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Lee J, Simpson L, Li Y, Becker S, Zou F, Zhang X, Bai L. Transcription factor condensates, 3D clustering, and gene expression enhancement of the MET regulon. eLife 2024; 13:RP96028. [PMID: 39347738 PMCID: PMC11441978 DOI: 10.7554/elife.96028] [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: 10/01/2024] Open
Abstract
Some transcription factors (TFs) can form liquid-liquid phase separated (LLPS) condensates. However, the functions of these TF condensates in 3-Dimentional (3D) genome organization and gene regulation remain elusive. In response to methionine (met) starvation, budding yeast TF Met4 and a few co-activators, including Met32, induce a set of genes involved in met biosynthesis. Here, we show that the endogenous Met4 and Met32 form co-localized puncta-like structures in yeast nuclei upon met depletion. Recombinant Met4 and Met32 form mixed droplets with LLPS properties in vitro. In relation to chromatin, Met4 puncta co-localize with target genes, and at least a subset of these target genes is clustered in 3D in a Met4-dependent manner. A MET3pr-GFP reporter inserted near several native Met4-binding sites becomes co-localized with Met4 puncta and displays enhanced transcriptional activity. A Met4 variant with a partial truncation of an intrinsically disordered region (IDR) shows less puncta formation, and this mutant selectively reduces the reporter activity near Met4-binding sites to the basal level. Overall, these results support a model where Met4 and co-activators form condensates to bring multiple target genes into a vicinity with higher local TF concentrations, which facilitates a strong response to methionine depletion.
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Affiliation(s)
- James Lee
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, United States
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, United States
- Microbiology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, United States
| | - Leman Simpson
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, United States
- Department of Chemistry, The Pennsylvania State University, Universtiy Park, United States
| | - Yi Li
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, United States
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, United States
| | - Samuel Becker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, United States
| | - Fan Zou
- Department of Physics, The Pennsylvania State University, University Park, United States
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, Universtiy Park, United States
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, United States
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, United States
- Department of Physics, The Pennsylvania State University, University Park, United States
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2
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Lee J, Simpson L, Li Y, Becker S, Zou F, Zhang X, Bai L. Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579062. [PMID: 38370634 PMCID: PMC10871269 DOI: 10.1101/2024.02.06.579062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Some transcription factors (TFs) can form liquid-liquid phase separated (LLPS) condensates. However, the functions of these TF condensates in 3D genome organization and gene regulation remain elusive. In response to methionine (met) starvation, budding yeast TF Met4 and a few co-activators, including Met32, induce a set of genes involved in met biosynthesis. Here, we show that the endogenous Met4 and Met32 form co-localized puncta-like structures in yeast nuclei upon met depletion. Recombinant Met4 and Met32 form mixed droplets with LLPS properties in vitro. In relation to chromatin, Met4 puncta co-localize with target genes, and at least a subset of these target genes is clustered in 3D in a Met4-dependent manner. A MET3pr-GFP reporter inserted near several native Met4 binding sites becomes co-localized with Met4 puncta and displays enhanced transcriptional activity. A Met4 variant with a partial truncation of an intrinsically disordered region (IDR) shows less puncta formation, and this mutant selectively reduces the reporter activity near Met4 binding sites to the basal level. Overall, these results support a model where Met4 and co-activators form condensates to bring multiple target genes into a vicinity with higher local TF concentrations, which facilitates a strong response to methionine depletion.
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Affiliation(s)
- James Lee
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Leman Simpson
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Yi Li
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Samuel Becker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Fan Zou
- Department of Physics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Physics, The Pennsylvania State University, University Park, PA, 16802, USA
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Dias JD, Sarica N, Cournac A, Koszul R, Neuveut C. Crosstalk between Hepatitis B Virus and the 3D Genome Structure. Viruses 2022; 14:445. [PMID: 35216038 PMCID: PMC8877387 DOI: 10.3390/v14020445] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/04/2022] [Accepted: 02/14/2022] [Indexed: 12/17/2022] Open
Abstract
Viruses that transcribe their DNA within the nucleus have to adapt to the existing cellular mechanisms that govern transcriptional regulation. Recent technological breakthroughs have highlighted the highly hierarchical organization of the cellular genome and its role in the regulation of gene expression. This review provides an updated overview on the current knowledge on how the hepatitis B virus interacts with the cellular 3D genome and its consequences on viral and cellular gene expression. We also briefly discuss the strategies developed by other DNA viruses to co-opt and sometimes subvert cellular genome spatial organization.
