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Furuya H, Toda Y, Iwata A, Kanai M, Kato K, Kumagai T, Kageyama T, Tanaka S, Fujimura L, Sakamoto A, Hatano M, Suto A, Suzuki K, Nakajima H. Stage-specific GATA3 induction promotes ILC2 development after lineage commitment. Nat Commun 2024; 15:5610. [PMID: 38969652 PMCID: PMC11226602 DOI: 10.1038/s41467-024-49881-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: 03/27/2023] [Accepted: 06/24/2024] [Indexed: 07/07/2024] Open
Abstract
Group 2 innate lymphoid cells (ILC2s) are a subset of innate lymphocytes that produce type 2 cytokines, including IL-4, IL-5, and IL-13. GATA3 is a critical transcription factor for ILC2 development at multiple stages. However, when and how GATA3 is induced to the levels required for ILC2 development remains unclear. Herein, we identify ILC2-specific GATA3-related tandem super-enhancers (G3SE) that induce high GATA3 in ILC2-committed precursors. G3SE-deficient mice exhibit ILC2 deficiency in the bone marrow, lung, liver, and small intestine with minimal impact on other ILC lineages or Th2 cells. Single-cell RNA-sequencing and subsequent flow cytometry analysis show that GATA3 induction mechanism, which is required for entering the ILC2 stage, is lost in IL-17RB+PD-1- late ILC2-committed precursor stage in G3SE-deficient mice. Cnot6l, part of the CCR4-NOT deadenylase complex, is a possible GATA3 target during ILC2 development. Our findings implicate a stage-specific regulatory mechanism for GATA3 expression during ILC2 development.
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Affiliation(s)
- Hiroki Furuya
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yosuke Toda
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Arifumi Iwata
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.
| | - Mizuki Kanai
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kodai Kato
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takashi Kumagai
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takahiro Kageyama
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shigeru Tanaka
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Lisa Fujimura
- Biomedical Research Center, Chiba University, Chiba, Japan
| | - Akemi Sakamoto
- Biomedical Research Center, Chiba University, Chiba, Japan
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masahiko Hatano
- Biomedical Research Center, Chiba University, Chiba, Japan
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Akira Suto
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kotaro Suzuki
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroshi Nakajima
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.
- Chiba University Synergy Institute for Futuristic Mucosal Vaccine Research and Development (cSIMVa), Chiba, Japan.
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2
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Kumagai T, Iwata A, Furuya H, Kato K, Okabe A, Toda Y, Kanai M, Fujimura L, Sakamoto A, Kageyama T, Tanaka S, Suto A, Hatano M, Kaneda A, Nakajima H. A distal enhancer of GATA3 regulates Th2 differentiation and allergic inflammation. Proc Natl Acad Sci U S A 2024; 121:e2320727121. [PMID: 38923989 PMCID: PMC11228505 DOI: 10.1073/pnas.2320727121] [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: 11/24/2023] [Accepted: 05/15/2024] [Indexed: 06/28/2024] Open
Abstract
Asthma is a widespread airway disorder where GATA3-dependent Type-2 helper T (Th2) cells and group 2 innate lymphoid cells (ILC2s) play vital roles. Asthma-associated single nucleotide polymorphisms (SNPs) are enriched in a region located 926-970 kb downstream from GATA3 in the 10p14 (hG900). However, it is unknown how hG900 affects the pathogenesis of allergic airway inflammation. To investigate the roles of the asthma-associated GATA3 enhancer region in experimental allergic airway inflammation, we first examined the correlation between GATA3 expression and the activation of the hG900 region was analyzed by flow cytometry and ChIP-qPCR. We found that The activation of enhancers in the hG900 region was strongly correlated to the levels of GATA3 in human peripheral T cell subsets. We next generated mice lacking the mG900 region (mG900KO mice) were generated by the CRISPR-Cas9 system, and the development and function of helper T cells and ILCs in mG900KO mice were analyzed in steady-state conditions and allergic airway inflammation induced by papain or house dust mite (HDM). The deletion of the mG900 did not affect the development of lymphocytes in steady-state conditions or allergic airway inflammation induced by papain. However, mG900KO mice exhibited reduced allergic inflammation and Th2 differentiation in the HDM-induced allergic airway inflammation. The analysis of the chromatin conformation around Gata3 by circular chromosome conformation capture coupled to high-throughput sequencing (4C-seq) revealed that the mG900 region interacted with the transcription start site of Gata3 with an influencing chromatin conformation in Th2 cells. These findings indicate that the mG900 region plays a pivotal role in Th2 differentiation and thus enhances allergic airway inflammation.
