1
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Hou PX, Fan Q, Zhang Q, Liu JJ, Wu Q. M6A-induced transcription factor IRF5 contributes to the progression of cervical cancer by upregulating PPP6C. Clin Exp Pharmacol Physiol 2024; 51:e13868. [PMID: 38745265 DOI: 10.1111/1440-1681.13868] [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: 02/21/2024] [Revised: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 05/16/2024]
Abstract
Cervical cancer (CC) is a gynaecological malignancy tumour that seriously threatens women's health. Recent evidence has identified that interferon regulatory factor 5 (IRF5), a nucleoplasm shuttling protein, is a pivotal transcription factor regulating the growth and metastasis of various human tumours. This study aimed to investigate the function and molecular basis of IRF5 in CC development. IRF5, protein phosphatase 6 catalytic subunit (PPP6C) and methyltransferase-like 3 (METTL3) mRNA levels were evaluated by quantitative real-time (qRT)-polymerase chain reaction (PCR). IRF5, PPP6C, METTL3, B-cell lymphoma 2 and Bax protein levels were detected using western blot. Cell proliferation, migration, invasion, angiogenesis and apoptosis were determined by using colony formation, 5-ethynyl-2'-deoxyuridine (EdU), transwell, tube formation assay and flow cytometry assay, respectively. Glucose uptake and lactate production were measured using commercial kits. Xenograft tumour assay in vivo was used to explore the role of IRF5. After JASPAR predication, binding between IRF5 and PPP6C promoter was verified using chromatin immunoprecipitation and dual-luciferase reporter assays. Moreover, the interaction between METTL3 and IRF5 was verified using methylated RNA immunoprecipitation (MeRIP). IRF5, PPP6C and METTL3 were highly expressed in CC tissues and cells. IRF5 silencing significantly inhibited cell proliferation, migration, invasion, angiogenesis and glycolytic metabolism in CC cells, while induced cell apoptosis. Furthermore, the absence of IRF5 hindered tumour growth in vivo. At the molecular level, IRF5 might bind with PPP6C to positively regulate the expression of PPP6C mRNA. Meanwhile, IRF5 was identified as a downstream target of METTL3-mediated m6A modification. METTL3-mediated m6A modification of mRNA might promote CC malignant progression by regulating PPP6C, which might provide a promising therapeutic target for CC treatment.
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Affiliation(s)
- Peng-Xiao Hou
- Department of Traditional Chinese Medicine, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Qian Fan
- Department of Traditional Chinese Medicine, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Qin Zhang
- Department of Traditional Chinese Medicine, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jia-Jia Liu
- Department of Tumor, Shanxi Traditional Chinese Medicine Institute, Taiyuan, China
| | - Qian Wu
- Department of Traditional Chinese Medicine, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
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2
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Wu K, Dhillon N, Bajor A, Abrahamsson S, Kamakaka RT. Yeast heterochromatin stably silences only weak regulatory elements by altering burst duration. Cell Rep 2024; 43:113983. [PMID: 38517895 PMCID: PMC11141299 DOI: 10.1016/j.celrep.2024.113983] [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: 08/24/2023] [Revised: 12/25/2023] [Accepted: 03/06/2024] [Indexed: 03/24/2024] Open
Abstract
Transcriptional silencing in Saccharomyces cerevisiae involves the generation of a chromatin state that stably represses transcription. Using multiple reporter assays, a diverse set of upstream activating sequence enhancers and core promoters were investigated for their susceptibility to silencing. We show that heterochromatin stably silences only weak and stress-induced regulatory elements but is unable to stably repress housekeeping gene regulatory elements, and the partial repression of these elements did not result in bistable expression states. Permutation analysis of enhancers and promoters indicates that both elements are targets of repression. Chromatin remodelers help specific regulatory elements to resist repression, most probably by altering nucleosome mobility and changing transcription burst duration. The strong enhancers/promoters can be repressed if silencer-bound Sir1 is increased. Together, our data suggest that the heterochromatic locus has been optimized to stably silence the weak mating-type gene regulatory elements but not strong housekeeping gene regulatory sequences.
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Affiliation(s)
- Kenneth Wu
- Department of MCD Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Namrita Dhillon
- Department of MCD Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Antone Bajor
- Electrical Engineering Department, Baskin School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Sara Abrahamsson
- Electrical Engineering Department, Baskin School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Rohinton T Kamakaka
- Department of MCD Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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3
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Zhang Z, Zhang Y. Transcriptional regulation of cancer stem cell: regulatory factors elucidation and cancer treatment strategies. J Exp Clin Cancer Res 2024; 43:99. [PMID: 38561775 PMCID: PMC10986082 DOI: 10.1186/s13046-024-03021-y] [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: 12/04/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
Cancer stem cells (CSCs) were first discovered in the 1990s, revealing the mysteries of cancer origin, migration, recurrence and drug-resistance from a new perspective. The expression of pluripotent genes and complex signal regulatory networks are significant features of CSC, also act as core factors to affect the characteristics of CSC. Transcription is a necessary link to regulate the phenotype and potential of CSC, involving chromatin environment, nucleosome occupancy, histone modification, transcription factor (TF) availability and cis-regulatory elements, which suffer from ambient pressure. Especially, the expression and activity of pluripotent TFs are deeply affected by both internal and external factors, which is the foundation of CSC transcriptional regulation in the current research framework. Growing evidence indicates that regulating epigenetic modifications to alter cancer stemness is effective, and some special promoters and enhancers can serve as targets to influence the properties of CSC. Clarifying the factors that regulate CSC transcription will assist us directly target key stem genes and TFs, or hinder CSC transcription through environmental and other related factors, in order to achieve the goal of inhibiting CSC and tumors. This paper comprehensively reviews the traditional aspects of transcriptional regulation, and explores the progress and insights of the impact on CSC transcription and status through tumor microenvironment (TME), hypoxia, metabolism and new meaningful regulatory factors in conjunction with the latest research. Finally, we present opinions on omnidirectional targeting CSCs transcription to eliminate CSCs and address tumor resistance.
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Affiliation(s)
- Zhengyue Zhang
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, People's Republic of China
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, People's Republic of China
| | - Yanjie Zhang
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, People's Republic of China.
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, People's Republic of China.
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4
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Hwang DW, Maekiniemi A, Singer RH, Sato H. Real-time single-molecule imaging of transcriptional regulatory networks in living cells. Nat Rev Genet 2024; 25:272-285. [PMID: 38195868 DOI: 10.1038/s41576-023-00684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
Abstract
Gene regulatory networks drive the specific transcriptional programmes responsible for the diversification of cell types during the development of multicellular organisms. Although our knowledge of the genes involved in these dynamic networks has expanded rapidly, our understanding of how transcription is spatiotemporally regulated at the molecular level over a wide range of timescales in the small volume of the nucleus remains limited. Over the past few decades, advances in the field of single-molecule fluorescence imaging have enabled real-time behaviours of individual transcriptional components to be measured in living cells and organisms. These efforts are now shedding light on the dynamic mechanisms of transcription, revealing not only the temporal rules but also the spatial coordination of underlying molecular interactions during various biological events.
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Affiliation(s)
- Dong-Woo Hwang
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Anna Maekiniemi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Robert H Singer
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Hanae Sato
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
- Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan.
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5
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Pomp W, Meeussen JVW, Lenstra TL. Transcription factor exchange enables prolonged transcriptional bursts. Mol Cell 2024; 84:1036-1048.e9. [PMID: 38377994 PMCID: PMC10962226 DOI: 10.1016/j.molcel.2024.01.020] [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: 05/11/2023] [Revised: 11/27/2023] [Accepted: 01/24/2024] [Indexed: 02/22/2024]
Abstract
Single-molecule imaging inside living cells has revealed that transcription factors (TFs) bind to DNA transiently, but a long-standing question is how this transient binding is related to transcription activation. Here, we devised a microscopy method to simultaneously measure transient TF binding at a single locus and the effect of these binding events on transcription. We show that DNA binding of the yeast TF Gal4 activates transcription of a target gene within a few seconds, with at least ∼20% efficiency and with a high initiation rate of ∼1 RNA/s. Gal4 DNA dissociation decreases transcription rapidly. Moreover, at a gene with multiple binding sites, individual Gal4 molecules only rarely stay bound throughout the entire burst but instead frequently exchange during a burst to increase the transcriptional burst duration. Our results suggest a mechanism for enhancer regulation in more complex eukaryotes, where TF cooperativity and exchange enable robust and responsive transcription regulation.
