive activity. SUMOylation influences Bonus's subnuclear localization, its association with chromatin and interaction with SetDB1. Finally, we showed that Bonus SUMOylation is mediated by the SUMO E3-ligase Su(var)2-10, revealing that although SUMOylation of TIF1 proteins is conserved between insects and mammals, both the mechanism and specific site of modification is different in the two taxa. Together, our work identified Bonus as a regulator of tissue-specific gene expression and revealed the importance of SUMOylation as a regulator of complex formation in the context of transcriptional repression.
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Affiliation(s)
- Baira Godneeva
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA 91125, USA
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria Ninova
- University of California, Riverside, Riverside, CA 92521, USA
| | - Katalin Fejes Tóth
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA 91125, USA
| | - Alexei A. Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA 91125, USA
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20
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Pickles S, Zanetti Alepuz D, Koike Y, Yue M, Tong J, Liu P, Zhou Y, Jansen-West K, Daughrity LM, Song Y, DeTure M, Oskarsson B, Graff-Radford NR, Boeve BF, Petersen RC, Josephs KA, Dickson DW, Ward ME, Dong L, Prudencio M, Cook CN, Petrucelli L. CRISPR interference to evaluate modifiers of C9ORF72-mediated toxicity in FTD. Front Cell Dev Biol 2023; 11:1251551. [PMID: 37614226 PMCID: PMC10443592 DOI: 10.3389/fcell.2023.1251551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 07/26/2023] [Indexed: 08/25/2023] Open
Abstract
Treatments for neurodegenerative disease, including Frontotemporal dementia (FTD) and Amyotrophic lateral sclerosis (ALS), remain rather limited, underscoring the need for greater mechanistic insight and disease-relevant models. Our ability to develop novel disease models of genetic risk factors, disease modifiers, and other FTD/ALS-relevant targets is impeded by the significant amount of time and capital required to develop conventional knockout and transgenic mice. To overcome these limitations, we have generated a novel CRISPRi interference (CRISPRi) knockin mouse. CRISPRi uses a catalytically dead form of Cas9, fused to a transcriptional repressor to knockdown protein expression, following the introduction of single guide RNA against the gene of interest. To validate the utility of this model we have selected the TAR DNA binding protein (TDP-43) splicing target, stathmin-2 (STMN2). STMN2 RNA is downregulated in FTD/ALS due to loss of TDP-43 activity and STMN2 loss is suggested to play a role in ALS pathogenesis. The involvement of STMN2 loss of function in FTD has yet to be determined. We find that STMN2 protein levels in familial FTD cases are significantly reduced compared to controls, supporting that STMN2 depletion may be involved in the pathogenesis of FTD. Here, we provide proof-of-concept that we can simultaneously knock down Stmn2 and express the expanded repeat in the Chromosome 9 open reading frame 72 (C9ORF72) gene, successfully replicating features of C9-associated pathology. Of interest, depletion of Stmn2 had no effect on expression or deposition of dipeptide repeat proteins (DPRs), but significantly decreased the number of phosphorylated Tdp-43 (pTdp-43) inclusions. We submit that our novel CRISPRi mouse provides a versatile and rapid method to silence gene expression in vivo and propose this model will be useful to understand gene function in isolation or in the context of other neurodegenerative disease models.
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Affiliation(s)
- Sarah Pickles
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
- Neuroscience Graduate Program, Mayo Graduate School, Mayo Clinic, Jacksonville, FL, United States
| | | | - Yuka Koike
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | - Mei Yue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | - Jimei Tong
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | - Pinghu Liu
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Yugui Zhou
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Karen Jansen-West
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | | | - Yuping Song
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | - Michael DeTure
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
| | - Björn Oskarsson
- Department of Neurology, Mayo Clinic, Jacksonville, FL, United States
| | | | - Bradley F. Boeve
- Department of Neurology, Mayo Clinic, Rochester, MN, United States
| | | | - Keith A. Josephs
- Department of Neurology, Mayo Clinic, Rochester, MN, United States
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
- Neuroscience Graduate Program, Mayo Graduate School, Mayo Clinic, Jacksonville, FL, United States
- Department of Neurology, Mayo Clinic, Jacksonville, FL, United States
| | - Michael E. Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Lijin Dong
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
- Neuroscience Graduate Program, Mayo Graduate School, Mayo Clinic, Jacksonville, FL, United States
| | - Casey N. Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
- Neuroscience Graduate Program, Mayo Graduate School, Mayo Clinic, Jacksonville, FL, United States
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
- Neuroscience Graduate Program, Mayo Graduate School, Mayo Clinic, Jacksonville, FL, United States
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21
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Baniulyte G, Durham SA, Merchant LE, Sammons MA. Shared Gene Targets of the ATF4 and p53 Transcriptional Networks. Mol Cell Biol 2023; 43:426-449. [PMID: 37533313 PMCID: PMC10448979 DOI: 10.1080/10985549.2023.2229225] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 08/04/2023] Open
Abstract
The master tumor suppressor p53 regulates multiple cell fate decisions, such as cell cycle arrest and apoptosis, via transcriptional control of a broad gene network. Dysfunction in the p53 network is common in cancer, often through mutations that inactivate p53 or other members of the pathway. Induction of tumor-specific cell death by restoration of p53 activity without off-target effects has gained significant interest in the field. In this study, we explore the gene regulatory mechanisms underlying a putative anticancer strategy involving stimulation of the p53-independent integrated stress response (ISR). Our data demonstrate the p53 and ISR pathways converge to independently regulate common metabolic and proapoptotic genes. We investigated the architecture of multiple gene regulatory elements bound by p53 and the ISR effector ATF4 controlling this shared regulation. We identified additional key transcription factors that control basal and stress-induced regulation of these shared p53 and ATF4 target genes. Thus, our results provide significant new molecular and genetic insight into gene regulatory networks and transcription factors that are the target of numerous antitumor therapies.
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Affiliation(s)
- Gabriele Baniulyte
- Department of Biological Sciences, The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
| | - Serene A. Durham
- Department of Biological Sciences, The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
| | - Lauren E. Merchant
- Department of Biological Sciences, The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
| | - Morgan A. Sammons
- Department of Biological Sciences, The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
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22
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Baniulyte G, Durham SA, Merchant LE, Sammons MA. Shared gene targets of the ATF4 and p53 transcriptional networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532778. [PMID: 36993734 PMCID: PMC10055071 DOI: 10.1101/2023.03.15.532778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The master tumor suppressor p53 regulates multiple cell fate decisions, like cell cycle arrest and apoptosis, via transcriptional control of a broad gene network. Dysfunction in the p53 network is common in cancer, often through mutations that inactivate p53 or other members of the pathway. Induction of tumor-specific cell death by restoration of p53 activity without off-target effects has gained significant interest in the field. In this study, we explore the gene regulatory mechanisms underlying a putative anti-cancer strategy involving stimulation of the p53-independent Integrated Stress Response (ISR). Our data demonstrate the p53 and ISR pathways converge to independently regulate common metabolic and pro-apoptotic genes. We investigated the architecture of multiple gene regulatory elements bound by p53 and the ISR effector ATF4 controlling this shared regulation. We identified additional key transcription factors that control basal and stress-induced regulation of these shared p53 and ATF4 target genes. Thus, our results provide significant new molecular and genetic insight into gene regulatory networks and transcription factors that are the target of numerous antitumor therapies.
