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Salafranca J, Ko JK, Mukherjee AK, Fritzsche M, van Grinsven E, Udalova IA. Neutrophil nucleus: shaping the past and the future. J Leukoc Biol 2023; 114:585-594. [PMID: 37480361 PMCID: PMC10673716 DOI: 10.1093/jleuko/qiad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023] Open
Abstract
Neutrophils are innate immune cells that are key to protecting the host against infection and maintaining body homeostasis. However, if dysregulated, they can contribute to disease, such as in cancer or chronic autoinflammatory disorders. Recent studies have highlighted the heterogeneity in the neutrophil compartment and identified the presence of immature neutrophils and their precursors in these pathologies. Therefore, understanding neutrophil maturity and the mechanisms through which they contribute to disease is critical. Neutrophils were first characterized morphologically by Ehrlich in 1879 using microscopy, and since then, different technologies have been used to assess neutrophil maturity. The advances in the imaging field, including state-of-the-art microscopy and machine learning algorithms for image analysis, reinforce the use of neutrophil nuclear morphology as a fundamental marker of maturity, applicable for objective classification in clinical diagnostics. New emerging approaches, such as the capture of changes in chromatin topology, will provide mechanistic links between the nuclear shape, chromatin organization, and transcriptional regulation during neutrophil maturation.
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Affiliation(s)
- Julia Salafranca
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Jacky Ka Ko
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Ananda K Mukherjee
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Marco Fritzsche
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Erinke van Grinsven
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Irina A Udalova
- The Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
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2
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Huang J, Wu C, Kloeber JA, Gao H, Gao M, Zhu Q, Chang Y, Zhao F, Guo G, Luo K, Dai H, Liu S, Huang Q, Kim W, Zhou Q, Zhu S, Wu Z, Tu X, Yin P, Deng M, Wang L, Yuan J, Lou Z. SLFN5-mediated chromatin dynamics sculpt higher-order DNA repair topology. Mol Cell 2023; 83:1043-1060.e10. [PMID: 36854302 PMCID: PMC10467573 DOI: 10.1016/j.molcel.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 12/23/2022] [Accepted: 02/01/2023] [Indexed: 03/02/2023]
Abstract
Repair of DNA double-strand breaks (DSBs) elicits three-dimensional (3D) chromatin topological changes. A recent finding reveals that 53BP1 assembles into a 3D chromatin topology pattern around DSBs. How this formation of a higher-order structure is configured and regulated remains enigmatic. Here, we report that SLFN5 is a critical factor for 53BP1 topological arrangement at DSBs. Using super-resolution imaging, we find that SLFN5 binds to 53BP1 chromatin domains to assemble a higher-order microdomain architecture by driving damaged chromatin dynamics at both DSBs and deprotected telomeres. Mechanistically, we propose that 53BP1 topology is shaped by two processes: (1) chromatin mobility driven by the SLFN5-LINC-microtubule axis and (2) the assembly of 53BP1 oligomers mediated by SLFN5. In mammals, SLFN5 deficiency disrupts the DSB repair topology and impairs non-homologous end joining, telomere fusions, class switch recombination, and sensitivity to poly (ADP-ribose) polymerase inhibitor. We establish a molecular mechanism that shapes higher-order chromatin topologies to safeguard genomic stability.
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Affiliation(s)
- Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Chenming Wu
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA; Medical Scientist Training Program, Mayo Clinic, Rochester, MN 55905, USA
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yiming Chang
- Jinzhou Medical University, Shanghai East Hospital, Shanghai 200120, China
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Haiming Dai
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Sijia Liu
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Qiru Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Wootae Kim
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Shouhai Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zheming Wu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xinyi Tu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Yuan
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200092, China.
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA.