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Affiliation(s)
- Wim Pomp
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Joseph V W Meeussen
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
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6
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Yang JH, Hansen AS. Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00710-6. [PMID: 38413840 DOI: 10.1038/s41580-024-00710-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2024] [Indexed: 02/29/2024]
Abstract
The primary regulators of metazoan gene expression are enhancers, originally functionally defined as DNA sequences that can activate transcription at promoters in an orientation-independent and distance-independent manner. Despite being crucial for gene regulation in animals, what mechanisms underlie enhancer selectivity for promoters, and more fundamentally, how enhancers interact with promoters and activate transcription, remain poorly understood. In this Review, we first discuss current models of enhancer-promoter interactions in space and time and how enhancers affect transcription activation. Next, we discuss different mechanisms that mediate enhancer selectivity, including repression, biochemical compatibility and regulation of 3D genome structure. Through 3D polymer simulations, we illustrate how the ability of 3D genome folding mechanisms to mediate enhancer selectivity strongly varies for different enhancer-promoter interaction mechanisms. Finally, we discuss how recent technical advances may provide new insights into mechanisms of enhancer-promoter interactions and how technical biases in methods such as Hi-C and Micro-C and imaging techniques may affect their interpretation.
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Affiliation(s)
- Jin H Yang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
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7
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Meeussen JVW, Lenstra TL. Time will tell: comparing timescales to gain insight into transcriptional bursting. Trends Genet 2024; 40:160-174. [PMID: 38216391 PMCID: PMC10860890 DOI: 10.1016/j.tig.2023.11.003] [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: 09/13/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 01/14/2024]
Abstract
Recent imaging studies have captured the dynamics of regulatory events of transcription inside living cells. These events include transcription factor (TF) DNA binding, chromatin remodeling and modification, enhancer-promoter (E-P) proximity, cluster formation, and preinitiation complex (PIC) assembly. Together, these molecular events culminate in stochastic bursts of RNA synthesis, but their kinetic relationship remains largely unclear. In this review, we compare the timescales of upstream regulatory steps (input) with the kinetics of transcriptional bursting (output) to generate mechanistic models of transcription dynamics in single cells. We highlight open questions and potential technical advances to guide future endeavors toward a quantitative and kinetic understanding of transcription regulation.
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Affiliation(s)
- Joseph V W Meeussen
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066CX, The Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066CX, The Netherlands.
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8
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Yin J, Ding N, Yu J, Wang Z, Fu L, Li Y, Li X, Xu J. Systematic analysis of DNA methylation-mediated TF dysregulation on lncRNAs reveals critical roles in tumor immunity. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102058. [PMID: 38028194 PMCID: PMC10630662 DOI: 10.1016/j.omtn.2023.102058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023]
Abstract
Emerging evidence suggests that DNA methylation affects transcriptional regulation and expression perturbations of long non-coding RNAs (lncRNAs) in cancer. However, a comprehensive investigation into the transcriptional control of DNA methylation-mediated dysregulation of transcription factors (TFs) on lncRNAs has been lacking. Here, we integrated the transcriptome, methylome, and regulatome across 21 human cancers and systematically identified the transcriptional regulation of DNA methylation-mediated TF dysregulations (DMTDs) on lncRNAs. Our findings reveal that TF regulation of lncRNAs is significantly impacted by DNA methylation. Comparative analysis of DMTDs on mRNAs revealed a conserved pattern of TFs involvement. Pan-cancer Methylation TFs (MethTFs) and Methylation LncRNAs (MethLncRNAs) were identified, and were found to be closely associated with cancer hallmarks and clinical features. In-depth analysis of co-expressed mRNAs with pan-cancer MethLncRNAs unveiled frequent disruptions in cancer immunity, particularly in the context of inflammatory response. Furthermore, we identified five immune-related network modules that contribute to immune cell infiltration in cancer. Immune-related subtypes were subsequently classified, characterized by high levels of immune cell infiltration, expression of immunomodulatory genes, and relevant immune cytolytic activity score, major histocompatibility complex score, response to chemotherapy, and prognosis. Our findings provide valuable insights into cancer immunity from the epigenetic and transcriptional regulation perspective.
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Affiliation(s)
- Jiaqi Yin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Na Ding
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jiaxin Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Zishan Wang
- Department of Genetics and Genomic Sciences, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Limei Fu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yongsheng Li
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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9
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Fu Y, Clark F, Nomikou S, Tsirigos A, Lionnet T. Connecting Chromatin Structures to Gene Regulation Using Dynamic Polymer Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566032. [PMID: 37986912 PMCID: PMC10659377 DOI: 10.1101/2023.11.07.566032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The transfer of regulatory information between distal loci on chromatin is thought to involve physical proximity, but key biophysical features of these contacts remain unclear. For instance, it is unknown how close and for how long two loci need to be in order to productively interact. The main challenge is that it is currently impossible to measure chromatin dynamics with high spatiotemporal resolution at scale. Polymer simulations provide an accessible and rigorous way to test biophysical models of chromatin regulation, yet there is a lack of simple and general methods for extracting the values of model parameters. Here we adapt the Nelder-Mead simplex optimization algorithm to select the best polymer model matching a given Hi-C dataset, using the MYC locus as an example. The model's biophysical parameters predict a compartmental rearrangement of the MYC locus in leukemia, which we validate with single-cell measurements. Leveraging trajectories predicted by the model, we find that loci with similar Hi-C contact frequencies can exhibit widely different contact dynamics. Interestingly, the frequency of productive interactions between loci exhibits a non-linear relationship with their Hi-C contact frequency when we enforce a specific capture radius and contact duration. These observations are consistent with recent experimental observations and suggest that the dynamic ensemble of chromatin configurations, rather than average contact matrices, is required to fully predict long-range chromatin interactions.
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Affiliation(s)
- Yi Fu
- Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016, USA
| | - Finnegan Clark
- Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016, USA
| | | | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
- Department of Medicine, Division of Precision Medicine, NYU School of Medicine, New York, NY 10016, USA
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA
| | - Timothee Lionnet
- Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
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10
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Schleussner N, Cauchy P, Franke V, Giefing M, Fornes O, Vankadari N, Assi SA, Costanza M, Weniger MA, Akalin A, Anagnostopoulos I, Bukur T, Casarotto MG, Damm F, Daumke O, Edginton-White B, Gebhardt JCM, Grau M, Grunwald S, Hansmann ML, Hartmann S, Huber L, Kärgel E, Lusatis S, Noerenberg D, Obier N, Pannicke U, Fischer A, Reisser A, Rosenwald A, Schwarz K, Sundararaj S, Weilemann A, Winkler W, Xu W, Lenz G, Rajewsky K, Wasserman WW, Cockerill PN, Scheidereit C, Siebert R, Küppers R, Grosschedl R, Janz M, Bonifer C, Mathas S. Transcriptional reprogramming by mutated IRF4 in lymphoma. Nat Commun 2023; 14:6947. [PMID: 37935654 PMCID: PMC10630337 DOI: 10.1038/s41467-023-41954-8] [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: 11/29/2022] [Accepted: 09/20/2023] [Indexed: 11/09/2023] Open
Abstract
Disease-causing mutations in genes encoding transcription factors (TFs) can affect TF interactions with their cognate DNA-binding motifs. Whether and how TF mutations impact upon the binding to TF composite elements (CE) and the interaction with other TFs is unclear. Here, we report a distinct mechanism of TF alteration in human lymphomas with perturbed B cell identity, in particular classic Hodgkin lymphoma. It is caused by a recurrent somatic missense mutation c.295 T > C (p.Cys99Arg; p.C99R) targeting the center of the DNA-binding domain of Interferon Regulatory Factor 4 (IRF4), a key TF in immune cells. IRF4-C99R fundamentally alters IRF4 DNA-binding, with loss-of-binding to canonical IRF motifs and neomorphic gain-of-binding to canonical and non-canonical IRF CEs. IRF4-C99R thoroughly modifies IRF4 function by blocking IRF4-dependent plasma cell induction, and up-regulates disease-specific genes in a non-canonical Activator Protein-1 (AP-1)-IRF-CE (AICE)-dependent manner. Our data explain how a single mutation causes a complex switch of TF specificity and gene regulation and open the perspective to specifically block the neomorphic DNA-binding activities of a mutant TF.