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Affiliation(s)
- Gabriele Baniulyte
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Serene A. Durham
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Lauren E. Merchant
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Morgan A. Sammons
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
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23
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Jayanthi BE, Jayanthi S, Segatori L. Design of Oscillatory Networks through Post-Translational Control of Network Components. SYNTHETIC BIOLOGY AND ENGINEERING 2023; 1:10004. [PMID: 38590452 PMCID: PMC11000592 DOI: 10.35534/sbe.2023.10004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Many essential functions in biological systems, including cell cycle progression and circadian rhythm regulation, are governed by the periodic behaviors of specific molecules. These periodic behaviors arise from the precise arrangement of components in biomolecular networks that generate oscillatory output signals. The dynamic properties of individual components of these networks, such as maturation delays and degradation rates, often play a key role in determining the network's oscillatory behavior. In this study, we explored the post-translational modulation of network components as a means to generate genetic circuits with oscillatory behaviors and perturb the oscillation features. Specifically, we used the NanoDeg platform-A bifunctional molecule consisting of a target-specific nanobody and a degron tag-to control the degradation rates of the circuit's components and predicted the effect of NanoDeg-mediated post-translational depletion of a key circuit component on the behavior of a series of proto-oscillating network topologies. We modeled the behavior of two main classes of oscillators, namely relaxation oscillator topologies (the activator-repressor and the Goodwin oscillator) and ring oscillator topologies (repressilators). We identified two main mechanisms by which non-oscillating networks could be induced to oscillate through post-translational modulation of network components: an increase in the separation of timescales of network components and mitigation of the leaky expression of network components. These results are in agreement with previous findings describing the effect of timescale separation and mitigation of leaky expression on oscillatory behaviors. This work thus validates the use of tools to control protein degradation rates as a strategy to modulate existing oscillatory signals and construct oscillatory networks. In addition, this study provides the design rules to implement such an approach based on the control of protein degradation rates using the NanoDeg platform, which does not require genetic manipulation of the network components and can be adapted to virtually any cellular protein. This work also establishes a framework to explore the use of tools for post-translational perturbations of biomolecular networks and generates desired behaviors of the network output.
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Affiliation(s)
- Brianna E.K. Jayanthi
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX 77005, USA
| | - Shridhar Jayanthi
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Laura Segatori
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX 77005, USA
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
- Department of Chemical & Biomolecular Engineering, Rice University, Houston, TX 77005, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
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24
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Han JL, Entcheva E. Gene Modulation with CRISPR-based Tools in Human iPSC-Cardiomyocytes. Stem Cell Rev Rep 2023; 19:886-905. [PMID: 36656467 PMCID: PMC9851124 DOI: 10.1007/s12015-023-10506-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 01/20/2023]
Abstract
Precise control of gene expression (knock-out, knock-in, knockdown or overexpression) is at the heart of functional genomics - an approach to dissect the contribution of a gene/protein to the system's function. The development of a human in vitro system that can be patient-specific, induced pluripotent stem cells, iPSC, and the ability to obtain various cell types of interest, have empowered human disease modeling and therapeutic development. Scalable tools have been deployed for gene modulation in these cells and derivatives, including pharmacological means, DNA-based RNA interference and standard RNA interference (shRNA/siRNA). The CRISPR/Cas9 gene editing system, borrowed from bacteria and adopted for use in mammalian cells a decade ago, offers cell-specific genetic targeting and versatility. Outside genome editing, more subtle, time-resolved gene modulation is possible by using a catalytically "dead" Cas9 enzyme linked to an effector of gene transcription in combination with a guide RNA. The CRISPRi / CRISPRa (interference/activation) system evolved over the last decade as a scalable technology for performing functional genomics with libraries of gRNAs. Here, we review key developments of these approaches and their deployment in cardiovascular research. We discuss specific use with iPSC-cardiomyocytes and the challenges in further translation of these techniques.
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Affiliation(s)
- Julie Leann Han
- Department of Biomedical Engineering, The George Washington University, 800 22nd St NW, Suite 5000, Washington, DC, 20052, USA
| | - Emilia Entcheva
- Department of Biomedical Engineering, The George Washington University, 800 22nd St NW, Suite 5000, Washington, DC, 20052, USA.
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25
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Bhokisham N, Laudermilch E, Traeger LL, Bonilla TD, Ruiz-Estevez M, Becker JR. CRISPR-Cas System: The Current and Emerging Translational Landscape. Cells 2023; 12:cells12081103. [PMID: 37190012 DOI: 10.3390/cells12081103] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
CRISPR-Cas technology has rapidly changed life science research and human medicine. The ability to add, remove, or edit human DNA sequences has transformative potential for treating congenital and acquired human diseases. The timely maturation of the cell and gene therapy ecosystem and its seamless integration with CRISPR-Cas technologies has enabled the development of therapies that could potentially cure not only monogenic diseases such as sickle cell anemia and muscular dystrophy, but also complex heterogenous diseases such as cancer and diabetes. Here, we review the current landscape of clinical trials involving the use of various CRISPR-Cas systems as therapeutics for human diseases, discuss challenges, and explore new CRISPR-Cas-based tools such as base editing, prime editing, CRISPR-based transcriptional regulation, CRISPR-based epigenome editing, and RNA editing, each promising new functionality and broadening therapeutic potential. Finally, we discuss how the CRISPR-Cas system is being used to understand the biology of human diseases through the generation of large animal disease models used for preclinical testing of emerging therapeutics.