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Affiliation(s)
- Takashi Kumagai
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Arifumi Iwata
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Hiroki Furuya
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Kodai Kato
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
- Health and Disease Omics Center, Chiba University, Chiba260-8670, Japan
| | - Yosuke Toda
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Mizuki Kanai
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Lisa Fujimura
- Biomedical Research Center, Chiba University, Chiba260-8670, Japan
| | - Akemi Sakamoto
- Biomedical Research Center, Chiba University, Chiba260-8670, Japan
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Takahiro Kageyama
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Shigeru Tanaka
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Akira Suto
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Masahiko Hatano
- Biomedical Research Center, Chiba University, Chiba260-8670, Japan
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
- Health and Disease Omics Center, Chiba University, Chiba260-8670, Japan
| | - Hiroshi Nakajima
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
- Chiba University Synergy Institute for Futuristic Mucosal Vaccine Research and Development, Chiba260-8670, Japan
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3
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Morimoto K, Suzuki H, Kuno A, Daitoku Y, Tanimoto Y, Kato K, Murata K, Sugiyama F, Mizuno S. Regional random mutagenesis driven by multiple sgRNAs and diverse on-target genome editing events to identify functionally important elements in non-coding regions. Open Biol 2024; 14:240007. [PMID: 38565160 PMCID: PMC10987234 DOI: 10.1098/rsob.240007] [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: 01/05/2024] [Accepted: 02/06/2024] [Indexed: 04/04/2024] Open
Abstract
Functional regions that regulate biological phenomena are interspersed throughout eukaryotic genomes. The most definitive approach for identifying such regions is to confirm the phenotype of cells or organisms in which specific regions have been mutated or removed from the genome. This approach is invaluable for the functional analysis of genes with a defined functional element, the protein-coding sequence. By contrast, no functional analysis platforms have been established for the study of cis-elements or microRNA cluster regions consisting of multiple microRNAs with functional overlap. Whole-genome mutagenesis approaches, such as via N-ethyl-N-nitrosourea and gene trapping, have greatly contributed to elucidating the function of coding genes. These methods almost never induce deletions of genomic regions or multiple mutations within a narrow region. In other words, cis-elements and microRNA clusters cannot be effectively targeted in such a manner. Herein, we established a novel region-specific random mutagenesis method named CRISPR- and transposase-based regional mutagenesis (CTRL-mutagenesis). We demonstrate that CTRL-mutagenesis randomly induces diverse mutations within target regions in murine embryonic stem cells. Comparative analysis of mutants harbouring subtly different mutations within the same region would facilitate the further study of cis-element and microRNA clusters.
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Affiliation(s)
- Kento Morimoto
- Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
- Research Fellow of the Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Hayate Suzuki
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Akihiro Kuno
- Department of Anatomy and Embryology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoko Daitoku
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoko Tanimoto
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kanako Kato
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kazuya Murata
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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4
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Fang D, Healy A, Zhu J. Differential regulation of lineage-determining transcription factor expression in innate lymphoid cell and adaptive T helper cell subsets. Front Immunol 2023; 13:1081153. [PMID: 36685550 PMCID: PMC9846361 DOI: 10.3389/fimmu.2022.1081153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023] Open
Abstract
CD4 T helper (Th) cell subsets, including Th1, Th2 and Th17 cells, and their innate counterparts innate lymphoid cell (ILC) subsets consisting of ILC1s, ILC2s and ILC3s, display similar effector cytokine-producing capabilities during pro-inflammatory immune responses. These lymphoid cell subsets utilize the same set of lineage-determining transcription factors (LDTFs) for their differentiation, development and functions. The distinct ontogeny and developmental niches between Th cells and ILCs indicate that they may adopt different external signals for the induction of LDTF during lineage commitment. Increasing evidence demonstrates that many conserved cis-regulatory elements at the gene loci of LDTFs are often preferentially utilized for the induction of LDTF expression during Th cell differentiation and ILC development at different stages. In this review, we discuss the functions of lineage-related cis-regulatory elements in inducing T-bet, GATA3 or RORγt expression based on the genetic evidence provided in recent publications. We also review and compare the upstream signals involved in LDTF induction in Th cells and ILCs both in vitro and in vivo. Finally, we discuss the possible mechanisms and physiological importance of regulating LDTF dynamic expression during ILC development and activation.