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Affiliation(s)
- Nikolai Schleussner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Pierre Cauchy
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- University Medical Center Freiburg, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Vedran Franke
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center, Berlin, Germany
| | - Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, 60-479, Poland
- Institute of Human Genetics, Christian-Albrechts-University Kiel, 24105, Kiel, Germany
| | - Oriol Fornes
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Naveen Vankadari
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Mariantonia Costanza
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, 45122, Essen, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center, Berlin, Germany
| | - Ioannis Anagnostopoulos
- Institute of Pathology, Universität Würzburg and Comprehensive Cancer Centre Mainfranken (CCCMF), Würzburg, Germany
| | - Thomas Bukur
- TRON gGmbH - Translationale Onkologie an der Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Marco G Casarotto
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Frederik Damm
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
| | - Oliver Daumke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Structural Biology, 13125, Berlin, Germany
| | - Benjamin Edginton-White
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Michael Grau
- Department of Physics, University of Marburg, 35052, Marburg, Germany
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Stephan Grunwald
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Structural Biology, 13125, Berlin, Germany
| | - Martin-Leo Hansmann
- Frankfurt Institute of Advanced Studies, Frankfurt am Main, Germany
- Institute for Pharmacology and Toxicology, Goethe University, Frankfurt am Main, Germany
| | - Sylvia Hartmann
- Dr. Senckenberg Institute of Pathology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Lionel Huber
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Eva Kärgel
- Signal Transduction in Tumor Cells, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Simone Lusatis
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Daniel Noerenberg
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
| | - Nadine Obier
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ulrich Pannicke
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Anja Fischer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Anja Reisser
- Department of Physics, Institute of Biophysics, Ulm University, Ulm, Germany
| | - Andreas Rosenwald
- Institute of Pathology, Universität Würzburg and Comprehensive Cancer Centre Mainfranken (CCCMF), Würzburg, Germany
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg-Hessen, Ulm, Germany
| | - Srinivasan Sundararaj
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Andre Weilemann
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Wiebke Winkler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Wendan Xu
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Georg Lenz
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Klaus Rajewsky
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Immune Regulation and Cancer, 13125, Berlin, Germany
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Claus Scheidereit
- Signal Transduction in Tumor Cells, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel, 24105, Kiel, Germany
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Ralf Küppers
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, 45122, Essen, Germany
| | - Rudolf Grosschedl
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Martin Janz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stephan Mathas
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Biology of Malignant Lymphomas, 13125, Berlin, Germany.
- Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117, Berlin, Germany.
- Experimental and Clinical Research Center (ECRC), a joint cooperation between Charité and MDC, Berlin, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
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11
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Zhao L, Ge T, Cheng T, Wang Q, Cui M, Yuan H, Zhao L. Fine-tuning gene expression of regulator AdmX for improved biosynthesis of andrimid in Erwinia persicina BST187. Appl Microbiol Biotechnol 2023; 107:6775-6788. [PMID: 37715803 DOI: 10.1007/s00253-023-12770-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/17/2023] [Accepted: 09/01/2023] [Indexed: 09/18/2023]
Abstract
Andrimid is a potent antibiotic that inhibits acetyl-CoA carboxylase. However, its low biological yield and complex chemical synthesis have hindered its large-scale application. In this study, we found that the LysR-type transcriptional activator AdmX controls andrimid yield by adjusting its expression level in the andrimid-producing bacterium Erwinia persicina strain BST187. Our results showed that gradually increasing of admX transcriptional levels significantly improved andrimid yield, while the yield declined when admX was overexpressed excessively. To further estimate the effect of AdmX on andrimid promotion, we fitted and developed a model which was y = -0.5576x2 + 61.945x + 800.63 (R2 = 0.9591), where x represents the admX transcriptional level and y represents andrimid yield. Andrimid yield of admX overexpression strain BST187ΔadmX/pET28a-Pgap-1::admX was greatly improved by 260%, which was reported for the first time that andrimid yield could be promoted by genetic engineering. Thus, this study provides important insights that the biosynthesis of andrimid would be improved by bioengineering and sheds lights on the potential application of andrimid in both biomedicine and bioagricultural manipulation with its large-scale production in the future. KEY POINTS: • Andrimid production can be greatly promoted by genetic engineering on non-model chassis. • The relationship between AdmX abundance and andrimid yield in Erwinia persicina strain BST187 might be parabolic. • Erwinia persicina BST187 combined with chassis modification enable the promising applications in andrimid industrialization.
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Affiliation(s)
- Lunqiang Zhao
- Key Laboratory of Engineering Biology for Low Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Tongling Ge
- Key Laboratory of Engineering Biology for Low Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Tingfeng Cheng
- Key Laboratory of Engineering Biology for Low Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Qing Wang
- Key Laboratory of Engineering Biology for Low Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Meijie Cui
- Key Laboratory of Engineering Biology for Low Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Hongli Yuan
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lei Zhao
- Key Laboratory of Engineering Biology for Low Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China.
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12
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Abstract
Cells must tightly regulate their gene expression programs and yet rapidly respond to acute biochemical and biophysical cues within their environment. This information is transmitted to the nucleus through various signaling cascades, culminating in the activation or repression of target genes. Transcription factors (TFs) are key mediators of these signals, binding to specific regulatory elements within chromatin. While live-cell imaging has conclusively proven that TF-chromatin interactions are highly dynamic, how such transient interactions can have long-term impacts on developmental trajectories and disease progression is still largely unclear. In this review, we summarize our current understanding of the dynamic nature of TF functions, starting with a historical overview of early live-cell experiments. We highlight key factors that govern TF dynamics and how TF dynamics, in turn, affect downstream transcriptional bursting. Finally, we conclude with open challenges and emerging technologies that will further our understanding of transcriptional regulation.
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Affiliation(s)
- Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
- Department of Physics, University of Maryland, College Park, Maryland, USA;
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, Maryland, USA;
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
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13
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Wu K, Dhillon N, Bajor A, Abrahamson S, Kamakaka RT. Yeast Heterochromatin Only Stably Silences Weak Regulatory Elements by Altering Burst Duration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.05.561072. [PMID: 37873261 PMCID: PMC10592971 DOI: 10.1101/2023.10.05.561072] [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
The interplay between nucleosomes and transcription factors leads to programs of gene expression. Transcriptional silencing involves the generation of a chromatin state that represses transcription and is faithfully propagated through DNA replication and cell division. Using multiple reporter assays, including directly visualizing transcription in single cells, we investigated a diverse set of UAS enhancers and core promoters for their susceptibility to heterochromatic gene silencing. These results show that heterochromatin only stably silences weak and stress induced regulatory elements but is unable to stably repress housekeeping gene regulatory elements and the partial repression did not result in bistable expression states. Permutation analysis of different UAS enhancers and core promoters indicate that both elements function together to determine the susceptibility of regulatory sequences to repression. Specific histone modifiers and chromatin remodellers function in an enhancer specific manner to aid these elements to resist repression suggesting that Sir proteins likely function in part by reducing nucleosome mobility. We also show that the strong housekeeping regulatory elements can be repressed if silencer bound Sir1 is increased, suggesting that Sir1 is a limiting component in silencing. Together, our data suggest that the heterochromatic locus has been optimized to stably silence the weak mating type gene regulatory elements but not strong housekeeping gene regulatory sequences which could help explain why these genes are often found at the boundaries of silenced domains.