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3
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Feng Y, Wang P, Cai L, Zhan M, He F, Wang J, Li Y, Gega E, Zhang W, Zhao W, Xin Y, Chen X, Ruan Y, Lu L. 3D-Epigenomic Regulation of Gene Transcription in Hepatocellular Carcinoma. Adv Genet (Hoboken) 2022; 3:2100010. [PMID: 36911294 PMCID: PMC9993472 DOI: 10.1002/ggn2.202100010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 05/03/2022] [Indexed: 11/10/2022]
Abstract
The fundamental cause of transcription dysregulation in hepatocellular carcinoma (HCC) remains elusive. To investigate the underlying mechanisms, comprehensive 3D-epigenomic analyses are performed in cellular models of THLE2 (a normal hepatocytes cell line) and HepG2 (a hepatocellular carcinoma cell line) using integrative approaches for chromatin topology, genomic and epigenomic variation, and transcriptional output. Comparing the 3D-epigenomes in THLE2 and HepG2 reveal that most HCC-associated genes are organized in complex chromatin interactions mediated by RNA polymerase II (RNAPII). Incorporation of genome-wide association studies (GWAS) data enables the identification of non-coding genetic variants that are enriched in distal enhancers connecting to the promoters of HCC-associated genes via long-range chromatin interactions, highlighting their functional roles. Interestingly, CTCF binding and looping proximal to HCC-associated genes appear to form chromatin architectures that overarch RNAPII-mediated chromatin interactions. It is further demonstrated that epigenetic variants by DNA hypomethylation at a subset of CTCF motifs proximal to HCC-associated genes can modify chromatin topological configuration, which in turn alter RNAPII-mediated chromatin interactions and lead to dysregulation of transcription. Together, the 3D-epigenomic analyses provide novel insights of multifaceted interplays involving genetics, epigenetics, and chromatin topology in HCC cells.
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Affiliation(s)
- Yuliang Feng
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China.,The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Liuyang Cai
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Meixiao Zhan
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
| | - Fan He
- Department of Interventional Radiology Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology) Shenzhen Guangdong 518020 P. R. China
| | - Jiahui Wang
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Yong Li
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
| | - Eva Gega
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Wei Zhang
- Department of Interventional Radiology Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology) Shenzhen Guangdong 518020 P. R. China
| | - Wei Zhao
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
| | - Yongjie Xin
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
| | - Xudong Chen
- Department of Interventional Radiology Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology) Shenzhen Guangdong 518020 P. R. China
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA
| | - Ligong Lu
- Zhuhai Precision Medical Center Zhuhai People's Hospital Zhuhai Hospital Affiliated with Jinan University Zhuhai Guangdong 519000 P. R. China
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4
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Nazer E. To be or not be (in the LAD): emerging roles of lamin proteins in transcriptional regulation. Biochem Soc Trans 2022:BST20210858. [PMID: 35437578 DOI: 10.1042/BST20210858] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 12/21/2022]
Abstract
Lamins are components of the nuclear lamina, a protein meshwork that underlies the nuclear membrane. Lamins interact with chromatin in transcriptionally silent regions defined as lamina-associated-domains (LADs). However, recent studies have shown that lamins regulate active transcription inside LADs. In addition, ChIP-seq analysis has shown that lamins interact with lamin-dependent promoters and enhancers located in the interior of the nucleus. Moreover, functional studies suggest that lamins regulate transcription at associated-promoters and long-range chromatin interactions of key developmental gene programs. This review will discuss emerging, non-canonical functions of lamins in controlling non-silent genes located both inside and outside of LADs, focusing on transcriptional regulation and chromatin organization in Drosophila and mammals as metazoan model organisms.