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Affiliation(s)
- Difeng Fang
- *Correspondence: Difeng Fang, ; Jinfang Zhu,
| | | | - Jinfang Zhu
- *Correspondence: Difeng Fang, ; Jinfang Zhu,
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5
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Kasal DN, Liang Z, Hollinger MK, O'Leary CY, Lisicka W, Sperling AI, Bendelac A. A Gata3 enhancer necessary for ILC2 development and function. Proc Natl Acad Sci U S A 2021; 118:e2106311118. [PMID: 34353913 PMCID: PMC8364216 DOI: 10.1073/pnas.2106311118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The type 2 helper effector program is driven by the master transcription factor GATA3 and can be expressed by subsets of both innate lymphoid cells (ILCs) and adaptive CD4+ T helper (Th) cells. While ILC2s and Th2 cells acquire their type 2 differentiation program under very different contexts, the distinct regulatory mechanisms governing this common program are only partially understood. Here we show that the differentiation of ILC2s, and their concomitant high level of GATA3 expression, are controlled by a Gata3 enhancer, Gata3 +674/762, that plays only a minimal role in Th2 cell differentiation. Mice lacking this enhancer exhibited defects in several but not all type 2 inflammatory responses, depending on the respective degree of ILC2 and Th2 cell involvement. Our study provides molecular insights into the different gene regulatory pathways leading to the acquisition of the GATA3-driven type 2 helper effector program in innate and adaptive lymphocytes.
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Affiliation(s)
- Darshan N Kasal
- Committee on Immunology, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
| | - Zhitao Liang
- Committee on Immunology, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
| | - Maile K Hollinger
- Committee on Immunology, University of Chicago, Chicago, IL 60637
- Department of Medicine, Section of Pulmonary and Critical Care, University of Chicago, Chicago, IL 60637
| | | | - Wioletta Lisicka
- Committee on Immunology, University of Chicago, Chicago, IL 60637
- Department of Medicine, Section of Gastroenterology, University of Chicago, Chicago, IL 60637
| | - Anne I Sperling
- Committee on Immunology, University of Chicago, Chicago, IL 60637
- Department of Medicine, Section of Pulmonary and Critical Care, University of Chicago, Chicago, IL 60637
| | - Albert Bendelac
- Committee on Immunology, University of Chicago, Chicago, IL 60637;
- Department of Pathology, University of Chicago, Chicago, IL 60637
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6
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Yang R, Weisshaar M, Mele F, Benhsaien I, Dorgham K, Han J, Croft CA, Notarbartolo S, Rosain J, Bastard P, Puel A, Fleckenstein B, Glimcher LH, Di Santo JP, Ma CS, Gorochov G, Bousfiha A, Abel L, Tangye SG, Casanova JL, Bustamante J, Sallusto F. High Th2 cytokine levels and upper airway inflammation in human inherited T-bet deficiency. J Exp Med 2021; 218:e20202726. [PMID: 34160550 PMCID: PMC8225679 DOI: 10.1084/jem.20202726] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/16/2021] [Accepted: 05/27/2021] [Indexed: 12/20/2022] Open
Abstract
We have described a child suffering from Mendelian susceptibility to mycobacterial disease (MSMD) due to autosomal recessive, complete T-bet deficiency, which impairs IFN-γ production by innate and innate-like adaptive, but not mycobacterial-reactive purely adaptive, lymphocytes. Here, we explore the persistent upper airway inflammation (UAI) and blood eosinophilia of this patient. Unlike wild-type (WT) T-bet, the mutant form of T-bet from this patient did not inhibit the production of Th2 cytokines, including IL-4, IL-5, IL-9, and IL-13, when overexpressed in T helper 2 (Th2) cells. Moreover, Herpesvirus saimiri-immortalized T cells from the patient produced abnormally large amounts of Th2 cytokines, and the patient had markedly high plasma IL-5 and IL-13 concentrations. Finally, the patient's CD4+ αβ T cells produced most of the Th2 cytokines in response to chronic stimulation, regardless of their antigen specificities, a phenotype reversed by the expression of WT T-bet. T-bet deficiency thus underlies the excessive production of Th2 cytokines, particularly IL-5 and IL-13, by CD4+ αβ T cells, causing blood eosinophilia and UAI. The MSMD of this patient results from defective IFN-γ production by innate and innate-like adaptive lymphocytes, whereas the UAI and eosinophilia result from excessive Th2 cytokine production by adaptive CD4+ αβ T lymphocytes.