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Affiliation(s)
- João Diogo Dias
- Laboratoire de Virologie Moléculaire, Institut de Génétique Humaine, CNRS, Université de Montpellier, 34000 Montpellier, France; (J.D.D.); (N.S.)
| | - Nazim Sarica
- Laboratoire de Virologie Moléculaire, Institut de Génétique Humaine, CNRS, Université de Montpellier, 34000 Montpellier, France; (J.D.D.); (N.S.)
| | - Axel Cournac
- Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, Institut Pasteur, Université de Paris, 75015 Paris, France; (A.C.); (R.K.)
| | - Romain Koszul
- Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, Institut Pasteur, Université de Paris, 75015 Paris, France; (A.C.); (R.K.)
| | - Christine Neuveut
- Laboratoire de Virologie Moléculaire, Institut de Génétique Humaine, CNRS, Université de Montpellier, 34000 Montpellier, France; (J.D.D.); (N.S.)
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Chemically Induced Chromosomal Interaction (CICI) method to study chromosome dynamics and its biological roles. Nat Commun 2022; 13:757. [PMID: 35140210 PMCID: PMC8828778 DOI: 10.1038/s41467-022-28416-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/14/2022] [Indexed: 01/01/2023] Open
Abstract
Numerous intra- and inter-chromosomal contacts have been mapped in eukaryotic genomes, but it remains challenging to link these 3D structures to their regulatory functions. To establish the causal relationships between chromosome conformation and genome functions, we develop a method, Chemically Induced Chromosomal Interaction (CICI), to selectively perturb the chromosome conformation at targeted loci. Using this method, long-distance chromosomal interactions can be induced dynamically between intra- or inter-chromosomal loci pairs, including the ones with very low Hi-C contact frequencies. Measurement of CICI formation time allows us to probe chromosome encounter dynamics between different loci pairs across the cell cycle. We also conduct two functional tests of CICI. We perturb the chromosome conformation near a DNA double-strand break and observe altered donor preference in homologous recombination; we force interactions between early and late-firing DNA replication origins and find no significant changes in replication timing. These results suggest that chromosome conformation plays a deterministic role in homology-directed DNA repair, but not in the establishment of replication timing. Overall, our study demonstrates that CICI is a powerful tool to study chromosome dynamics and 3D genome function. Methods to selectively manipulate specific long-distance chromosomal interactions are limited. Here the authors develop a method called Chemically Induced Chromosomal Interaction (CICI) to engineer interactions and demonstrate that 3D conformation plays a causal role in establishing donor DNA preference during DNA repair.
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Shen C, Feng X, Mao T, Yang D, Zou J, Zao X, Deng Q, Chen X, Lu F. Yin-Yang 1 and HBx protein activate HBV transcription by mediating the spatial interaction of cccDNA minichromosome with cellular chromosome 19p13.11. Emerg Microbes Infect 2021; 9:2455-2464. [PMID: 33084547 PMCID: PMC7671595 DOI: 10.1080/22221751.2020.1840311] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
HBV cccDNA stably exists in the nuclei of infected cells as an episomal munichromosome which is responsible for viral persistence and failure of current antiviral treatments. However, the regulatory mechanism of cccDNA transcription by viral and host cellular factors is not well understood. In this study, we investigated whether cccDNA could be recruited into a specific region of the nucleus via specific interaction with a cellular chromatin to regulate its transcription activity. To investigate this hypothesis, we used chromosome conformation capture (3C) technology to search for the potential interaction of cccDNA and cellular chromatin through rcccDNA transfection in hepatoma cells and found that cccDNA is specifically associated with human chromosome 19p13.11 region, which contains a highly active enhancer element. We also confirmed that cellular transcription factor Yin-Yang 1 (YY1) and viral protein HBx mediated the spatial regulation of HBV cccDNA transcription by 19p13.11 enhancer. Thus, These findings indicate that YY1 and HBx mediate the recruitment of HBV cccDNA minichromosomes to 19p13.11 region for transcription activation, and YY1 may present as a novel therapeutic target against HBV infection.
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Affiliation(s)
- Congle Shen
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People's Republic of China
| | - Xiaoyu Feng
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People's Republic of China
| | - Tianhao Mao
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People's Republic of China
| | - Danli Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People's Republic of China
| | - Jun Zou
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People's Republic of China
| | - Xiaobin Zao
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People's Republic of China
| | - Qiang Deng
- Key Laboratory of Medical Molecular Virology (MOE & MOH), School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Xiangmei Chen
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People's Republic of China
| | - Fengmin Lu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People's Republic of China
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Condensin action and compaction. Curr Genet 2018; 65:407-415. [PMID: 30361853 DOI: 10.1007/s00294-018-0899-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 10/18/2018] [Accepted: 10/20/2018] [Indexed: 12/20/2022]
Abstract
Condensin is a multi-subunit protein complex that belongs to the family of structural maintenance of chromosomes (SMC) complexes. Condensins regulate chromosome structure in a wide range of processes including chromosome segregation, gene regulation, DNA repair and recombination. Recent research defined the structural features and molecular activities of condensins, but it is unclear how these activities are connected to the multitude of phenotypes and functions attributed to condensins. In this review, we briefly discuss the different molecular mechanisms by which condensins may regulate global chromosome compaction, organization of topologically associated domains, clustering of specific loci such as tRNA genes, rDNA segregation, and gene regulation.