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5
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Mas G, Santoro F, Blanco E, Gamarra Figueroa GP, Le Dily F, Frigè G, Vidal E, Mugianesi F, Ballaré C, Gutierrez A, Sparavier A, Marti-Renom MA, Minucci S, Di Croce L. In vivo temporal resolution of acute promyelocytic leukemia progression reveals a role of Klf4 in suppressing early leukemic transformation. Genes Dev 2022; 36:451-467. [PMID: 35450883 PMCID: PMC9067408 DOI: 10.1101/gad.349115.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/25/2022] [Indexed: 11/25/2022]
Abstract
In this study, Mas et al. used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts that express the fusion protein PML-RARα as a paradigm to temporally dissect the dynamic changes in the epigenome, transcriptome, and genome architecture induced during oncogenic transformation. Their multiomics-integrated analysis identified Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis, and they characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression and demonstrated that ectopic Klf4 overexpression can suppress self-renewal and reverse the differentiation block induced by PML-RARα. Genome organization plays a pivotal role in transcription, but how transcription factors (TFs) rewire the structure of the genome to initiate and maintain the programs that lead to oncogenic transformation remains poorly understood. Acute promyelocytic leukemia (APL) is a fatal subtype of leukemia driven by a chromosomal translocation between the promyelocytic leukemia (PML) and retinoic acid receptor α (RARα) genes. We used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts that express the fusion protein PML-RARα as a paradigm to temporally dissect the dynamic changes in the epigenome, transcriptome, and genome architecture induced during oncogenic transformation. We found that PML-RARα initiates a continuum of topologic alterations, including switches from A to B compartments, transcriptional repression, loss of active histone marks, and gain of repressive histone marks. Our multiomics-integrated analysis identifies Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis. Furthermore, we characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression and demonstrated that ectopic Klf4 overexpression can suppress self-renewal and reverse the differentiation block induced by PML-RARα. Our study provides a comprehensive in vivo temporal dissection of the epigenomic and topological reprogramming induced by an oncogenic TF and illustrates how topological architecture can be used to identify new drivers of malignant transformation.
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Affiliation(s)
- Glòria Mas
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Fabio Santoro
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | | | - François Le Dily
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Gianmaria Frigè
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Francesca Mugianesi
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Cecilia Ballaré
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Arantxa Gutierrez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Aleksandra Sparavier
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Marc A Marti-Renom
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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6
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Belver L, Albero R, Ferrando AA. Deregulation of enhancer structure, function, and dynamics in acute lymphoblastic leukemia. Trends Immunol 2021; 42:418-431. [PMID: 33858773 PMCID: PMC8091164 DOI: 10.1016/j.it.2021.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/25/2022]
Abstract
Enhancers control dynamic changes in gene expression and orchestrate the tightly controlled transcriptional circuitries that direct and coordinate cell growth, proliferation, survival, lineage commitment, and differentiation during lymphoid development. Enhancer hijacking and neoenhancer formation at oncogene loci, as well as aberrant activation of oncogene-associated enhancers, can induce constitutive activation of self-perpetuating oncogenic transcriptional circuitries, and contribute to the malignant transformation of immature lymphoid progenitors in acute lymphoblastic leukemia (ALL). In this review, we present recent discoveries of the role of enhancer dynamics in mouse and human lymphoid development, and discuss how genetic and epigenetic alterations of enhancer function can promote leukemogenesis, and potential strategies for targeting the enhancer machinery in the treatment of ALL.
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Affiliation(s)
- Laura Belver
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA; Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, 08916, Spain
| | - Robert Albero
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA; Department of Systems Biology, Columbia University, New York, NY, 10032, USA; Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA; Department of Pathology, Columbia University Medical Center, New York, NY, 10032, USA.