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Affiliation(s)
- Rui Yang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Marc Weisshaar
- Institute of Microbiology, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland
| | - Federico Mele
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland, Bellinzona, Switzerland
| | - Ibtihal Benhsaien
- Laboratory of Clinical Immunology, Inflammation, and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, Casablanca, Morocco
- Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, Centre Hospitalo-Universitaire Averroes, Casablanca, Morocco
| | - Karim Dorgham
- Sorbonne University, Institut national de la santé et de la recherche médicale, Center for Immunology and Microbial Infections-Paris, Paris, France
| | - Jing Han
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Carys A. Croft
- Innate Immunity Unit, Institut Pasteur, Paris, France
- Institut national de la santé et de la recherche médicale U1223, Paris, France
- University of Paris, Paris, France
| | - Samuele Notarbartolo
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland, Bellinzona, Switzerland
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut national de la santé et de la recherche médicale Unité Mixte de Recherches 1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Paul Bastard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut national de la santé et de la recherche médicale Unité Mixte de Recherches 1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut national de la santé et de la recherche médicale Unité Mixte de Recherches 1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Bernhard Fleckenstein
- Institute for Clinical and Molecular Virology, University Erlangen-Nuremberg, Erlangen, Germany
| | - Laurie H. Glimcher
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Department of Immunology, Harvard Medical School, Boston, MA
| | - James P. Di Santo
- Innate Immunity Unit, Institut Pasteur, Paris, France
- Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Cindy S. Ma
- Garvan Institute of Medical Research, Darlinghurst, Australia
- St. Vincent’s Clinical School, Faculty of Medicine and Health, University of New South Wales, Sydney, Darlinghurst, Australia
| | - Guy Gorochov
- Sorbonne University, Institut national de la santé et de la recherche médicale, Center for Immunology and Microbial Infections-Paris, Paris, France
- Assistance Publique–Hôpitaux de Paris, Department of Immunology, Paris, France
| | - Aziz Bousfiha
- Laboratory of Clinical Immunology, Inflammation, and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, Casablanca, Morocco
- Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, Centre Hospitalo-Universitaire Averroes, Casablanca, Morocco
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut national de la santé et de la recherche médicale Unité Mixte de Recherches 1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Stuart G. Tangye
- Garvan Institute of Medical Research, Darlinghurst, Australia
- St. Vincent’s Clinical School, Faculty of Medicine and Health, University of New South Wales, Sydney, Darlinghurst, Australia
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut national de la santé et de la recherche médicale Unité Mixte de Recherches 1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- Howard Hughes Medical Institute, New York, NY
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut national de la santé et de la recherche médicale Unité Mixte de Recherches 1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Federica Sallusto
- Institute of Microbiology, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland, Bellinzona, Switzerland
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7
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Hosokawa H, Rothenberg EV. How transcription factors drive choice of the T cell fate. Nat Rev Immunol 2021; 21:162-176. [PMID: 32918063 PMCID: PMC7933071 DOI: 10.1038/s41577-020-00426-6] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2020] [Indexed: 12/21/2022]
Abstract
Recent evidence has elucidated how multipotent blood progenitors transform their identities in the thymus and undergo commitment to become T cells. Together with environmental signals, a core group of transcription factors have essential roles in this process by directly activating and repressing specific genes. Many of these transcription factors also function in later T cell development, but control different genes. Here, we review how these transcription factors work to change the activities of specific genomic loci during early intrathymic development to establish T cell lineage identity. We introduce the key regulators and highlight newly emergent insights into the rules that govern their actions. Whole-genome deep sequencing-based analysis has revealed unexpectedly rich relationships between inherited epigenetic states, transcription factor-DNA binding affinity thresholds and influences of given transcription factors on the activities of other factors in the same cells. Together, these mechanisms determine T cell identity and make the lineage choice irreversible.
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Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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8
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Kucinski I, Wilson NK, Hannah R, Kinston SJ, Cauchy P, Lenaerts A, Grosschedl R, Göttgens B. Interactions between lineage-associated transcription factors govern haematopoietic progenitor states. EMBO J 2020; 39:e104983. [PMID: 33103827 PMCID: PMC7737608 DOI: 10.15252/embj.2020104983|] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Recent advances in molecular profiling provide descriptive datasets of complex differentiation landscapes including the haematopoietic system, but the molecular mechanisms defining progenitor states and lineage choice remain ill-defined. Here, we employed a cellular model of murine multipotent haematopoietic progenitors (Hoxb8-FL) to knock out 39 transcription factors (TFs) followed by RNA-Seq analysis, to functionally define a regulatory network of 16,992 regulator/target gene links. Focussed analysis of the subnetworks regulated by the B-lymphoid TF Ebf1 and T-lymphoid TF Gata3 revealed a surprising role in common activation of an early myeloid programme. Moreover, Gata3-mediated repression of Pax5 emerges as a mechanism to prevent precocious B-lymphoid differentiation, while Hox-mediated activation of Meis1 suppresses myeloid differentiation. To aid interpretation of large transcriptomics datasets, we also report a new method that visualises likely transitions that a progenitor will undergo following regulatory network perturbations. Taken together, this study reveals how molecular network wiring helps to establish a multipotent progenitor state, with experimental approaches and analysis tools applicable to dissecting a broad range of both normal and perturbed cellular differentiation landscapes.