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Affiliation(s)
- Kenneth Wu
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Namrita Dhillon
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Antone Bajor
- Electrical Engineering Department, Baskin School of Engineering, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Sara Abrahamson
- Electrical Engineering Department, Baskin School of Engineering, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Rohinton T. Kamakaka
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
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14
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Vu HN, Valdimarsson MM, Sigurbjörnsdóttir S, Bergsteinsdóttir K, Debbache J, Bismuth K, Swing DA, Hallsson JH, Larue L, Arnheiter H, Copeland NG, Jenkins NA, Heidarsson PO, Steingrímsson E. Novel mechanisms of MITF regulation and melanoma predisposition identified in a mouse suppressor screen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.551952. [PMID: 37786677 PMCID: PMC10541597 DOI: 10.1101/2023.08.04.551952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
MITF, a basic-Helix-Loop-Helix Zipper (bHLHZip) transcription factor, plays vital roles in melanocyte development and functions as an oncogene. To explore MITF regulation and its role in melanoma, we conducted a genetic screen for suppressors of the Mitf-associated pigmentation phenotype. An intragenic Mitf mutation was identified, leading to termination of MITF at the K316 SUMOylation site and loss of the C-end intrinsically disordered region (IDR). The resulting protein is more nuclear but less stable than wild-type MITF and retains DNA-binding ability. Interestingly, as a dimer, it can translocate wild-type and mutant MITF partners into the nucleus, improving its own stability and ensuring an active nuclear MITF supply. Interactions between K316 SUMOylation and S409 phosphorylation sites across monomers largely explain the observed effects. Notably, the recurrent melanoma-associated E318K mutation in MITF, which affects K316 SUMOylation, also alters protein regulation in concert with S409, unraveling a novel regulatory mechanism with unexpected disease insights.
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Affiliation(s)
- Hong Nhung Vu
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 102 Reykjavík, Iceland
| | - Matti Már Valdimarsson
- Department of Biochemistry, Science Institute, School of Engineering and Natural Sciences, University of Iceland, Sturlugata 7, 102 Reykjavík, Iceland
| | - Sara Sigurbjörnsdóttir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 102 Reykjavík, Iceland
| | - Kristín Bergsteinsdóttir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 102 Reykjavík, Iceland
| | - Julien Debbache
- Mammalian Development Section, NINDS, NIH, Bethesda, MD 20892-3706
| | - Keren Bismuth
- Mammalian Development Section, NINDS, NIH, Bethesda, MD 20892-3706
| | | | - Jón H. Hallsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 102 Reykjavík, Iceland
| | - Lionel Larue
- Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, 91405, Orsay, France
| | - Heinz Arnheiter
- Mammalian Development Section, NINDS, NIH, Bethesda, MD 20892-3706
| | - Neal G. Copeland
- Mouse Cancer Genetics Program, NCI, Frederick, MD 21702-1201
- Current address: Genetics Department, MD Anderson Cancer Center, Houston, TX 77030
| | - Nancy A. Jenkins
- Mouse Cancer Genetics Program, NCI, Frederick, MD 21702-1201
- Current address: Genetics Department, MD Anderson Cancer Center, Houston, TX 77030
| | - Petur O. Heidarsson
- Department of Biochemistry, Science Institute, School of Engineering and Natural Sciences, University of Iceland, Sturlugata 7, 102 Reykjavík, Iceland
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 102 Reykjavík, Iceland
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15
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Lerner J, Katznelson A, Zhang J, Zaret KS. Different chromatin-scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2. Cell Rep 2023; 42:112748. [PMID: 37405916 PMCID: PMC10529229 DOI: 10.1016/j.celrep.2023.112748] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/20/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Pioneer transcription factors interact with nucleosomes to scan silent, compact chromatin, enabling cooperative events that modulate gene activity. While at a subset of sites pioneer factors access chromatin by assisted loading with other transcription factors, the nucleosome-binding properties of pioneer factors enable them to initiate zygotic genome activation, embryonic development, and cellular reprogramming. To better understand nucleosome targeting in vivo, we assess whether pioneer factors FoxA1 and Sox2 target stable or unstable nucleosomes and find that they target DNase-resistant, stable nucleosomes, whereas HNF4A, a non-nucleosome binding factor, targets open, DNase-sensitive chromatin. Despite FOXA1 and SOX2 targeting similar proportions of DNase-resistant chromatin, using single-molecule tracking, we find that FOXA1 uses lower nucleoplasmic diffusion and longer residence times while SOX2 uses higher nucleoplasmic diffusion and shorter residence times to scan compact chromatin, while HNF4 scans compact chromatin much less efficiently. Thus, pioneer factors target compact chromatin through distinct processes.
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Affiliation(s)
- Jonathan Lerner
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Andrew Katznelson
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Jingchao Zhang
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA.
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16
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van Staalduinen J, van Staveren T, Grosveld F, Wendt KS. Live-cell imaging of chromatin contacts opens a new window into chromatin dynamics. Epigenetics Chromatin 2023; 16:27. [PMID: 37349773 PMCID: PMC10288748 DOI: 10.1186/s13072-023-00503-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023] Open
Abstract
Our understanding of the organization of the chromatin fiber within the cell nucleus has made great progress in the last few years. High-resolution techniques based on next-generation sequencing as well as optical imaging that can investigate chromatin conformations down to the single cell level have revealed that chromatin structure is highly heterogeneous at the level of the individual allele. While TAD boundaries and enhancer-promoter pairs emerge as hotspots of 3D proximity, the spatiotemporal dynamics of these different types of chromatin contacts remain largely unexplored. Investigation of chromatin contacts in live single cells is necessary to close this knowledge gap and further enhance the current models of 3D genome organization and enhancer-promoter communication. In this review, we first discuss the potential of single locus labeling to study architectural and enhancer-promoter contacts and provide an overview of the available single locus labeling techniques such as FROS, TALE, CRISPR-dCas9 and ANCHOR, and discuss the latest developments and applications of these systems.
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Affiliation(s)
- Jente van Staalduinen
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - Thomas van Staveren
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands.
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17
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Edwards DM, Davies P, Hebenstreit D. Synergising single-cell resolution and 4sU labelling boosts inference of transcriptional bursting. Genome Biol 2023; 24:138. [PMID: 37328900 DOI: 10.1186/s13059-023-02977-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 05/25/2023] [Indexed: 06/18/2023] Open
Abstract
Despite the recent rise of RNA-seq datasets combining single-cell (sc) resolution with 4-thiouridine (4sU) labelling, analytical methods exploiting their power to dissect transcriptional bursting are lacking. Here, we present a mathematical model and Bayesian inference implementation to facilitate genome-wide joint parameter estimation and confidence quantification (R package: burstMCMC). We demonstrate that, unlike conventional scRNA-seq, 4sU scRNA-seq resolves temporal parameters and furthermore boosts inference of dimensionless parameters via a synergy between single-cell resolution and 4sU labelling. We apply our method to published 4sU scRNA-seq data and linked with ChIP-seq data, we uncover previously obscured associations between different parameters and histone modifications.
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Affiliation(s)
- David M Edwards
- School of Life Sciences, University of Warwick, Coventry, UK.
| | - Philip Davies
- School of Life Sciences, University of Warwick, Coventry, UK
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18
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Single-molecule tracking (SMT): a window into live-cell transcription biochemistry. Biochem Soc Trans 2023; 51:557-569. [PMID: 36876879 DOI: 10.1042/bst20221242] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/07/2023]
Abstract
How molecules interact governs how they move. Single-molecule tracking (SMT) thus provides a unique window into the dynamic interactions of biomolecules within live cells. Using transcription regulation as a case study, we describe how SMT works, what it can tell us about molecular biology, and how it has changed our perspective on the inner workings of the nucleus. We also describe what SMT cannot yet tell us and how new technical advances seek to overcome its limitations. This ongoing progress will be imperative to address outstanding questions about how dynamic molecular machines function in live cells.