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7
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Imperador CHL, Bardella VB, Dos Anjos EHM, Rodrigues VLCC, Cabral-de-Mello DC, Mello MLS. Spatial Distribution of Heterochromatin Bodies in the Nuclei of Triatoma infestans (Klug). Microsc Microanal 2020; 26:567-574. [PMID: 32393416 DOI: 10.1017/s143192762000149x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Constitutive heterochromatin typically exhibits low gene density and is commonly found adjacent or close to the nuclear periphery, in contrast to transcriptionally active genes concentrated in the innermost nuclear region. In Triatoma infestans cells, conspicuous constitutive heterochromatin forms deeply stained structures named chromocenters. However, to the best of our knowledge, no information exists regarding whether these chromocenters acquire a precise topology in the cell nuclei or whether their 18S rDNA, which is important for ribosome function, faces the nuclear center preferentially. In this work, the spatial distribution of fluorescent Feulgen-stained chromocenters and the distribution of their 18S rDNA was analyzed in Malpighian tubule cells of T. infestans using confocal microscopy. The chromocenters were shown to be spatially positioned relatively close to the nuclear periphery, though not adjacent to it. The variable distance between the chromocenters and the nuclear periphery suggests mobility of these bodies within the cell nuclei. The distribution of 18S rDNA at the edge of the chromocenters was not found to face the nuclear interior exclusively. Because the genome regions containing 18S rDNA in the chromocenters also face the nuclear periphery, the proximity of the chromocenters to this nuclear region is not assumed to be associated with overall gene silencing.
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Affiliation(s)
- Carlos Henrique L Imperador
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), Rua Monteiro Lobato 255, 13083-862Campinas, SP, Brazil
| | - Vanessa B Bardella
- Department of Biology, Institute of Biosciences, State University of São Paulo (Unesp), Avenida 24-A, 1515, 13506-900Rio Claro, SP, Brazil
| | - Eli Heber M Dos Anjos
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), Rua Monteiro Lobato 255, 13083-862Campinas, SP, Brazil
| | - Vera L C C Rodrigues
- Superintendence for Control of Endemic Diseases (SUCEN), Rua Afonso Pessini, 86, 13845-206Mogi-Guaçu, SP, Brazil
| | - Diogo C Cabral-de-Mello
- Department of Biology, Institute of Biosciences, State University of São Paulo (Unesp), Avenida 24-A, 1515, 13506-900Rio Claro, SP, Brazil
| | - Maria Luiza S Mello
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), Rua Monteiro Lobato 255, 13083-862Campinas, SP, Brazil
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8
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Weiterer S, Meier‐Soelch J, Georgomanolis T, Mizi A, Beyerlein A, Weiser H, Brant L, Mayr‐Buro C, Jurida L, Beuerlein K, Müller H, Weber A, Tenekeci U, Dittrich‐Breiholz O, Bartkuhn M, Nist A, Stiewe T, van IJcken WFJ, Riedlinger T, Schmitz ML, Papantonis A, Kracht M. Distinct IL-1α-responsive enhancers promote acute and coordinated changes in chromatin topology in a hierarchical manner. EMBO J 2020; 39:e101533. [PMID: 31701553 PMCID: PMC6939198 DOI: 10.15252/embj.2019101533] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 09/27/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022] Open
Abstract
How cytokine-driven changes in chromatin topology are converted into gene regulatory circuits during inflammation still remains unclear. Here, we show that interleukin (IL)-1α induces acute and widespread changes in chromatin accessibility via the TAK1 kinase and NF-κB at regions that are highly enriched for inflammatory disease-relevant SNPs. Two enhancers in the extended chemokine locus on human chromosome 4 regulate the IL-1α-inducible IL8 and CXCL1-3 genes. Both enhancers engage in dynamic spatial interactions with gene promoters in an IL-1α/TAK1-inducible manner. Microdeletions of p65-binding sites in either of the two enhancers impair NF-κB recruitment, suppress activation and biallelic transcription of the IL8/CXCL2 genes, and reshuffle higher-order chromatin interactions as judged by i4C interactome profiles. Notably, these findings support a dominant role of the IL8 "master" enhancer in the regulation of sustained IL-1α signaling, as well as for IL-8 and IL-6 secretion. CRISPR-guided transactivation of the IL8 locus or cross-TAD regulation by TNFα-responsive enhancers in a different model locus supports the existence of complex enhancer hierarchies in response to cytokine stimulation that prime and orchestrate proinflammatory chromatin responses downstream of NF-κB.