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Affiliation(s)
- Iwo Kucinski
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Nicola K Wilson
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Rebecca Hannah
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Sarah J Kinston
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Pierre Cauchy
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Aurelie Lenaerts
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany,International Max Planck Research School for Molecular and Cellular BiologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Berthold Göttgens
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
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9
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Kucinski I, Wilson NK, Hannah R, Kinston SJ, Cauchy P, Lenaerts A, Grosschedl R, Göttgens B. Interactions between lineage-associated transcription factors govern haematopoietic progenitor states. EMBO J 2020; 39:e104983. [PMID: 33103827 PMCID: PMC7737608 DOI: 10.15252/embj.2020104983] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/26/2022] Open
Abstract
Recent advances in molecular profiling provide descriptive datasets of complex differentiation landscapes including the haematopoietic system, but the molecular mechanisms defining progenitor states and lineage choice remain ill-defined. Here, we employed a cellular model of murine multipotent haematopoietic progenitors (Hoxb8-FL) to knock out 39 transcription factors (TFs) followed by RNA-Seq analysis, to functionally define a regulatory network of 16,992 regulator/target gene links. Focussed analysis of the subnetworks regulated by the B-lymphoid TF Ebf1 and T-lymphoid TF Gata3 revealed a surprising role in common activation of an early myeloid programme. Moreover, Gata3-mediated repression of Pax5 emerges as a mechanism to prevent precocious B-lymphoid differentiation, while Hox-mediated activation of Meis1 suppresses myeloid differentiation. To aid interpretation of large transcriptomics datasets, we also report a new method that visualises likely transitions that a progenitor will undergo following regulatory network perturbations. Taken together, this study reveals how molecular network wiring helps to establish a multipotent progenitor state, with experimental approaches and analysis tools applicable to dissecting a broad range of both normal and perturbed cellular differentiation landscapes.
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Affiliation(s)
- Iwo Kucinski
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Nicola K Wilson
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Rebecca Hannah
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Sarah J Kinston
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Pierre Cauchy
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Aurelie Lenaerts
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
- International Max Planck Research School for Molecular and Cellular BiologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Berthold Göttgens
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
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10
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Chan WF, Coughlan HD, Iannarella N, Smyth GK, Johanson TM, Keenan CR, Allan RS. Identification and characterization of the long noncoding RNA Dreg1 as a novel regulator of Gata3. Immunol Cell Biol 2020; 99:323-332. [PMID: 32970351 DOI: 10.1111/imcb.12408] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/22/2020] [Indexed: 01/05/2023]
Abstract
The eukaryotic genome is three-dimensionally segregated into discrete globules of topologically associating domains (TADs), within which numerous cis-regulatory elements such as enhancers and promoters interact to regulate gene expression. In this study, we identify a T-cell-specific sub-TAD containing the Gata3 locus, and reveal a previously uncharacterized long noncoding RNA (Dreg1) within a distant enhancer lying approximately 280 kb downstream of Gata3. Dreg1 expression is highly correlated with that of Gata3 during early immune system development and T helper type 2 cell differentiation. Inhibition and overexpression of Dreg1 suggest that it may be involved in the establishment, but not in the maintenance of Gata3 expression. Overall, we propose that Dreg1 is a novel regulator of Gata3 and may inform therapeutic strategies in diseases such allergy and lymphoma, where Gata3 has a pathological role.