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19
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Song Q, Ruffalo M, Bar-Joseph Z. Using single cell atlas data to reconstruct regulatory networks. Nucleic Acids Res 2023; 51:e38. [PMID: 36762475 PMCID: PMC10123116 DOI: 10.1093/nar/gkad053] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 12/16/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Inference of global gene regulatory networks from omics data is a long-term goal of systems biology. Most methods developed for inferring transcription factor (TF)-gene interactions either relied on a small dataset or used snapshot data which is not suitable for inferring a process that is inherently temporal. Here, we developed a new computational method that combines neural networks and multi-task learning to predict RNA velocity rather than gene expression values. This allows our method to overcome many of the problems faced by prior methods leading to more accurate and more comprehensive set of identified regulatory interactions. Application of our method to atlas scale single cell data from 6 HuBMAP tissues led to several validated and novel predictions and greatly improved on prior methods proposed for this task.
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Affiliation(s)
- Qi Song
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Matthew Ruffalo
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.,Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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20
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A multimorphic mutation in IRF4 causes human autosomal dominant combined immunodeficiency. Sci Immunol 2023; 8:eade7953. [PMID: 36662884 PMCID: PMC10825898 DOI: 10.1126/sciimmunol.ade7953] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/22/2022] [Indexed: 01/22/2023]
Abstract
Interferon regulatory factor 4 (IRF4) is a transcription factor (TF) and key regulator of immune cell development and function. We report a recurrent heterozygous mutation in IRF4, p.T95R, causing an autosomal dominant combined immunodeficiency (CID) in seven patients from six unrelated families. The patients exhibited profound susceptibility to opportunistic infections, notably Pneumocystis jirovecii, and presented with agammaglobulinemia. Patients' B cells showed impaired maturation, decreased immunoglobulin isotype switching, and defective plasma cell differentiation, whereas their T cells contained reduced TH17 and TFH populations and exhibited decreased cytokine production. A knock-in mouse model of heterozygous T95R showed a severe defect in antibody production both at the steady state and after immunization with different types of antigens, consistent with the CID observed in these patients. The IRF4T95R variant maps to the TF's DNA binding domain, alters its canonical DNA binding specificities, and results in a simultaneous multimorphic combination of loss, gain, and new functions for IRF4. IRF4T95R behaved as a gain-of-function hypermorph by binding to DNA with higher affinity than IRF4WT. Despite this increased affinity for DNA, the transcriptional activity on IRF4 canonical genes was reduced, showcasing a hypomorphic activity of IRF4T95R. Simultaneously, IRF4T95R functions as a neomorph by binding to noncanonical DNA sites to alter the gene expression profile, including the transcription of genes exclusively induced by IRF4T95R but not by IRF4WT. This previously undescribed multimorphic IRF4 pathophysiology disrupts normal lymphocyte biology, causing human disease.
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21
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Onufriev AV. Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome. Front Mol Biosci 2023; 10:1067787. [PMID: 37143824 PMCID: PMC10151541 DOI: 10.3389/fmolb.2023.1067787] [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: 10/12/2022] [Accepted: 01/16/2023] [Indexed: 05/06/2023] Open
Abstract
Stability of a protein-ligand complex may be sensitive to pH of its environment. Here we explore, computationally, stability of a set of protein-nucleic acid complexes using fundamental thermodynamic linkage relationship. The nucleosome, as well as an essentially random selection of 20 protein complexes with DNA or RNA, are included in the analysis. An increase in intra-cellular/intra-nuclear pH destabilizes most complexes, including the nucleosome. We propose to quantify the effect by ΔΔG0.3-the change in the binding free energy due to pH increase of 0.3 units, corresponding to doubling of the H + activity; variations of pH of this amplitude can occur in living cells, including in the course of the cell cycle, and in cancer cells relative to normal ones. We suggest, based on relevant experimental findings, a threshold of biological significance of 1 2 k B T ( ∼ 0.3 k c a l / m o l ) for changes of stability of chromatin-related protein-DNA complexes: a change in the binding affinity above the threshold may have biological consequences. We find that for 70% of the examined complexes, Δ Δ G 0.3 > 1 2 k B T (for 10%, ΔΔG0.3 is between 3 and 4 k B T). Thus, small but relevant variations of intra-nuclear pH of 0.3 may have biological consequences for many protein-nucleic acid complexes. The binding affinity between the histone octamer and its DNA, which directly affects the DNA accessibility in the nucleosome, is predicted to be highly sensitive to intra-nuclear pH. A variation of 0.3 units results in ΔΔG0.3 ∼ 10k B T ( ∼ 6 k c a l / m o l ) ; for spontaneous unwrapping of 20 bp long entry/exit fragments of the nucleosomal DNA, ΔΔG0.3 = 2.2k B T; partial disassembly of the nucleosome into the tetrasome is characterized by ΔΔG0.3 = 5.2k B T. The predicted pH -induced modulations of the nucleosome stability are significant enough to suggest that they may have consequences relevant to the biological function of the nucleosome. Accessibility of the nucleosomal DNA is predicted to positively correlate with pH variations during the cell cycle; an increase in intra-cellular pH seen in cancer cells is predicted to lead to a more accessible nucleosomal DNA; a drop in pH associated with apoptosis is predicted to make nucleosomal DNA less accessible. We speculate that processes that depend on accessibility to the DNA in the nucleosomes, such as transcription or DNA replication, might become upregulated due to relatively small, but nevertheless realistic increases of intra-nuclear pH.
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Affiliation(s)
- Alexey V. Onufriev
- Department of Physics, Virginia Tech, Blacksburg, Blacksburg, VA, United States
- Department of Computer Science, Virginia Tech, Blacksburg, Blacksburg, VA, United States
- Center from Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, United States
- *Correspondence: Alexey V. Onufriev,
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22
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Ball DA, Jalloh B, Karpova TS. Impact of Saccharomyces cerevisiae on the Field of Single-Molecule Biophysics. Int J Mol Sci 2022; 23:ijms232415895. [PMID: 36555532 PMCID: PMC9781480 DOI: 10.3390/ijms232415895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/10/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
Cellular functions depend on the dynamic assembly of protein regulator complexes at specific cellular locations. Single Molecule Tracking (SMT) is a method of choice for the biochemical characterization of protein dynamics in vitro and in vivo. SMT follows individual molecules in live cells and provides direct information about their behavior. SMT was successfully applied to mammalian models. However, mammalian cells provide a complex environment where protein mobility depends on numerous factors that are difficult to control experimentally. Therefore, yeast cells, which are unicellular and well-studied with a small and completely sequenced genome, provide an attractive alternative for SMT. The simplicity of organization, ease of genetic manipulation, and tolerance to gene fusions all make yeast a great model for quantifying the kinetics of major enzymes, membrane proteins, and nuclear and cellular bodies. However, very few researchers apply SMT techniques to yeast. Our goal is to promote SMT in yeast to a wider research community. Our review serves a dual purpose. We explain how SMT is conducted in yeast cells, and we discuss the latest insights from yeast SMT while putting them in perspective with SMT of higher eukaryotes.