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Affiliation(s)
| | - Ethan Laudermilch
- Corporate Research Material Labs, 3M Center, 3M Company, Maplewood, MN 55144, USA
| | - Lindsay L Traeger
- Corporate Research Material Labs, 3M Center, 3M Company, Maplewood, MN 55144, USA
| | - Tonya D Bonilla
- Corporate Research Material Labs, 3M Center, 3M Company, Maplewood, MN 55144, USA
| | | | - Jordan R Becker
- Corporate Research Material Labs, 3M Center, 3M Company, Maplewood, MN 55144, USA
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26
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Sapozhnikov DM, Szyf M. The PROTECTOR strategy employs dCas orthologs to sterically shield off-target sites from CRISPR/Cas activity. Sci Rep 2023; 13:2280. [PMID: 36759683 PMCID: PMC9911626 DOI: 10.1038/s41598-023-29332-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Off-target mutagenesis of CRISPR/Cas systems must be solved to facilitate safe gene therapy. Here, we report a novel approach, termed "PROTECTOR", to shield known off-target sites by directing the binding of an orthologous nuclease-dead Cas protein to the off-target site to sterically interfere with Cas activity. We show that this method reduces off-target mutation rates of two well-studied guide RNAs without compromising on-target activity and that it can be used in combination with high-fidelity Cas enzymes to further reduce off-target editing. This expands the suite of off-target mitigation strategies and offers an ability to protect off-target sites even when their sequences are fully identical to target sites.
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Affiliation(s)
- Daniel M Sapozhnikov
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada.
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada
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27
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B1 SINE-binding ZFP266 impedes mouse iPSC generation through suppression of chromatin opening mediated by reprogramming factors. Nat Commun 2023; 14:488. [PMID: 36717582 PMCID: PMC9887000 DOI: 10.1038/s41467-023-36097-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 01/13/2023] [Indexed: 01/31/2023] Open
Abstract
Induced pluripotent stem cell (iPSC) reprogramming is inefficient and understanding the molecular mechanisms underlying this inefficiency holds the key to successfully control cellular identity. Here, we report 24 reprogramming roadblock genes identified by CRISPR/Cas9-mediated genome-wide knockout (KO) screening. Of these, depletion of the predicted KRAB zinc finger protein (KRAB-ZFP) Zfp266 strongly and consistently enhances murine iPSC generation in several reprogramming settings, emerging as the most robust roadblock. We show that ZFP266 binds Short Interspersed Nuclear Elements (SINEs) adjacent to binding sites of pioneering factors, OCT4 (POU5F1), SOX2, and KLF4, and impedes chromatin opening. Replacing the KRAB co-suppressor with co-activator domains converts ZFP266 from an inhibitor to a potent facilitator of iPSC reprogramming. We propose that the SINE-KRAB-ZFP interaction is a critical regulator of chromatin accessibility at regulatory elements required for efficient cellular identity changes. In addition, this work serves as a resource to further illuminate molecular mechanisms hindering reprogramming.
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28
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Khor JM, Ettensohn CA. An optimized Tet-On system for conditional control of gene expression in sea urchins. Development 2023; 150:dev201373. [PMID: 36607745 PMCID: PMC10108607 DOI: 10.1242/dev.201373] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/28/2022] [Indexed: 01/07/2023]
Abstract
Sea urchins and other echinoderms are important experimental models for studying developmental processes. The lack of approaches for conditional gene perturbation, however, has made it challenging to investigate the late developmental functions of genes that have essential roles during early embryogenesis and genes that have diverse functions in multiple tissues. The doxycycline-controlled Tet-On system is a widely used molecular tool for temporally and spatially regulated transgene expression. Here, we optimized the Tet-On system to conditionally induce gene expression in sea urchin embryos. Using this approach, we explored the roles the MAPK signaling plays in skeletogenesis by expressing genes that perturb the pathway specifically in primary mesenchyme cells during later stages of development. We demonstrated the wide utility of the Tet-On system by applying it to a second sea urchin species and in cell types other than the primary mesenchyme cells. Our work provides a robust and flexible platform for the spatiotemporal regulation of gene expression in sea urchins, which will considerably enhance the utility of this prominent model system.
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Affiliation(s)
- Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Charles A. Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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29
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Fan TJ, Cui J. Human Endogenous Retroviruses in Diseases. Subcell Biochem 2023; 106:403-439. [PMID: 38159236 DOI: 10.1007/978-3-031-40086-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Human endogenous retroviruses (HERVs), which are conserved sequences of ancient retroviruses, are widely distributed in the human genome. Although most HERVs have been rendered inactive by evolution, some have continued to exhibit important cytological functions. HERVs in the human genome perform dual functions: on the one hand, they are involved in important physiological processes such as placental development and immune regulation; on the other hand, their aberrant expression is closely associated with the pathological processes of several diseases, such as cancers, autoimmune diseases, and viral infections. HERVs can also regulate a variety of host cellular functions, including the expression of protein-coding genes and regulatory elements that have evolved from HERVs. Here, we present recent research on the roles of HERVs in viral infections and cancers, including the dysregulation of HERVs in various viral infections, HERV-induced epigenetic modifications of histones (such as methylation and acetylation), and the potential mechanisms of HERV-mediated antiviral immunity. We also describe therapies to improve the efficacy of vaccines and medications either by directly or indirectly targeting HERVs, depending on the HERV.
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Affiliation(s)
- Tian-Jiao Fan
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
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30
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Yeo NC, Church GM. Perturbation of Gene Regulation by Genome Editing. Methods Mol Biol 2023; 2594:59-68. [PMID: 36264488 DOI: 10.1007/978-1-0716-2815-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The RNA-guided endonuclease Cas9 can be converted into a programmable transcriptional repressor. Here we describe a set of protocols for using the catalytically inactive dead Cas9 (dCas9)-based tools, including the bipartite super repressor consisting of the KRAB and MeCP2 domains, to achieve efficient and scalable gene silencing in mammalian cells.
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Affiliation(s)
- Nan Cher Yeo
- Precision Medicine Institute, University of Alabama-Birmingham, Birmingham, AL, USA.
- Department of Pharmacology and Toxicology, University of Alabama-Birmingham, Birmingham, AL, USA.
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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31
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The Modular Architecture of Metallothioneins Facilitates Domain Rearrangements and Contributes to Their Evolvability in Metal-Accumulating Mollusks. Int J Mol Sci 2022; 23:ijms232415824. [PMID: 36555472 PMCID: PMC9781358 DOI: 10.3390/ijms232415824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/05/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
Protein domains are independent structural and functional modules that can rearrange to create new proteins. While the evolution of multidomain proteins through the shuffling of different preexisting domains has been well documented, the evolution of domain repeat proteins and the origin of new domains are less understood. Metallothioneins (MTs) provide a good case study considering that they consist of metal-binding domain repeats, some of them with a likely de novo origin. In mollusks, for instance, most MTs are bidomain proteins that arose by lineage-specific rearrangements between six putative domains: α, β1, β2, β3, γ and δ. Some domains have been characterized in bivalves and gastropods, but nothing is known about the MTs and their domains of other Mollusca classes. To fill this gap, we investigated the metal-binding features of NpoMT1 of Nautilus pompilius (Cephalopoda class) and FcaMT1 of Falcidens caudatus (Caudofoveata class). Interestingly, whereas NpoMT1 consists of α and β1 domains and has a prototypical Cd2+ preference, FcaMT1 has a singular preference for Zn2+ ions and a distinct domain composition, including a new Caudofoveata-specific δ domain. Overall, our results suggest that the modular architecture of MTs has contributed to MT evolution during mollusk diversification, and exemplify how modularity increases MT evolvability.