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Affiliation(s)
- Sinah‐Sophia Weiterer
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Johanna Meier‐Soelch
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | | | - Athanasia Mizi
- Center for Molecular Medicine CologneUniversity of CologneCologneGermany
- Department of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | - Anna Beyerlein
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Hendrik Weiser
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Lilija Brant
- Department of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | - Christin Mayr‐Buro
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Liane Jurida
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Knut Beuerlein
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Helmut Müller
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Axel Weber
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Ulas Tenekeci
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Oliver Dittrich‐Breiholz
- Research Core Unit GenomicsInstitute of Physiological ChemistryMedical School HannoverHannoverGermany
| | - Marek Bartkuhn
- Institute for GeneticsJustus Liebig University GiessenGiessenGermany
| | - Andrea Nist
- Genomics Core Facility and Institute of Molecular OncologyPhilipps University MarburgMarburgGermany
| | - Thorsten Stiewe
- Genomics Core Facility and Institute of Molecular OncologyPhilipps University MarburgMarburgGermany
- Member of the German Center for Lung Research (DZL)GiessenGermany
| | | | - Tabea Riedlinger
- Institute of BiochemistryJustus Liebig University GiessenGiessenGermany
| | - M Lienhard Schmitz
- Member of the German Center for Lung Research (DZL)GiessenGermany
- Institute of BiochemistryJustus Liebig University GiessenGiessenGermany
| | - Argyris Papantonis
- Center for Molecular Medicine CologneUniversity of CologneCologneGermany
- Department of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | - Michael Kracht
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
- Member of the German Center for Lung Research (DZL)GiessenGermany
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9
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Moradpour M, Abdulah SNA. CRISPR/dCas9 platforms in plants: strategies and applications beyond genome editing. Plant Biotechnol J 2020; 18:32-44. [PMID: 31392820 PMCID: PMC6920162 DOI: 10.1111/pbi.13232] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/27/2019] [Accepted: 07/30/2019] [Indexed: 05/19/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) and Cas9-associated protein systems provide a powerful genetic manipulation tool that can drive plant research forward. Nuclease-dead Cas9 (dCas9) is an enzymatically inactive mutant of Cas9 in which its endonuclease activity is non-functional. The applications of CRISPR/dCas9 have expanded and diversified in recent years. Originally, dCas9 was used as a CRISPR/Cas9 re-engineering tool that enables targeted expression of any gene or multiple genes through recruitment of transcriptional effector domains without introducing irreversible DNA-damaging mutations. Subsequent applications have made use of its ability to recruit modifying enzymes and reporter proteins to DNA target sites. In this paper, the most recent progress in the applications of CRISPR/dCas9 in plants, which include gene activation and repression, epigenome editing, modulation of chromatin topology, live-cell chromatin imaging and DNA-free genetic modification, will be reviewed. The associated strategies for exploiting the CRISPR/dCas9 system for crop improvement with a dimer of the future of the CRISPR/dCas9 system in the functional genomics of crops and the development of traits will be briefly discussed.
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Affiliation(s)
- Mahdi Moradpour
- Laboratory of Science and TechnologyInstitute of Plantation StudiesUniversiti Putra MalaysiaSerdangSelangorMalaysia
| | - Siti Nor Akmar Abdulah
- Laboratory of Science and TechnologyInstitute of Plantation StudiesUniversiti Putra MalaysiaSerdangSelangorMalaysia
- Department of Agricultural TechnologyFaculty of AgricultureUniversiti Putra MalaysiaSerdangSelangorMalaysia
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10
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Abstract
DNA double-strand breaks (DSBs) elicit major chromatin changes. Using super-resolution microscopy in human cells, Ochs et al. unveil that the DSB response protein 53BP1 and its effector RIF1 organize DSB-flanking chromatin into circular micro-domains. These structures control the spatial distribution of DSB repair factors safeguarding genome integrity.