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23
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“Structure”-function relationships in eukaryotic transcription factors: The role of intrinsically disordered regions in gene regulation. Mol Cell 2022; 82:3970-3984. [DOI: 10.1016/j.molcel.2022.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/19/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
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24
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Johnstone CP, Galloway KE. Supercoiling-mediated feedback rapidly couples and tunes transcription. Cell Rep 2022; 41:111492. [PMID: 36261020 PMCID: PMC9624111 DOI: 10.1016/j.celrep.2022.111492] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/04/2022] [Accepted: 09/21/2022] [Indexed: 11/29/2022] Open
Abstract
Transcription induces a wave of DNA supercoiling, altering the binding affinity of RNA polymerases and reshaping the biochemical landscape of gene regulation. As supercoiling rapidly diffuses, transcription dynamically reshapes the regulation of proximal genes, forming a complex feedback loop. However, a theoretical framework is needed to integrate biophysical regulation with biochemical transcriptional regulation. To investigate the role of supercoiling-mediated feedback within multi-gene systems, we model transcriptional regulation under the influence of supercoiling-mediated polymerase dynamics, allowing us to identify patterns of expression that result from physical inter-gene coupling. We find that gene syntax—the relative ordering and orientation of genes—defines the expression profiles, variance, burst dynamics, and inter-gene correlation of two-gene systems. Furthermore, supercoiling can enhance or weaken biochemical regulation. Our results suggest that supercoiling couples behavior between neighboring genes, providing a regulatory mechanism that tunes transcriptional variance in engineered gene networks and explains the behavior of co-localized native circuits. Supercoiling-mediated feedback couples the transcription of proximal genes. Here, Johnstone and Galloway provide a framework for integrating biochemical gene regulation with the biophysical effects of DNA supercoiling. This unified model provides design principles for improving the performance of gene networks, developing novel regulatory functions, and accessing previously inaccessible regulatory dynamics.
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Affiliation(s)
| | - Kate E. Galloway
- Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA 02139, USA,Lead contact,Correspondence:
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25
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Kuhn T, Landge AN, Mörsdorf D, Coßmann J, Gerstenecker J, Čapek D, Müller P, Gebhardt JCM. Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model. Nat Commun 2022; 13:6101. [PMID: 36243734 PMCID: PMC9569377 DOI: 10.1038/s41467-022-33704-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022] Open
Abstract
The hindered diffusion model postulates that the movement of a signaling molecule through an embryo is affected by tissue geometry and binding-mediated hindrance, but these effects have not been directly demonstrated in vivo. Here, we visualize extracellular movement and binding of individual molecules of the activator-inhibitor signaling pair Nodal and Lefty in live developing zebrafish embryos using reflected light-sheet microscopy. We observe that diffusion coefficients of molecules are high in extracellular cavities, whereas mobility is reduced and bound fractions are high within cell-cell interfaces. Counterintuitively, molecules nevertheless accumulate in cavities, which we attribute to the geometry of the extracellular space by agent-based simulations. We further find that Nodal has a larger bound fraction than Lefty and shows a binding time of tens of seconds. Together, our measurements and simulations provide direct support for the hindered diffusion model and yield insights into the nanometer-to-micrometer-scale mechanisms that lead to macroscopic signal dispersal.
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Affiliation(s)
- Timo Kuhn
- grid.6582.90000 0004 1936 9748Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Amit N. Landge
- grid.9811.10000 0001 0658 7699University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - David Mörsdorf
- grid.418026.90000 0004 0492 0357Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany ,grid.10420.370000 0001 2286 1424University of Vienna, Department of Neurosciences and Developmental Biology, Djerassiplatz 1, 1030 Vienna, Austria
| | - Jonas Coßmann
- grid.6582.90000 0004 1936 9748Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Johanna Gerstenecker
- grid.6582.90000 0004 1936 9748Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Daniel Čapek
- grid.9811.10000 0001 0658 7699University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Patrick Müller
- grid.9811.10000 0001 0658 7699University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany ,grid.418026.90000 0004 0492 0357Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - J. Christof M. Gebhardt
- grid.6582.90000 0004 1936 9748Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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26
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Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila. Nat Commun 2022; 13:5375. [PMID: 36104317 PMCID: PMC9474875 DOI: 10.1038/s41467-022-32973-y] [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: 01/25/2022] [Accepted: 08/25/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractThe spatial organization of chromatin at the scale of topologically associating domains (TADs) and below displays large cell-to-cell variations. Up until now, how this heterogeneity in chromatin conformation is shaped by chromatin condensation, TAD insulation, and transcription has remained mostly elusive. Here, we used Hi-M, a multiplexed DNA-FISH imaging technique providing developmental timing and transcriptional status, to show that the emergence of TADs at the ensemble level partially segregates the conformational space explored by single nuclei during the early development of Drosophila embryos. Surprisingly, a substantial fraction of nuclei display strong insulation even before TADs emerge. Moreover, active transcription within a TAD leads to minor changes to the local inter- and intra-TAD chromatin conformation in single nuclei and only weakly affects insulation to the neighboring TAD. Overall, our results indicate that multiple parameters contribute to shaping the chromatin architecture of single nuclei at the TAD scale.
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27
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Shahein A, López-Malo M, Istomin I, Olson EJ, Cheng S, Maerkl SJ. Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance. Nat Commun 2022; 13:5273. [PMID: 36071116 PMCID: PMC9452512 DOI: 10.1038/s41467-022-32971-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/25/2022] [Indexed: 11/10/2022] Open
Abstract
Binding to binding site clusters has yet to be characterized in depth, and the functional relevance of low-affinity clusters remains uncertain. We characterized transcription factor binding to low-affinity clusters in vitro and found that transcription factors can bind concurrently to overlapping sites, challenging the notion of binding exclusivity. Furthermore, small clusters with binding sites an order of magnitude lower in affinity give rise to high mean occupancies at physiologically-relevant transcription factor concentrations. To assess whether the observed in vitro occupancies translate to transcriptional activation in vivo, we tested low-affinity binding site clusters in a synthetic and native gene regulatory network in S. cerevisiae. In both systems, clusters of low-affinity binding sites generated transcriptional output comparable to single or even multiple consensus sites. This systematic characterization demonstrates that clusters of low-affinity binding sites achieve substantial occupancies, and that this occupancy can drive expression in eukaryotic promoters.
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Affiliation(s)
- Amir Shahein
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Maria López-Malo
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ivan Istomin
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Evan J Olson
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Shiyu Cheng
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sebastian J Maerkl
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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28
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Kenworthy CA, Haque N, Liou SH, Chandris P, Wong V, Dziuba P, Lavis LD, Liu WL, Singer RH, Coleman RA. Bromodomains regulate dynamic targeting of the PBAF chromatin-remodeling complex to chromatin hubs. Biophys J 2022; 121:1738-1752. [PMID: 35364106 PMCID: PMC9117891 DOI: 10.1016/j.bpj.2022.03.027] [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: 07/23/2021] [Revised: 09/20/2021] [Accepted: 03/24/2022] [Indexed: 11/12/2022] Open
Abstract
Chromatin remodelers actively target arrays of acetylated nucleosomes at select enhancers and promoters to facilitate or shut down the repeated recruitment of RNA polymerase II during transcriptional bursting. It is poorly understood how chromatin remodelers such as PBAF dynamically target different chromatin states inside a live cell. Our live-cell single-molecule fluorescence microscopy study reveals chromatin hubs throughout the nucleus where PBAF rapidly cycles on and off the genome. Deletion of PBAF's bromodomains impairs targeting and stable engagement of chromatin in hubs. Dual color imaging reveals that PBAF targets both euchromatic and heterochromatic hubs with distinct genome-binding kinetic profiles that mimic chromatin stability. Removal of PBAF's bromodomains stabilizes H3.3 binding within chromatin, indicating that bromodomains may play a direct role in remodeling of the nucleosome. Our data suggests that PBAF's dynamic bromodomain-mediated engagement of a nucleosome may reflect the chromatin-remodeling potential of differentially bound chromatin states.