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32
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Stoll GA, Pandiloski N, Douse CH, Modis Y. Structure and functional mapping of the KRAB-KAP1 repressor complex. EMBO J 2022; 41:e111179. [PMID: 36341546 PMCID: PMC9753469 DOI: 10.15252/embj.2022111179] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
Transposable elements are a genetic reservoir from which new genes and regulatory elements can emerge. However, expression of transposable elements can be pathogenic and is therefore tightly controlled. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) recruit the co-repressor KRAB-associated protein 1 (KAP1/TRIM28) to regulate many transposable elements, but how KRAB-ZFPs and KAP1 interact remains unclear. Here, we report the crystal structure of the KAP1 tripartite motif (TRIM) in complex with the KRAB domain from a human KRAB-ZFP, ZNF93. Structure-guided mutations in the KAP1-KRAB binding interface abolished repressive activity in an epigenetic transcriptional silencing assay. Deposition of H3K9me3 over thousands of loci is lost genome-wide in cells expressing a KAP1 variant with mutations that abolish KRAB binding. Our work identifies and functionally validates the KRAB-KAP1 molecular interface, which is critical for a central transcriptional control axis in vertebrates. In addition, the structure-based prediction of KAP1 recruitment efficiency will enable optimization of KRABs used in CRISPRi.
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Affiliation(s)
- Guido A Stoll
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUK,Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)University of Cambridge School of Clinical MedicineCambridgeUK
| | - Ninoslav Pandiloski
- Department of Experimental Medical Science, Lund Stem Cell CenterLund UniversityLundSweden
| | - Christopher H Douse
- Department of Experimental Medical Science, Lund Stem Cell CenterLund UniversityLundSweden
| | - Yorgo Modis
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUK,Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)University of Cambridge School of Clinical MedicineCambridgeUK
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33
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Taka JRH, Sun Y, Goldstone DC. Mapping the interaction between Trim28 and the
KRAB
domain at the center of Trim28 silencing of endogenous retroviruses. Protein Sci 2022; 31:e4436. [PMID: 36173157 PMCID: PMC9601868 DOI: 10.1002/pro.4436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 12/03/2022]
Abstract
Transcription of endogenous retroviral elements are tightly regulated during development by members of the KRAB‐containing zinc finger proteins (KRAB‐ZFPs) and the co‐repressor Trim28 (also known as Kap‐1 or Tif1β). KRAB‐ZFPs form the largest family of transcription regulators in mammals and initiate transcriptional silencing by tethering Trim28 to a target locus. Subsequently, Trim28 recruits chromatin modifying effectors resulting in the formation of heterochromatin. In the present study, we identify surface exposed residues on the central six turns of the Trim28 coiled‐coil region forming the binding interface for the KRAB domain. Using AlphaFold2 (AF2) we provide high confidence models of the interface between Trim28 and the KRAB domain and identified leucine 301 on each chain of the Trim28 monomer to act as a pin extending into a hydrophobic pocket on the KRAB domain surface. Site directed mutations in the Trim28‐KRAB binding interface abolished binding to the KRAB domain. Our work provides a detailed understanding of the specific interactions between the KRAB domain and the Trim28 coiled‐coil and how this interaction may be regulated during silencing events.
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Affiliation(s)
- Jamie R. H. Taka
- School of Biological Sciences University of Auckland Auckland New Zealand
| | - Yunyuan Sun
- School of Biological Sciences University of Auckland Auckland New Zealand
| | - David C. Goldstone
- School of Biological Sciences University of Auckland Auckland New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery Auckland New Zealand
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34
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Raskó T, Pande A, Radscheit K, Zink A, Singh M, Sommer C, Wachtl G, Kolacsek O, Inak G, Szvetnik A, Petrakis S, Bunse M, Bansal V, Selbach M, Orbán TI, Prigione A, Hurst LD, Izsvák Z. A Novel Gene Controls a New Structure: PiggyBac Transposable Element-Derived 1, Unique to Mammals, Controls Mammal-Specific Neuronal Paraspeckles. Mol Biol Evol 2022; 39:6661922. [PMID: 36205081 PMCID: PMC9538788 DOI: 10.1093/molbev/msac175] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although new genes can arrive from modes other than duplication, few examples are well characterized. Given high expression in some human brain subregions and a putative link to psychological disorders [e.g., schizophrenia (SCZ)], suggestive of brain functionality, here we characterize piggyBac transposable element-derived 1 (PGBD1). PGBD1 is nonmonotreme mammal-specific and under purifying selection, consistent with functionality. The gene body of human PGBD1 retains much of the original DNA transposon but has additionally captured SCAN and KRAB domains. Despite gene body retention, PGBD1 has lost transposition abilities, thus transposase functionality is absent. PGBD1 no longer recognizes piggyBac transposon-like inverted repeats, nonetheless PGBD1 has DNA binding activity. Genome scale analysis identifies enrichment of binding sites in and around genes involved in neuronal development, with association with both histone activating and repressing marks. We focus on one of the repressed genes, the long noncoding RNA NEAT1, also dysregulated in SCZ, the core structural RNA of paraspeckles. DNA binding assays confirm specific binding of PGBD1 both in the NEAT1 promoter and in the gene body. Depletion of PGBD1 in neuronal progenitor cells (NPCs) results in increased NEAT1/paraspeckles and differentiation. We conclude that PGBD1 has evolved core regulatory functionality for the maintenance of NPCs. As paraspeckles are a mammal-specific structure, the results presented here show a rare example of the evolution of a novel gene coupled to the evolution of a contemporaneous new structure.
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Affiliation(s)
- Tamás Raskó
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | | | | | - Annika Zink
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Manvendra Singh
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Christian Sommer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Gerda Wachtl
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, Budapest, Hungary,Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Orsolya Kolacsek
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, Budapest, Hungary
| | - Gizem Inak
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Attila Szvetnik
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Spyros Petrakis
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece
| | - Mario Bunse
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Vikas Bansal
- Biomedical Data Science and Machine Learning Group, German Center for Neurodegenerative Diseases, Tübingen 72076, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, Budapest, Hungary
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
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35
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Mariot V, Dumonceaux J. Gene Editing to Tackle Facioscapulohumeral Muscular Dystrophy. Front Genome Ed 2022; 4:937879. [PMID: 35910413 PMCID: PMC9334676 DOI: 10.3389/fgeed.2022.937879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is a skeletal muscle disease caused by the aberrant expression of the DUX4 gene in the muscle tissue. To date, different therapeutic approaches have been proposed, targeting DUX4 at the DNA, RNA or protein levels. The recent development of the clustered regularly interspaced short-palindromic repeat (CRISPR) based technology opened new avenues of research, and FSHD is no exception. For the first time, a cure for genetic muscular diseases can be considered. Here, we describe CRISPR-based strategies that are currently being investigated for FSHD. The different approaches include the epigenome editing targeting the DUX4 gene and its promoter, gene editing targeting the polyadenylation of DUX4 using TALEN, CRISPR/cas9 or adenine base editing and the CRISPR-Cas9 genome editing for SMCHD1. We also discuss challenges facing the development of these gene editing based therapeutics.