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Moreau P, Cournac A, Palumbo GA, Marbouty M, Mortaza S, Thierry A, Cairo S, Lavigne M, Koszul R, Neuveut C. Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin. Nat Commun 2018; 9:4268. [PMID: 30323189 PMCID: PMC6189100 DOI: 10.1038/s41467-018-06739-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 09/19/2018] [Indexed: 01/05/2023] Open
Abstract
Whether non-integrated viral DNAs distribute randomly or target specific positions within the higher-order architecture of mammalian genomes remains largely unknown. Here we use Hi-C and viral DNA capture (CHi-C) in primary human hepatocytes infected by either hepatitis B virus (HBV) or adenovirus type 5 (Ad5) virus to show that they adopt different strategies in their respective positioning at active chromatin. HBV contacts preferentially CpG islands (CGIs) enriched in Cfp1 a factor required for its transcription. These CGIs are often associated with highly expressed genes (HEG) and genes deregulated during infection. Ad5 DNA interacts preferentially with transcription start sites (TSSs) and enhancers of HEG, as well as genes upregulated during infection. These results show that DNA viruses use different strategies to infiltrate genomic 3D networks and target specific regions. This targeting may facilitate the recruitment of transcription factors necessary for their own replication and contribute to the deregulation of cellular gene expression.
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Affiliation(s)
- Pierrick Moreau
- Institut Pasteur, Unité Hepacivirus et Immunité Innée, 75015, Paris, France.,CNRS, UMR 3569, 75015, Paris, France.,Institut Pasteur, Département de Virologie, Paris, France
| | - Axel Cournac
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015, Paris, France.,CNRS, UMR 3525, 75015, Paris, France
| | - Gianna Aurora Palumbo
- Institut Pasteur, Unité Hepacivirus et Immunité Innée, 75015, Paris, France.,CNRS, UMR 3569, 75015, Paris, France.,Institut Pasteur, Département de Virologie, Paris, France
| | - Martial Marbouty
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015, Paris, France.,CNRS, UMR 3525, 75015, Paris, France
| | - Shogofa Mortaza
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015, Paris, France.,CNRS, UMR 3525, 75015, Paris, France
| | - Agnes Thierry
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015, Paris, France.,CNRS, UMR 3525, 75015, Paris, France
| | - Stefano Cairo
- XenTech, Research and Development Department, 91000, Evry, France
| | - Marc Lavigne
- Institut Pasteur, Département de Virologie, Paris, France.,Institut Cochin-INSERM U1016-CNRS UMR8104, Université Paris Descartes, Paris, France
| | - Romain Koszul
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015, Paris, France. .,CNRS, UMR 3525, 75015, Paris, France.
| | - Christine Neuveut
- Institut Pasteur, Unité Hepacivirus et Immunité Innée, 75015, Paris, France. .,CNRS, UMR 3569, 75015, Paris, France. .,Institut Pasteur, Département de Virologie, Paris, France.
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Nikolaou C. Invisible cities: segregated domains in the yeast genome with distinct structural and functional attributes. Curr Genet 2017; 64:247-258. [PMID: 28780612 DOI: 10.1007/s00294-017-0731-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 02/07/2023]
Abstract
Recent advances in our understanding of the three-dimensional organization of the eukaryotic nucleus have rendered the spatial distribution of genes increasingly relevant. In a recent work (Tsochatzidou et al., Nucleic Acids Res 45:5818-5828, 2017), we proposed the existence of a functional compartmentalization of the yeast genome according to which, genes occupying the chromosomal regions at the nuclear periphery have distinct structural, functional and evolutionary characteristics compared to their centromeric-proximal counterparts. Around the same time, it was also shown that the genome of Saccharomyces cerevisiae is organized in topologically associated domains (TADs), which are largely associated with the replication timing. In this work, we proceed to investigate whether such units of three-dimensional genomic organization can be linked to transcriptional activity as a driving force for the shaping of genomic architecture. Through the application of a simple boundary-calling criterion in genome-wide 3C data, we define ~100 TAD-like domains which can be clustered in six different classes with radically different nucleosomal organizations, significant variations in transcription factor binding and uneven chromosomal distribution. Approximately ~20% of the genome is found to be confined in regions with "closed" chromatin structure around gene promoters. Most interestingly, we find both "open" and "closed" regions to be segregated, in the sense that they tend to avoid inter-chromosomal interactions. Our data further enforce the notion of a marked compartmentalization of the yeast genome in isolated territories, with implications in its function and evolution.
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Affiliation(s)
- Christoforos Nikolaou
- Computational Genomics Group, Department of Biology, University of Crete, 70013, Herakleion, Greece.
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