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Affiliation(s)
- Wing Fuk Chan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Hannah D Coughlan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Nadia Iannarella
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Christine R Keenan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
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11
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Sun Y, Jin Z, Zhang X, Cui T, Zhang W, Shao S, Li H, Wang N. GATA Binding Protein 3 Is a Direct Target of Kruppel-Like Transcription Factor 7 and Inhibits Chicken Adipogenesis. Front Physiol 2020; 11:610. [PMID: 32587528 PMCID: PMC7298121 DOI: 10.3389/fphys.2020.00610] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/15/2020] [Indexed: 12/21/2022] Open
Abstract
Kruppel-like transcription factor 7 (KLF7) is a negative regulator of adipogenesis, however, its precise mechanism is poorly understood. Our previous KLF7 ChIP-seq analysis showed that one of the KLF7 binding peaks was present upstream of GATA binding protein 3 (GATA3) in chicken preadipocytes. In the present study, we identified GATA3 as a target of KLF7. Overexpression analysis showed KLF7 markedly enhanced the endogenous expression of GATA3 in the immortalized chicken preadipcyte cell line (ICP2), and the luciferase reporter assay showed that KLF7 overexpression increased the reporter gene activity of the cloned upstream region (-5285/-4336 relative to the translation initiation codon ATG) of GATA3 in ICP2 and DF1 cells, and mutation of the putative KLF7 binding site abolished the promotive effect of KLF7 overexpression on the reporter gene activity of the cloned GATA3 upstream region. ChIP-qPCR further demonstrated that KLF7 directly bound to the GATA3 upstream region. Gene expression analysis showed that GATA3 mRNA expression in abdominal adipose tissue was significantly higher in lean chicken line than in the fat line at 2, 3, and 6 weeks of age. In addition, GATA3 mRNA expression markedly decreased during the preadipocyte differentiation. Furthermore, a functional study showed that GATA3 overexpression inhibited the differentiation of the ICP2 cells. Taken together, our results demonstrated that KLF7 inhibits chicken adipogenesis, at least in part through direct upregulation of GATA3.
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Affiliation(s)
- Yingning Sun
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Zhao Jin
- College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, China
| | - Xinyang Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Tingting Cui
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Wenjian Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Shuli Shao
- College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, China
| | - Hui Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Ning Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
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12
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Bai X, Shi S, Ai B, Jiang Y, Liu Y, Han X, Xu M, Pan Q, Wang F, Wang Q, Zhang J, Li X, Feng C, Li Y, Wang Y, Song Y, Feng K, Li C. ENdb: a manually curated database of experimentally supported enhancers for human and mouse. Nucleic Acids Res 2020; 48:D51-D57. [PMID: 31665430 PMCID: PMC7145688 DOI: 10.1093/nar/gkz973] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/10/2019] [Accepted: 10/16/2019] [Indexed: 12/30/2022] Open
Abstract
Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons. Enhancers, as well as their associated target genes, and transcription factors (TFs) that bind to them, are highly associated with human disease and biological processes. Although some enhancer databases have been published, most only focus on enhancers identified by high-throughput experimental techniques. Therefore, it is highly desirable to construct a comprehensive resource of manually curated enhancers and their related information based on low-throughput experimental evidences. Here, we established a comprehensive manually-curated enhancer database for human and mouse, which provides a resource for experimentally supported enhancers, and to annotate the detailed information of enhancers. The current release of ENdb documents 737 experimentally validated enhancers and their related information, including 384 target genes, 263 TFs, 110 diseases and 153 functions in human and mouse. Moreover, the enhancer-related information was supported by experimental evidences, such as RNAi, in vitro knockdown, western blotting, qRT-PCR, luciferase reporter assay, chromatin conformation capture (3C) and chromosome conformation capture-on-chip (4C) assays. ENdb provides a user-friendly interface to query, browse and visualize the detailed information of enhancers. The database is available at http://www.licpathway.net/ENdb.
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Affiliation(s)
- Xuefeng Bai
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Shanshan Shi
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yong Jiang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yuejuan Liu
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Xiaole Han
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Mingcong Xu
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Qi Pan
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Fan Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Qiuyu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Xuecang Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yanyu Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yuezhu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yiwei Song
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Ke Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Chunquan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
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13
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Chen CH, Zheng R, Tokheim C, Dong X, Fan J, Wan C, Tang Q, Brown M, Liu JS, Meyer CA, Liu XS. Determinants of transcription factor regulatory range. Nat Commun 2020; 11:2472. [PMID: 32424124 PMCID: PMC7235260 DOI: 10.1038/s41467-020-16106-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/14/2020] [Indexed: 01/03/2023] Open
Abstract
Characterization of the genomic distances over which transcription factor (TF) binding influences gene expression is important for inferring target genes from TF chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Here we systematically examine the relationship between thousands of TF and histone modification ChIP-seq data sets with thousands of gene expression profiles. We develop a model for integrating these data, which reveals two classes of TFs with distinct ranges of regulatory influence, chromatin-binding preferences, and auto-regulatory properties. We find that the regulatory range of the same TF bound within different topologically associating domains (TADs) depend on intrinsic TAD properties such as local gene density and G/C content, but also on the TAD chromatin states. Our results suggest that considering TF type, binding distance to gene locus, as well as chromatin context is important in identifying implicated TFs from GWAS SNPs.