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Affiliation(s)
- Virginie Mariot
- NIHR Biomedical Research Centre, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, University College London, London, United Kingdom
| | - Julie Dumonceaux
- NIHR Biomedical Research Centre, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, University College London, London, United Kingdom
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36
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Wang T, Yao Y, Hu X, Zhao Y. Message in hand: the application of CRISPRi, RNAi, and LncRNA in adenocarcinoma. Med Oncol 2022; 39:148. [PMID: 35834017 DOI: 10.1007/s12032-022-01727-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
Gene editing interference technology has been flourishing for more than 30 years. It has always been a common means to interfere with the expression of particular genes. Today it has shown a broad application prospect in clinical treatment, especially in adenocarcinoma treatment. In just a few years, the CRISPRi technology has attracted much z attention with its precise targeting and convenient operability significantly promoted the transformation from bench to bedside, and won the Nobel Prize in Chemistry 2020. In recent years, the importance of non-coding RNA has led LncRNA research to the center. At the same time, it also recalls the surprises obtained in laboratory and clinic research by RNAi technologies such as microRNA, siRNA, and shRNA at the beginning of the century. Therefore, this article focuses on CRISPRi, RNAi, and LncRNA to review their gene interference mechanisms currently expected to be translational research. Their applications and differences in adenocarcinoma research will also be described powerfully. It will provide a helpful reference for scientists to understand better and apply several RNA interference technologies.
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Affiliation(s)
- Ting Wang
- Cancer Research Institute, Guangdong Medical University, Dongguan, 523808, China
- Pathology Department, Guangdong Medical University, Dongguan, 523808, China
| | - Yunhong Yao
- Pathology Department, Guangdong Medical University, Dongguan, 523808, China
| | - Xinrong Hu
- Cancer Research Institute, Guangdong Medical University, Dongguan, 523808, China.
- Pathology Department, Guangdong Medical University, Dongguan, 523808, China.
| | - Yi Zhao
- Cancer Research Institute, Guangdong Medical University, Dongguan, 523808, China.
- Microbiology and Immunology Department, Guangdong Medical University, Dongguan, 523808, China.
- Department of Traditional Chinese Medicine, The First Dongguan Affiliated Hospital of Guangdong Medical University, Dongguan, 523713, China.
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37
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Lensch S, Herschl MH, Ludwig CH, Sinha J, Hinks MM, Mukund A, Fujimori T, Bintu L. Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells. eLife 2022; 11:e75115. [PMID: 35678392 PMCID: PMC9183234 DOI: 10.7554/elife.75115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/23/2022] [Indexed: 12/02/2022] Open
Abstract
In mammalian cells genes that are in close proximity can be transcriptionally coupled: silencing or activating one gene can affect its neighbors. Understanding these dynamics is important for natural processes, such as heterochromatin spreading during development and aging, and when designing synthetic gene regulation circuits. Here, we systematically dissect this process in single cells by recruiting and releasing repressive chromatin regulators at dual-gene synthetic reporters, and measuring how fast gene silencing and reactivation spread as a function of intergenic distance and configuration of insulator elements. We find that silencing by KRAB, associated with histone methylation, spreads between two genes within hours, with a time delay that increases with distance. This fast KRAB-mediated spreading is not blocked by the classical cHS4 insulators. Silencing by histone deacetylase HDAC4 of the upstream gene can also facilitate background silencing of the downstream gene by PRC2, but with a days-long delay that does not change with distance. This slower silencing can sometimes be stopped by insulators. Gene reactivation of neighboring genes is also coupled, with strong promoters and insulators determining the order of reactivation. Our data can be described by a model of multi-gene regulation that builds upon previous knowledge of heterochromatin spreading, where both gene silencing and gene reactivation can act at a distance, allowing for coordinated dynamics via chromatin regulator recruitment.
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Affiliation(s)
- Sarah Lensch
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Michael H Herschl
- University of California, Berkeley—University of California, San Francisco Graduate Program in BioengineeringBerkeleyUnited States
| | - Connor H Ludwig
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Joydeb Sinha
- Department of Chemical and Systems Biology, Stanford UniversityStanfordUnited States
| | - Michaela M Hinks
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Adi Mukund
- Biophysics Program, Stanford UniversityStanfordUnited States
| | - Taihei Fujimori
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford UniversityStanfordUnited States
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38
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Das D, Singha DL, Paswan RR, Chowdhury N, Sharma M, Reddy PS, Chikkaputtaiah C. Recent advancements in CRISPR/Cas technology for accelerated crop improvement. PLANTA 2022; 255:109. [PMID: 35460444 DOI: 10.1007/s00425-022-03894-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Precise genome engineering approaches could be perceived as a second paradigm for targeted trait improvement in crop plants, with the potential to overcome the constraints imposed by conventional CRISPR/Cas technology. The likelihood of reduced agricultural production due to highly turbulent climatic conditions increases as the global population expands. The second paradigm of stress-resilient crops with enhanced tolerance and increased productivity against various stresses is paramount to support global production and consumption equilibrium. Although traditional breeding approaches have substantially increased crop production and yield, effective strategies are anticipated to restore crop productivity even further in meeting the world's increasing food demands. CRISPR/Cas, which originated in prokaryotes, has surfaced as a coveted genome editing tool in recent decades, reshaping plant molecular biology in unprecedented ways and paving the way for engineering stress-tolerant crops. CRISPR/Cas is distinguished by its efficiency, high target specificity, and modularity, enables precise genetic modification of crop plants, allowing for the creation of allelic variations in the germplasm and the development of novel and more productive agricultural practices. Additionally, a slew of advanced biotechnologies premised on the CRISPR/Cas methodologies have augmented fundamental research and plant synthetic biology toolkits. Here, we describe gene editing tools, including CRISPR/Cas and its imitative tools, such as base and prime editing, multiplex genome editing, chromosome engineering followed by their implications in crop genetic improvement. Further, we comprehensively discuss the latest developments of CRISPR/Cas technology including CRISPR-mediated gene drive, tissue-specific genome editing, dCas9 mediated epigenetic modification and programmed self-elimination of transgenes in plants. Finally, we highlight the applicability and scope of advanced CRISPR-based techniques in crop genetic improvement.