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Affiliation(s)
- Pierre Caron
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, F-75013, Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, F-75013, Paris, France.
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11
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Abstract
This Outlook by Weidemann et al. highlights two recent studies, one of which, by Mermet et al., is in this issue of Genes & Development. They examine how “time of day”-dependent changes in chromatin drive core clock oscillations and show that waking up involves highly dynamic changes in the three dimensional positioning of genes within the cell. Each spring, we get out of bed 1 h ahead of our biological wake-up time due to the misalignment of internal clocks with the light–dark cycle. Genetic discoveries revealed that clock genes encode transcription factors that are expressed throughout many tissues, yet a gap has remained in understanding the temporal dynamics of transcription. Two groups now apply circular chromosome conformation capture and high-throughput sequencing to dissect how “time of day”-dependent changes in chromatin drive core clock oscillations. A surprise is the finding that disruption of enhancer–promoter contacts within chromatin leads to an advance in the “wake-up” time of mice. Furthermore, the assembly of transcriptionally active domains of chromatin requires the ordered recruitment of core clock transcription factors each day. These studies show that waking up involves highly dynamic changes in the three-dimensional positioning of genes within the cell.
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Affiliation(s)
- Benjamin J Weidemann
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Kathryn Moynihan Ramsey
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Joseph Bass
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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12
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Mermet J, Yeung J, Hurni C, Mauvoisin D, Gustafson K, Jouffe C, Nicolas D, Emmenegger Y, Gobet C, Franken P, Gachon F, Naef F. Clock-dependent chromatin topology modulates circadian transcription and behavior. Genes Dev 2018; 32:347-358. [PMID: 29572261 PMCID: PMC5900709 DOI: 10.1101/gad.312397.118] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/02/2018] [Indexed: 12/27/2022]
Abstract
The circadian clock in animals orchestrates widespread oscillatory gene expression programs, which underlie 24-h rhythms in behavior and physiology. Several studies have shown the possible roles of transcription factors and chromatin marks in controlling cyclic gene expression. However, how daily active enhancers modulate rhythmic gene transcription in mammalian tissues is not known. Using circular chromosome conformation capture (4C) combined with sequencing (4C-seq), we discovered oscillatory promoter-enhancer interactions along the 24-h cycle in the mouse liver and kidney. Rhythms in chromatin interactions were abolished in arrhythmic Bmal1 knockout mice. Deleting a contacted intronic enhancer element in the Cryptochrome 1 (Cry1) gene was sufficient to compromise the rhythmic chromatin contacts in tissues. Moreover, the deletion reduced the daily dynamics of Cry1 transcriptional burst frequency and, remarkably, shortened the circadian period of locomotor activity rhythms. Our results establish oscillating and clock-controlled promoter-enhancer looping as a regulatory layer underlying circadian transcription and behavior.
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Affiliation(s)
- Jérôme Mermet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jake Yeung
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Clémence Hurni
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Daniel Mauvoisin
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Kyle Gustafson
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Céline Jouffe
- Nestle Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Damien Nicolas
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Yann Emmenegger
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Cédric Gobet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Nestle Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Paul Franken
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Frédéric Gachon
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Nestle Institute of Health Sciences, CH-1015 Lausanne, Switzerland
| | - Félix Naef
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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13
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Stadler MR, Haines JE, Eisen MB. Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo. eLife 2017; 6:29550. [PMID: 29148971 PMCID: PMC5739541 DOI: 10.7554/elife.29550] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 11/13/2017] [Indexed: 11/13/2022] Open
Abstract
High-throughput assays of three-dimensional interactions of chromosomes have shed considerable light on the structure of animal chromatin. Despite this progress, the precise physical nature of observed structures and the forces that govern their establishment remain poorly understood. Here we present high resolution Hi-C data from early Drosophila embryos. We demonstrate that boundaries between topological domains of various sizes map to DNA elements that resemble classical insulator elements: short genomic regions sensitive to DNase digestion that are strongly bound by known insulator proteins and are frequently located between divergent promoters. Further, we show a striking correspondence between these elements and the locations of mapped polytene interband regions. We believe it is likely this relationship between insulators, topological boundaries, and polytene interbands extends across the genome, and we therefore propose a model in which decompaction of boundary-insulator-interband regions drives the organization of interphase chromosomes by creating stable physical separation between adjacent domains.