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Affiliation(s)
- Charles A. Kenworthy
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York
| | - Nayem Haque
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York
| | - Shu-Hao Liou
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York
| | - Panagiotis Chandris
- Section on High Resolution Optical Imaging, National Institute on Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Vincent Wong
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York
| | - Patrycja Dziuba
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia
| | - Wei-Li Liu
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York
| | - Robert H. Singer
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia
| | - Robert A. Coleman
- Gruss-Lipper Biophotonics Center, Department of Cell Biology, Albert Einstein College of Medicine, New York,Corresponding author
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29
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Transcription activation is enhanced by multivalent interactions independent of phase separation. Mol Cell 2022; 82:1878-1893.e10. [DOI: 10.1016/j.molcel.2022.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 02/28/2022] [Accepted: 04/11/2022] [Indexed: 12/23/2022]
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30
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Kuchler O, Gerlach J, Vomhof T, Hettich J, Steinmetz J, Gebhardt JCM, Michaelis J, Knöll B. Single-molecule tracking (SMT) and localization of SRF and MRTF transcription factors during neuronal stimulation and differentiation. Open Biol 2022; 12:210383. [PMID: 35537478 PMCID: PMC9090491 DOI: 10.1098/rsob.210383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In cells, proteins encoded by the same gene do not all behave uniformly but engage in functional subpopulations induced by spatial or temporal segregation. While conventional microscopy has limitations in revealing such spatial and temporal diversity, single-molecule tracking (SMT) microscopy circumvented this problem and allows for high-resolution imaging and quantification of dynamic single-molecule properties. Particularly in the nucleus, SMT has identified specific DNA residence times of transcription factors (TFs), DNA-bound TF fractions and positions of transcriptional hot-spots upon cell stimulation. By contrast to cell stimulation, SMT has not been employed to follow dynamic TF changes along stages of cell differentiation. Herein, we analysed the serum response factor (SRF), a TF involved in the differentiation of many cell types to study nuclear single-molecule dynamics in neuronal differentiation. Our data in living mouse hippocampal neurons show dynamic changes in SRF DNA residence time and SRF DNA-bound fraction between the stages of adhesion, neurite growth and neurite differentiation in axon and dendrites. Using TALM (tracking and localization microscopy), we identified nuclear positions of SRF clusters and observed changes in their numbers and size during differentiation. Furthermore, we show that the SRF cofactor MRTF-A (myocardin-related TF or MKL1) responds to cell activation by enhancing the long-bound DNA fraction. Finally, a first SMT colocalization study of two proteins was performed in living cells showing enhanced SRF/MRTF-A colocalization upon stimulation. In summary, SMT revealed modulation of dynamic TF properties during cell stimulation and differentiation.
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Affiliation(s)
- Oliver Kuchler
- Institute of Neurobiochemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany,Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Jule Gerlach
- Institute of Neurobiochemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany,Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Thomas Vomhof
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Johannes Hettich
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Julia Steinmetz
- Department of Statistics, TU Dortmund University, August-Schmidt Straße 1, 44227 Dortmund, Germany
| | | | - Jens Michaelis
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Bernd Knöll
- Institute of Neurobiochemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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31
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de Jonge WJ, Patel HP, Meeussen JVW, Lenstra TL. Following the tracks: how transcription factor binding dynamics control transcription. Biophys J 2022; 121:1583-1592. [PMID: 35337845 PMCID: PMC9117886 DOI: 10.1016/j.bpj.2022.03.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/28/2022] [Accepted: 03/21/2022] [Indexed: 11/29/2022] Open
Abstract
Transcription, the process of copying genetic information from DNA to messenger RNA, is regulated by sequence-specific DNA binding proteins known as transcription factors (TFs). Recent advances in single-molecule tracking (SMT) technologies have enabled visualization of individual TF molecules as they diffuse and interact with the DNA in the context of living cells. These SMT studies have uncovered multiple populations of DNA binding events characterized by their distinctive DNA residence times. In this perspective, we review recent insights into how these residence times relate to specific and non-specific DNA binding, as well as the contribution of TF domains on the DNA binding dynamics. We discuss different models that aim to link transient DNA binding by TFs to bursts of transcription and present an outlook for how future advances in microscopy development may broaden our understanding of the dynamics of the molecular steps that underlie transcription activation.
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Affiliation(s)
- Wim J de Jonge
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Heta P Patel
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Joseph V W Meeussen
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands.
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32
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Facilitated Dissociation of Nucleoid Associated Proteins from DNA in the Bacterial Confinement. Biophys J 2022; 121:1119-1133. [PMID: 35257784 PMCID: PMC9034294 DOI: 10.1016/j.bpj.2022.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/04/2021] [Accepted: 03/01/2022] [Indexed: 11/20/2022] Open
Abstract
Transcription machinery depends on the temporal formation of protein-DNA complexes. Recent experiments demonstrated that not only the formation but also the lifetime of such complexes can affect the transcriptional machinery. In parallel, in vitro single-molecule studies showed that nucleoid-associated proteins (NAPs) leave the DNA rapidly as the bulk concentration of the protein increases via facilitated dissociation (FD). Nevertheless, whether such a concentration-dependent mechanism is functional in a bacterial cell, in which NAP levels and the 3d chromosomal structure are often coupled, is not clear a priori. Here, by using extensive coarse-grained molecular simulations, we model the unbinding of specific and nonspecific dimeric NAPs from a high-molecular-weight circular DNA molecule in a cylindrical structure mimicking the cellular confinement of a bacterial chromosome. Our simulations confirm that physiologically relevant peak protein levels (tens of micromolar) lead to highly compact chromosomal structures. This compaction results in rapid off rates (shorter DNA residence times) for specifically DNA-binding NAPs, such as the factor for inversion stimulation, which mostly dissociate via a segmental jump mechanism. Contrarily, for nonspecific NAPs, which are more prone to leave their binding sites via 1d sliding, the off rates decrease as the protein levels increase. The simulations with restrained chromosome models reveal that chromosome compaction is in favor of faster dissociation but only for specific proteins, and nonspecific proteins are not affected by the chromosome compaction. Overall, our results suggest that the cellular concentration level of a structural DNA-binding protein can be highly intermingled with its DNA residence time.
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33
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Hettich J, Gebhardt JCM. Periodic synchronization of isolated network elements facilitates simulating and inferring gene regulatory networks including stochastic molecular kinetics. BMC Bioinformatics 2022; 23:13. [PMID: 34986805 PMCID: PMC8729106 DOI: 10.1186/s12859-021-04541-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/16/2021] [Indexed: 11/10/2022] Open
Abstract
Background The temporal progression of many fundamental processes in cells and organisms, including homeostasis, differentiation and development, are governed by gene regulatory networks (GRNs). GRNs balance fluctuations in the output of their genes, which trace back to the stochasticity of molecular interactions. Although highly desirable to understand life processes, predicting the temporal progression of gene products within a GRN is challenging when considering stochastic events such as transcription factor–DNA interactions or protein production and degradation.
Results We report a method to simulate and infer GRNs including genes and biochemical reactions at molecular detail. In our approach, we consider each network element to be isolated from other elements during small time intervals, after which we synchronize molecule numbers across all network elements. Thereby, the temporal behaviour of network elements is decoupled and can be treated by local stochastic or deterministic solutions. We demonstrate the working principle of this modular approach with a repressive gene cascade comprising four genes. By considering a deterministic time evolution within each time interval for all elements, our method approaches the solution of the system of deterministic differential equations associated with the GRN. By allowing genes to stochastically switch between on and off states or by considering stochastic production of gene outputs, we are able to include increasing levels of stochastic detail and approximate the solution of a Gillespie simulation. Thereby, CaiNet is able to reproduce noise-induced bi-stability and oscillations in dynamically complex GRNs. Notably, our modular approach further allows for a simple consideration of deterministic delays. We further infer relevant regulatory connections and steady-state parameters of a GRN of up to ten genes from steady-state measurements by identifying each gene of the network with a single perceptron in an artificial neuronal network and using a gradient decent method originally designed to train recurrent neural networks. To facilitate setting up GRNs and using our simulation and inference method, we provide a fast computer-aided interactive network simulation environment, CaiNet. Conclusion We developed a method to simulate GRNs at molecular detail and to infer the topology and steady-state parameters of GRNs. Our method and associated user-friendly framework CaiNet should prove helpful to analyze or predict the temporal progression of reaction networks or GRNs in cellular and organismic biology. CaiNet is freely available at https://gitlab.com/GebhardtLab/CaiNet. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04541-6.