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Affiliation(s)
- Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Dhanawantari L Singha
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Ricky Raj Paswan
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Naimisha Chowdhury
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Monica Sharma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Palakolanu Sudhakar Reddy
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India.
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39
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Tak YE, Boulay G, Lee L, Iyer S, Perry NT, Schultz HT, Garcia SP, Broye L, Horng JE, Rengarajan S, Naigles B, Volorio A, Sander JD, Gong J, Riggi N, Joung JK, Rivera MN. Genome-wide functional perturbation of human microsatellite repeats using engineered zinc finger transcription factors. CELL GENOMICS 2022; 2. [PMID: 35967079 PMCID: PMC9374162 DOI: 10.1016/j.xgen.2022.100119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Y. Esther Tak
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Gaylor Boulay
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lukuo Lee
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sowmya Iyer
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Nicholas T. Perry
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Hayley T. Schultz
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sara P. Garcia
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Liliane Broye
- Institute of Pathology, Department of Experimental Pathology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Joy E. Horng
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Shruthi Rengarajan
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Beverly Naigles
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Angela Volorio
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Institute of Pathology, Department of Experimental Pathology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Jeffry D. Sander
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Jingyi Gong
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Nicolò Riggi
- Institute of Pathology, Department of Experimental Pathology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
- Corresponding author
| | - J. Keith Joung
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Corresponding author
| | - Miguel N. Rivera
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Corresponding author
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40
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Olechnowicz A, Oleksiewicz U, Machnik M. KRAB-ZFPs and cancer stem cells identity. Genes Dis 2022. [PMID: 37492743 PMCID: PMC10363567 DOI: 10.1016/j.gendis.2022.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Studies on carcinogenesis continue to provide new information about different disease-related processes. Among others, much research has focused on the involvement of cancer stem cells (CSCs) in tumor initiation and progression. Studying the similarities and differences between CSCs and physiological stem cells (SCs) allows for a better understanding of cancer biology. Recently, it was shown that stem cell identity is partially governed by the Krϋppel-associated box domain zinc finger proteins (KRAB-ZFPs), the biggest family of transcription regulators. Several KRAB-ZFP factors exert a known effect in tumor cells, acting as tumor suppressor genes (TSGs) or oncogenes, yet their role in CSCs is still poorly characterized. Here, we review recent studies regarding the influence of KRAB-ZFPs and their cofactor protein TRIM28 on CSCs phenotype, stemness features, migration and invasion potential, metastasis, and expression of parental markers.
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41
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Mori L, Valente ST. Cure and Long-Term Remission Strategies. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2407:391-428. [PMID: 34985678 DOI: 10.1007/978-1-0716-1871-4_26] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The majority of virally suppressed individuals will experience rapid viral rebound upon antiretroviral therapy (ART) interruption, providing a strong rationale for the development of cure strategies. Moreover, despite ART virological control, HIV infection is still associated with chronic immune activation, inflammation, comorbidities, and accelerated aging. These effects are believed to be due, in part, to low-grade persistent transcription and trickling production of viral proteins from the pool of latent proviruses constituting the viral reservoir. In recent years there has been an increasing interest in developing what has been termed a functional cure for HIV. This approach entails the long-term, durable control of viral expression in the absence of therapy, preventing disease progression and transmission, despite the presence of detectable integrated proviruses. One such strategy, the block-and-lock approach for a functional cure, proposes the epigenetic silencing of proviral expression, locking the virus in a profound latent state, from which reactivation is very unlikely. The proof-of-concept for this approach was demonstrated with the use of a specific small molecule targeting HIV transcription. Here we review the principles behind the block-and-lock approach and some of the additional strategies proposed to silence HIV expression.
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Affiliation(s)
- Luisa Mori
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Susana T Valente
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.
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42
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Advance of SOX Transcription Factors in Hepatocellular Carcinoma: From Role, Tumor Immune Relevance to Targeted Therapy. Cancers (Basel) 2022; 14:cancers14051165. [PMID: 35267473 PMCID: PMC8909699 DOI: 10.3390/cancers14051165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/12/2022] [Accepted: 02/18/2022] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Hepatocellular carcinoma (HCC) is one of the deadliest human health burdens worldwide. However, the molecular mechanism of HCC development is still not fully understood. Sex determining region Y-related high-mobility group box (SOX) transcription factors not only play pivotal roles in cell fate decisions during development but also participate in the initiation and progression of cancer. Given the significance of SOX factors in cancer and their ‘undruggable’ properties, we summarize the role and molecular mechanism of SOX family members in HCC and the regulatory effect of SOX factors in the tumor immune microenvironment (TIME) of various cancers. For the first time, we analyze the association between the levels of SOX factors and that of immune components in HCC, providing clues to the pivotal role of SOX factors in the TIME of HCC. We also discuss the opportunities and challenges of targeting SOX factors for cancer. Abstract Sex determining region Y (SRY)-related high-mobility group (HMG) box (SOX) factors belong to an evolutionarily conserved family of transcription factors that play essential roles in cell fate decisions involving numerous developmental processes. In recent years, the significance of SOX factors in the initiation and progression of cancers has been gradually revealed, and they act as potential therapeutic targets for cancer. However, the research involving SOX factors is still preliminary, given that their effects in some leading-edge fields such as tumor immune microenvironment (TIME) remain obscure. More importantly, as a class of ‘undruggable’ molecules, targeting SOX factors still face considerable challenges in achieving clinical translation. Here, we mainly focus on the roles and regulatory mechanisms of SOX family members in hepatocellular carcinoma (HCC), one of the fatal human health burdens worldwide. We then detail the role of SOX members in remodeling TIME and analyze the association between SOX members and immune components in HCC for the first time. In addition, we emphasize several alternative strategies involved in the translational advances of SOX members in cancer. Finally, we discuss the alternative strategies of targeting SOX family for cancer and propose the opportunities and challenges they face based on the current accumulated studies and our understanding.
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43
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Abstract
Terpenoids represent the largest group of secondary metabolites with variable structures and functions. Terpenoids are well known for their beneficial application in human life, such as pharmaceutical products, vitamins, hormones, anticancer drugs, cosmetics, flavors and fragrances, foods, agriculture, and biofuels. Recently, engineering microbial cells have been provided with a sustainable approach to produce terpenoids with high yields. Noticeably, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) system has emerged as one of the most efficient genome-editing technologies to engineer microorganisms for improving terpenoid production. In this review, we summarize the application of the CRISPR-Cas system for the production of terpenoids in microbial hosts such as Escherichia coli, Saccharomyces cerevisiae, Corynebacterium glutamicum, and Pseudomonas putida. CRISPR-Cas9 deactivated Cas9 (dCas9)-based CRISPR (CRISPRi), and the dCas9-based activator (CRISPRa) have been used in either individual or combinatorial systems to control the metabolic flux for enhancing the production of terpenoids. Finally, the prospects of using the CRISPR-Cas system in terpenoid production are also discussed.