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Affiliation(s)
- Michael R Stadler
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Jenna E Haines
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Michael B Eisen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States.,Department of Integrative Biology, University of California, Berkeley, CA, United States.,Howard Hughes Medical Institute, Berkeley, CA, United States
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14
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Bayarsaihan D. Deciphering the Epigenetic Code in Embryonic and Dental Pulp Stem Cells. Yale J Biol Med 2016; 89:539-563. [PMID: 28018144 PMCID: PMC5168831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A close cooperation between chromatin states, transcriptional modulation, and epigenetic modifications is required for establishing appropriate regulatory circuits underlying self-renewal and differentiation of adult and embryonic stem cells. A growing body of research has established that the epigenome topology provides a structural framework for engaging genes in the non-random chromosomal interactions to orchestrate complex processes such as cell-matrix interactions, cell adhesion and cell migration during lineage commitment. Over the past few years, the functional dissection of the epigenetic landscape has become increasingly important for understanding gene expression dynamics in stem cells naturally found in most tissues. Adult stem cells of the human dental pulp hold great promise for tissue engineering, particularly in the skeletal and tooth regenerative medicine. It is therefore likely that progress towards pulp regeneration will have a substantial impact on the clinical research. This review summarizes the current state of knowledge regarding epigenetic cues that have evolved to regulate the pluripotent differentiation potential of embryonic stem cells and the lineage determination of developing dental pulp progenitors.
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Affiliation(s)
- Dashzeveg Bayarsaihan
- Institute for System Genomics and Center for Regenerative Medicine and Skeletal Development, University of Connecticut Health Center, Farmington, CT, USA
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15
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Dong B, Almassalha LM, Stypula-Cyrus Y, Urban BE, Chandler JE, Nguyen TQ, Sun C, Zhang HF, Backman V. Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast. Proc Natl Acad Sci U S A 2016; 113:9716-21. [PMID: 27535934 DOI: 10.1073/pnas.1602202113] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Visualizing the nanoscale intracellular structures formed by nucleic acids, such as chromatin, in nonperturbed, structurally and dynamically complex cellular systems, will help expand our understanding of biological processes and open the next frontier for biological discovery. Traditional superresolution techniques to visualize subdiffractional macromolecular structures formed by nucleic acids require exogenous labels that may perturb cell function and change the very molecular processes they intend to study, especially at the extremely high label densities required for superresolution. However, despite tremendous interest and demonstrated need, label-free optical superresolution imaging of nucleotide topology under native nonperturbing conditions has never been possible. Here we investigate a photoswitching process of native nucleotides and present the demonstration of subdiffraction-resolution imaging of cellular structures using intrinsic contrast from unmodified DNA based on the principle of single-molecule photon localization microscopy (PLM). Using DNA-PLM, we achieved nanoscopic imaging of interphase nuclei and mitotic chromosomes, allowing a quantitative analysis of the DNA occupancy level and a subdiffractional analysis of the chromosomal organization. This study may pave a new way for label-free superresolution nanoscopic imaging of macromolecular structures with nucleotide topologies and could contribute to the development of new DNA-based contrast agents for superresolution imaging.
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16
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Abstract
Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.
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Affiliation(s)
- William A MacDonald
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Saqib S Sachani
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Carlee R White
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Mellissa R W Mann
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
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