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Affiliation(s)
- Chen-Hao Chen
- Department of Data Sciences, Dana-Farber Cancer Institute. Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Biological and Biomedical Science Program, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rongbin Zheng
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Collin Tokheim
- Department of Data Sciences, Dana-Farber Cancer Institute. Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xin Dong
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jingyu Fan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Changxin Wan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Qin Tang
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - Clifford A Meyer
- Department of Data Sciences, Dana-Farber Cancer Institute. Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - X Shirley Liu
- Department of Data Sciences, Dana-Farber Cancer Institute. Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Statistics, Harvard University, Cambridge, MA, USA.
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14
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Abstract
Specification of multipotent blood precursor cells in postnatal mice to become committed T-cell precursors involves a gene regulatory network of several interacting but functionally distinct modules. Many links of this network have been defined by perturbation tests and by functional genomics. However, using the network model to predict real-life kinetics of the commitment process is still difficult, partly due to the tenacity of repressive chromatin states, and to the ability of transcription factors to affect each other's binding site choices through competitive recruitment to alternative sites ("coregulator theft"). To predict kinetics, future models will need to incorporate mechanistic information about chromatin state change dynamics and more sophisticated understanding of the proteomics and cooperative DNA site choices of transcription factor complexes.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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15
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The transcription factor TCF-1 enforces commitment to the innate lymphoid cell lineage. Nat Immunol 2019; 20:1150-1160. [PMID: 31358996 PMCID: PMC6707869 DOI: 10.1038/s41590-019-0445-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 06/12/2019] [Indexed: 01/25/2023]
Abstract
Innate lymphoid cells (ILCs) play important functions in immunity and tissue homeostasis, but their development is poorly understood. Through the use of single-cell approaches, we examined the transcriptional and functional heterogeneity of ILC progenitors, and studied the precursor-product relationships that link the subsets identified. This analysis identified two successive stages of ILC development within T cell factor 1-positive (TCF-1+) early innate lymphoid progenitors (EILPs), which we named 'specified EILPs' and 'committed EILPs'. Specified EILPs generated dendritic cells, whereas this potential was greatly decreased in committed EILPs. TCF-1 was dispensable for the generation of specified EILPs, but required for the generation of committed EILPs. TCF-1 used a pre-existing regulatory landscape established in upstream lymphoid precursors to bind chromatin in EILPs. Our results provide insight into the mechanisms by which TCF-1 promotes developmental progression of ILC precursors, while constraining their dendritic cell lineage potential and enforcing commitment to ILC fate.
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16
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A Gata3 3' Distal Otic Vesicle Enhancer Directs Inner Ear-Specific Gata3 Expression. Mol Cell Biol 2018; 38:MCB.00302-18. [PMID: 30126893 DOI: 10.1128/mcb.00302-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/13/2018] [Indexed: 12/21/2022] Open
Abstract
Transcription factor GATA3 plays vital roles in inner ear development, while regulatory mechanisms controlling its inner ear-specific expression are undefined. We demonstrate that a cis-regulatory element lying 571 kb 3' to the Gata3 gene directs inner ear-specific Gata3 expression, which we refer to as the Gata3 otic vesicle enhancer (OVE). In transgenic murine embryos, a 1.5-kb OVE-directed lacZ reporter (TgOVE-LacZ) exhibited robust lacZ expression specifically in the otic vesicle (OV), an inner ear primordial tissue, and its derivative semicircular canal. To further define the regulatory activity of this OVE, we generated Cre transgenic mice in which Cre expression was directed by a 246-bp core sequence within the OVE element (TgcoreOVE-Cre). TgcoreOVE-Cre successfully marked the OV-derived inner ear tissues, including cochlea, semicircular canal and spiral ganglion, when crossed with ROSA26 lacZ reporter mice. Furthermore, Gata3 conditionally mutant mice, when crossed with the TgcoreOVE-Cre, showed hypoplasia throughout the inner ear tissues. These results demonstrate that OVE has a sufficient regulatory activity to direct Gata3 expression specifically in the otic vesicle and semicircular canal and that Gata3 expression driven by the OVE is crucial for normal inner ear development.