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Affiliation(s)
- Luan Luong Chu
- Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa University, Hanoi, Viet Nam.,Bioresource Research Center, Phenikaa University, Hanoi, Viet Nam
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44
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Zinc-finger protein 382 antagonises CDC25A and ZEB1 signaling pathway in breast cancer. Genes Dis 2022; 10:568-582. [DOI: 10.1016/j.gendis.2021.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 11/13/2021] [Accepted: 12/22/2021] [Indexed: 11/23/2022] Open
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45
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Lorenz P, Steinbeck F, Krause L, Thiesen HJ. The KRAB Domain of ZNF10 Guides the Identification of Specific Amino Acids That Transform the Ancestral KRAB-A-Related Domain Present in Human PRDM9 into a Canonical Modern KRAB-A Domain. Int J Mol Sci 2022; 23:1072. [PMID: 35162997 PMCID: PMC8835667 DOI: 10.3390/ijms23031072] [Citation(s) in RCA: 2] [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] [Received: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/14/2022] Open
Abstract
Krüppel-associated box (KRAB) zinc finger proteins are a large class of tetrapod transcription factors that usually exert transcriptional repression through recruitment of TRIM28/KAP1. The evolutionary root of modern KRAB domains (mKRAB) can be traced back to an ancestral motif (aKRAB) that occurs even in invertebrates. Here, we first stratified three subgroups of aKRAB sequences from the animal kingdom (PRDM9, SSX and coelacanth KZNF families) and defined ancestral subdomains for KRAB-A and KRAB-B. Using human ZNF10 mKRAB-AB as blueprints for function, we then identified the necessary amino acid changes that transform the inactive aKRAB-A of human PRDM9 into an mKRAB domain capable of mediating silencing and complexing TRIM28/KAP1 in human cells when employed as a hybrid with ZNF10-B. Full gain of function required replacement of residues KR by the conserved motif MLE (positionsA32-A34), which inserted an additional residue, and exchange of A9/S for F, A20/M for L, and A27/R for V. AlphaFold2 modelling documented an evolutionary conserved L-shaped body of two α-helices in all KRAB domains. It is transformed into a characteristic spatial arrangement typical for mKRAB-AB upon the amino acid replacements and in conjunction with a third helix supplied by mKRAB-B. Side-chains pointing outward from the core KRAB 3D structure may reveal a protein-protein interaction code enabling graded binding of TRIM28 to different KRAB domains. Our data provide basic insights into structure-function relationships and emulate transitions of KRAB during evolution.
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Affiliation(s)
- Peter Lorenz
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Felix Steinbeck
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Ludwig Krause
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Hans-Jürgen Thiesen
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
- Gesellschaft für Individualisierte Medizin (IndyMed) mbH, 17, 18055 Rostock, Germany
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46
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Iouranova A, Grun D, Rossy T, Duc J, Coudray A, Imbeault M, de Tribolet-Hardy J, Turelli P, Persat A, Trono D. KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences. Mob DNA 2022; 13:4. [PMID: 35042549 PMCID: PMC8767690 DOI: 10.1186/s13100-021-00260-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Transposable element-embedded regulatory sequences (TEeRS) and their KRAB-containing zinc finger protein (KZFP) controllers are increasingly recognized as modulators of gene expression. We aim to characterize the contribution of this system to gene regulation in early human development and germ cells. RESULTS Here, after studying genes driven by the long terminal repeat (LTR) of endogenous retroviruses, we identify the ape-restricted ZNF676 as the sequence-specific repressor of a subset of contemporary LTR12 integrants responsible for a large fraction of transpochimeric gene transcripts (TcGTs) generated during human early embryogenesis. We go on to reveal that the binding of this KZFP correlates with the epigenetic marking of these TEeRS in the germline, and is crucial to the control of genes involved in ciliogenesis/flagellogenesis, a biological process that dates back to the last common ancestor of eukaryotes. CONCLUSION These results illustrate how KZFPs and their TE targets contribute to the evolutionary turnover of transcription networks and participate in the transgenerational inheritance of epigenetic traits.
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Affiliation(s)
| | - Delphine Grun
- School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Tamara Rossy
- School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, EPFL, Lausanne, Switzerland
| | | | - Michael Imbeault
- School of Life Sciences, EPFL, Lausanne, Switzerland
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | | | | | - Didier Trono
- School of Life Sciences, EPFL, Lausanne, Switzerland.
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47
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Khandibharad S, Nimsarkar P, Singh S. Mechanobiology of immune cells: Messengers, receivers and followers in leishmaniasis aiding synthetic devices. CURRENT RESEARCH IN IMMUNOLOGY 2022; 3:186-198. [PMID: 36051499 PMCID: PMC9424266 DOI: 10.1016/j.crimmu.2022.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 11/03/2022] Open
Abstract
Cytokines are influential molecules which can direct cells behavior. In this review, cytokines are referred as messengers, immune cells which respond to cytokine stimulus are referred as receivers and the immune cells which gets modulated due to their plasticity induced by infectious pathogen leishmania, are referred as followers. The advantage of plasticity of cells is taken by the parasite to switch them from parasite eliminating form to parasite survival favoring form through a process called as reciprocity which is undergone by cytokines, wherein pro-inflammatory to anti-inflammatory switch occur rendering immune cell population to switch their phenotype. Detailed study of this switch can help in identification of important targets which can help in restoring the phenotype to parasite eliminating form and this can be done through synthetic circuit, finding its wider applicability in therapeutics. Cytokines as messengers for governing reciprocity in infection. Leishmania induces reciprocity modulating the immune cells plasticity. Reciprocity of cytokines identifies important target for therapeutics. Therapeutic targets aiding the design of synthetic devices to combat infection.