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Affiliation(s)
- Johannes Hettich
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - J Christof M Gebhardt
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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34
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A Protocol for Studying Transcription Factor Dynamics Using Fast Single-Particle Tracking and Spot-On Model-Based Analysis. Methods Mol Biol 2022; 2458:151-174. [PMID: 35103967 DOI: 10.1007/978-1-0716-2140-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Single-particle tracking (SPT) makes it possible to directly observe single protein diffusion dynamics in living cells over time. Thus, SPT has emerged as a powerful method to quantify the dynamics of nuclear proteins such as transcription factors (TFs). Here, we provide a protocol for conducting and analyzing SPT experiments with a focus on fast tracking ("fastSPT") of TFs in mammalian cells. First, we explore how to engineer and prepare cells for SPT experiments. Next, we examine how to optimize SPT experiments by imaging at low densities to minimize tracking errors and by using stroboscopic excitation to minimize motion-blur. Next, we discuss how to convert raw SPT data into single-particle trajectories. Finally, we illustrate how to analyze these trajectories using the kinetic modeling package Spot-On. We discuss how to use Spot-On to fit histograms of displacements and extract useful information such as the fraction of TFs that are bound and freely diffusing, and their associated diffusion coefficients.
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35
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Khamis H, Rudnizky S, Melamed P, Kaplan A. Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation. Nucleic Acids Res 2021; 49:10975-10987. [PMID: 34606618 PMCID: PMC8565314 DOI: 10.1093/nar/gkab843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/04/2021] [Accepted: 09/24/2021] [Indexed: 12/14/2022] Open
Abstract
The interaction of transcription factors with their response elements in DNA is emerging as a highly complex process, whose characterization requires measuring the full distribution of binding and dissociation times in a well-controlled assay. Here, we present a single-molecule assay that exploits the thermal fluctuations of a DNA hairpin to detect the association and dissociation of individual, unlabeled transcription factors. We demonstrate this new approach by following the binding of Egr1 to its consensus motif and the three binding sites found in the promoter of the Lhb gene, and find that both association and dissociation are modulated by the 9 bp core motif and the sequences around it. In addition, CpG methylation modulates the dissociation kinetics in a sequence and position-dependent manner, which can both stabilize or destabilize the complex. Together, our findings show how variations in sequence and methylation patterns synergistically extend the spectrum of a protein's binding properties, and demonstrate how the proposed approach can provide new insights on the function of transcription factors.
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Affiliation(s)
- Hadeel Khamis
- Faculty of Biology, Technion – Israel Institute of Technology, Haifa 32000, Israel
- Faculty of Physics, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Sergei Rudnizky
- Faculty of Biology, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion – Israel Institute of Technology, Haifa 32000, Israel
- Faculty of Biomedical Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
- Russell Berrie Nanotechnology Institute, Technion – Israel Institute of Technology, Haifa 32000, Israel
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36
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Pan L, Hoffmeister P, Turkiewicz A, Huynh NND, Große-Berkenbusch A, Knippschild U, Gebhardt JCM, Baumann B, Borggrefe T, Oswald F. Transcription Factor RBPJL Is Able to Repress Notch Target Gene Expression but Is Non-Responsive to Notch Activation. Cancers (Basel) 2021; 13:cancers13195027. [PMID: 34638511 PMCID: PMC8508133 DOI: 10.3390/cancers13195027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 12/01/2022] Open
Abstract
Simple Summary The transcription factor RBPJ is an integral part of the Notch signaling cascade. RBPJ can function as a coactivator when Notch signaling is activated but acts as a repressor in the absence of a Notch stimulus. Here, we characterized the function of RBPJL, a pancreas-specific paralog of RBPJ. Upon depletion of RBPJ using CRISPR/Cas9, we observed specific upregulation of Notch target gene expression. Reconstitution with RBPJL can compensate for the lack of RBPJ function in the repression of Notch target genes but is not able to mediate the Notch-dependent activation of gene expression. On the molecular level, we identified a limited capacity of RBPJL to interact with activated Notch1–4. Abstract The Notch signaling pathway is an evolutionary conserved signal transduction cascade present in almost all tissues and is required for embryonic and postnatal development, as well as for stem cell maintenance, but it is also implicated in tumorigenesis including pancreatic cancer and leukemia. The transcription factor RBPJ forms a coactivator complex in the presence of a Notch signal, whereas it represses Notch target genes in the absence of a Notch stimulus. In the pancreas, a specific paralog of RBPJ, called RBPJL, is expressed and found as part of the heterotrimeric PTF1-complex. However, the function of RBPJL in Notch signaling remains elusive. Using molecular modeling, biochemical and functional assays, as well as single-molecule time-lapse imaging, we show that RBPJL and RBPJ, despite limited sequence homology, possess a high degree of structural similarity. RBPJL is specifically expressed in the exocrine pancreas, whereas it is mostly undetectable in pancreatic tumour cell lines. Importantly, RBPJL is not able to interact with Notch−1 to −4 and it does not support Notch-mediated transactivation. However, RBPJL can bind to canonical RBPJ DNA elements and shows migration dynamics comparable to that of RBPJ in the nuclei of living cells. Importantly, RBPJL is able to interact with SHARP/SPEN, the central corepressor of the Notch pathway. In line with this, RBPJL is able to fully reconstitute transcriptional repression at Notch target genes in cells lacking RBPJ. Together, RBPJL can act as an antagonist of RBPJ, which renders cells unresponsive to the activation of Notch.
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Affiliation(s)
- Leiling Pan
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center Ulm, Ulm University, Albert-Einstein-Allee 23, 89081 Ulm, Germany; (L.P.); (P.H.)
| | - Philipp Hoffmeister
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center Ulm, Ulm University, Albert-Einstein-Allee 23, 89081 Ulm, Germany; (L.P.); (P.H.)
| | - Aleksandra Turkiewicz
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany;
| | - N. N. Duyen Huynh
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (N.N.D.H.); (A.G.-B.); (J.C.M.G.)
| | - Andreas Große-Berkenbusch
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (N.N.D.H.); (A.G.-B.); (J.C.M.G.)
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Surgery Center, Ulm University, Albert-Einstein-Allee 23, 89081 Ulm, Germany;
| | - J. Christof M. Gebhardt
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (N.N.D.H.); (A.G.-B.); (J.C.M.G.)
| | - Bernd Baumann
- Institute of Physiological Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany;
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany;
- Correspondence: (T.B.); (F.O.); Tel.: +49-731-500-44544 (F.O.)
| | - Franz Oswald
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center Ulm, Ulm University, Albert-Einstein-Allee 23, 89081 Ulm, Germany; (L.P.); (P.H.)
- Correspondence: (T.B.); (F.O.); Tel.: +49-731-500-44544 (F.O.)
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Mazzocca M, Colombo E, Callegari A, Mazza D. Transcription factor binding kinetics and transcriptional bursting: What do we really know? Curr Opin Struct Biol 2021; 71:239-248. [PMID: 34481381 DOI: 10.1016/j.sbi.2021.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 11/18/2022]
Abstract
In eukaryotes, transcription is a discontinuous process with mRNA being generated in bursts, after the binding of transcription factors (TFs) to regulatory elements on the genome. Live-cell single-molecule microscopy has highlighted that transcriptional bursting can be controlled by tuning TF/DNA binding kinetics. Yet the timescales of these two processes seem disconnected with TF/DNA interactions typically lasting orders of magnitude shorter than transcriptional bursts. To test models that could reconcile these discrepancies, reliable measurements of TF binding kinetics are needed, also accounting for the current limitations in performing these single-molecule measurements at specific regulatory elements. Here, we review the recent studies linking TF binding kinetics to transcriptional bursting and outline some current and future challenges that need to be addressed to provide a microscopic description of transcriptional regulation kinetics.
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Affiliation(s)
- Matteo Mazzocca
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Emanuele Colombo
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | | | - Davide Mazza
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.
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