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48
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Khang R, Jo A, Kang H, Kim H, Kwag E, Lee JY, Koo O, Park J, Kim HK, Jo DG, Hwang I, Ahn JY, Lee Y, Choi JY, Lee YS, Shin JH. Loss of zinc-finger protein 212 leads to Purkinje cell death and locomotive abnormalities with phospholipase D3 downregulation. Sci Rep 2021; 11:22745. [PMID: 34815492 PMCID: PMC8610974 DOI: 10.1038/s41598-021-02218-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 11/08/2021] [Indexed: 11/17/2022] Open
Abstract
Although Krüppel-associated box domain-containing zinc-finger proteins (K-ZNFs) may be associated with sophisticated gene regulation in higher organisms, the physiological functions of most K-ZNFs remain unknown. The Zfp212 protein was highly conserved in mammals and abundant in the brain; it was mainly expressed in the cerebellum (Cb). Zfp212 (mouse homolog of human ZNF212) knockout (Zfp212-KO) mice showed a reduction in survival rate compared to wild-type mice after 20 months of age. GABAergic Purkinje cell degeneration in the Cb and aberrant locomotion were observed in adult Zfp212-KO mice. To identify genes related to the ataxia-like phenotype of Zfp212-KO mice, 39 ataxia-associated genes in the Cb were monitored. Substantial alterations in the expression of ataxin 10, protein phosphatase 2 regulatory subunit beta, protein kinase C gamma, and phospholipase D3 (Pld3) were observed. Among them, Pld3 alone was tightly regulated by Flag-tagged ZNF212 overexpression or Zfp212 knockdown in the HT22 cell line. The Cyclic Amplification and Selection of Targets assay identified the TATTTC sequence as a recognition motif of ZNF212, and these motifs occurred in both human and mouse PLD3 gene promoters. Adeno-associated virus-mediated introduction of human ZNF212 into the Cb of 3-week-old Zfp212-KO mice prevented Purkinje cell death and motor behavioral deficits. We confirmed the reduction of Zfp212 and Pld3 in the Cb of an alcohol-induced cerebellar degeneration mouse model, suggesting that the ZNF212–PLD3 relationship is important for Purkinje cell survival.
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Affiliation(s)
- Rin Khang
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Areum Jo
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Hojin Kang
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Hanna Kim
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Eunsang Kwag
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Ji-Yeong Lee
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Okjae Koo
- Laboratory Animal Research Center, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,ToolGen, Seoul, 08501, South Korea
| | - Jinsu Park
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Hark Kyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Dong-Gyu Jo
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, South Korea.,Biomedical Institute for Convergence, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Inwoo Hwang
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Jee-Yin Ahn
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, 06351, South Korea
| | - Yunjong Lee
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, 06351, South Korea
| | - Jeong-Yun Choi
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, 06351, South Korea
| | - Yun-Song Lee
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, 06351, South Korea
| | - Joo-Ho Shin
- Department of Pharmacology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea. .,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea. .,Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, 06351, South Korea.
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Cesaro E, Lupo A, Rapuano R, Pastore A, Grosso M, Costanzo P. ZNF224 Protein: Multifaceted Functions Based on Its Molecular Partners. Molecules 2021; 26:molecules26206296. [PMID: 34684876 PMCID: PMC8537547 DOI: 10.3390/molecules26206296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 01/05/2023] Open
Abstract
The transcription factor ZNF224 is a Kruppel-like zinc finger protein that consists of 707 amino acids and contains 19 tandemly repeated C2H2 zinc finger domains that mediate DNA binding and protein-protein interactions. ZNF224 was originally identified as a transcriptional repressor of genes involved in energy metabolism, and it was demonstrated that ZNF224-mediated transcriptional repression needs the interaction of its KRAB repressor domain with the co-repressor KAP1 and its zinc finger domains 1-3 with the arginine methyltransferase PRMT5. Furthermore, the protein ZNF255 was identified as an alternative isoform of ZNF224 that possesses different domain compositions mediating distinctive functional interactions. Subsequent studies showed that ZNF224 is a multifunctional protein able to exert different transcriptional activities depending on the cell context and the variety of its molecular partners. Indeed, it has been shown that ZNF224 can act as a repressor, an activator and a cofactor for other DNA-binding transcription factors in different human cancers. Here, we provide a brief overview of the current knowledge on the multifaceted interactions of ZNF224 and the resulting different roles of this protein in various cellular contexts.
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Affiliation(s)
- Elena Cesaro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (M.G.)
- Correspondence: (E.C.); (P.C.)
| | - Angelo Lupo
- Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Italy; (A.L.); (R.R.)
| | - Roberta Rapuano
- Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Italy; (A.L.); (R.R.)
| | - Arianna Pastore
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (M.G.)
| | - Michela Grosso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (M.G.)
| | - Paola Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (M.G.)
- Correspondence: (E.C.); (P.C.)
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50
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Tan M, Redmond AK, Dooley H, Nozu R, Sato K, Kuraku S, Koren S, Phillippy AM, Dove ADM, Read T. The whale shark genome reveals patterns of vertebrate gene family evolution. eLife 2021; 10:e65394. [PMID: 34409936 PMCID: PMC8455134 DOI: 10.7554/elife.65394] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 08/18/2021] [Indexed: 02/06/2023] Open
Abstract
Chondrichthyes (cartilaginous fishes) are fundamental for understanding vertebrate evolution, yet their genomes are understudied. We report long-read sequencing of the whale shark genome to generate the best gapless chondrichthyan genome assembly yet with higher contig contiguity than all other cartilaginous fish genomes, and studied vertebrate genomic evolution of ancestral gene families, immunity, and gigantism. We found a major increase in gene families at the origin of gnathostomes (jawed vertebrates) independent of their genome duplication. We studied vertebrate pathogen recognition receptors (PRRs), which are key in initiating innate immune defense, and found diverse patterns of gene family evolution, demonstrating that adaptive immunity in gnathostomes did not fully displace germline-encoded PRR innovation. We also discovered a new toll-like receptor (TLR29) and three NOD1 copies in the whale shark. We found chondrichthyan and giant vertebrate genomes had decreased substitution rates compared to other vertebrates, but gene family expansion rates varied among vertebrate giants, suggesting substitution and expansion rates of gene families are decoupled in vertebrate genomes. Finally, we found gene families that shifted in expansion rate in vertebrate giants were enriched for human cancer-related genes, consistent with gigantism requiring adaptations to suppress cancer.
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Affiliation(s)
- Milton Tan
- Illinois Natural History Survey at University of Illinois Urbana-ChampaignChampaignUnited States
| | | | - Helen Dooley
- University of Maryland School of Medicine, Institute of Marine & Environmental TechnologyBaltimoreUnited States
| | - Ryo Nozu
- Okinawa Churashima Research Center, Okinawa Churashima FoundationOkinawaJapan
| | - Keiichi Sato
- Okinawa Churashima Research Center, Okinawa Churashima FoundationOkinawaJapan
- Okinawa Churaumi Aquarium, MotobuOkinawaJapan
| | - Shigehiro Kuraku
- RIKEN Center for Biosystems Dynamics Research (BDR), RIKENKobeJapan
| | - Sergey Koren
- National Human Genome Research Institute, National Institutes of HealthBethesdaUnited States
| | - Adam M Phillippy
- National Human Genome Research Institute, National Institutes of HealthBethesdaUnited States
| | | | - Timothy Read
- Department of Infectious Diseases, Emory University School of MedicineAtlantaUnited States
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