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17
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Sato Y, Tsukaguchi H, Morita H, Higasa K, Tran MTN, Hamada M, Usui T, Morito N, Horita S, Hayashi T, Takagi J, Yamaguchi I, Nguyen HT, Harada M, Inui K, Maruta Y, Inoue Y, Koiwa F, Sato H, Matsuda F, Ayabe S, Mizuno S, Sugiyama F, Takahashi S, Yoshimura A. A mutation in transcription factor MAFB causes Focal Segmental Glomerulosclerosis with Duane Retraction Syndrome. Kidney Int 2018; 94:396-407. [PMID: 29779709 DOI: 10.1016/j.kint.2018.02.025] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 01/24/2018] [Accepted: 02/08/2018] [Indexed: 01/02/2023]
Abstract
Focal segmental glomerulosclerosis (FSGS) is a leading cause of end-stage renal disease in children and adults. Genetic factors significantly contribute to early-onset FSGS, but the etiologies of most adult cases remain unknown. Genetic studies of monogenic syndromic FSGS exhibiting extra-renal manifestations have uncovered an unexpected biological role for genes in the development of both podocytes and other cellular lineages. To help define these roles, we studied two unrelated families with FSGS associated with Duane Retraction Syndrome, characterized by impaired horizontal eye movement due to cranial nerve malformation. All four affected individuals developed FSGS and Duane Retraction Syndrome in their first to second decade of life, manifested as restricted abduction together with globe retraction and narrowed palpebral fissure on attempted adduction. Hypoplasia of the abducens nerves and hearing impairment occurred in severely affected individuals. Genetic analyses revealed that affected individuals harbor a rare heterozygous substitution (p.Leu239Pro) in MAFB, a leucine zipper transcription factor. Luciferase assays with cultured monocytes indicated that the substitution significantly reduced transactivation of the F4/80 promoter, the known MAFB recognition element. Additionally, immunohistochemistry indicated reduced MAFB expression in the podocytes of patients. Structural modeling suggested that the p.Leu239Pro substitution in the DNA-binding domain possibly interferes with the stability of the adjacent zinc finger. Lastly, podocytes in neonatal mice with p.Leu239Pro displayed impaired differentiation. Thus, MAFB mutations impair development and/or maintenance of podocytes, abducens neurons and the inner ear. The interactions between MAFB and regulatory elements in these developing organs are likely highly specific based on spatiotemporal requirements.
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Affiliation(s)
- Yoshinori Sato
- Division of Nephrology, Department of Medicine, Showa University Fujigaoka Hospital, Fujigaoka, Japan
| | - Hiroyasu Tsukaguchi
- Second Department of Internal Medicine, Kansai Medical University, Hirakata, Japan.
| | - Hiroyuki Morita
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Koichiro Higasa
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Mai Thi Nhu Tran
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Michito Hamada
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Toshiaki Usui
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; Department of Nephrology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Naoki Morito
- Department of Nephrology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shoichiro Horita
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takao Hayashi
- Department of Ophthalmology, School of Medicine, Teikyo University, Tokyo, Japan
| | - Junko Takagi
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Izumi Yamaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Huan Thanh Nguyen
- Second Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Masayo Harada
- Department of Clinical Anatomy, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kiyoko Inui
- Division of Nephrology, Department of Medicine, Showa University Fujigaoka Hospital, Fujigaoka, Japan
| | - Yuichi Maruta
- Division of Nephrology, Department of Medicine, Showa University Fujigaoka Hospital, Fujigaoka, Japan
| | - Yoshihiko Inoue
- Division of Nephrology, Department of Medicine, Showa University Fujigaoka Hospital, Fujigaoka, Japan
| | - Fumihiko Koiwa
- Division of Nephrology, Department of Medicine, Showa University Fujigaoka Hospital, Fujigaoka, Japan
| | - Hiroshi Sato
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Center, Tsukuba, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; Laboratory Animal Resource Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Japan; Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Japan
| | - Ashio Yoshimura
- Division of Nephrology, Department of Medicine, Showa University Fujigaoka Hospital, Fujigaoka, Japan
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18
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Hosoya T, D'Oliveira Albanus R, Hensley J, Myers G, Kyono Y, Kitzman J, Parker SCJ, Engel JD. Global dynamics of stage-specific transcription factor binding during thymocyte development. Sci Rep 2018; 8:5605. [PMID: 29618724 PMCID: PMC5884796 DOI: 10.1038/s41598-018-23774-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/20/2018] [Indexed: 12/29/2022] Open
Abstract
In vertebrates, multiple transcription factors (TFs) bind to gene regulatory elements (promoters, enhancers, and silencers) to execute developmental expression changes. ChIP experiments are often used to identify where TFs bind to regulatory elements in the genome, but the requirement of TF-specific antibodies hampers analyses of tens of TFs at multiple loci. Here we tested whether TF binding predictions using ATAC-seq can be used to infer the identity of TFs that bind to functionally validated enhancers of the Cd4, Cd8, and Gata3 genes in thymocytes. We performed ATAC-seq at four distinct stages of development in mouse thymus, probing the chromatin accessibility landscape in double negative (DN), double positive (DP), CD4 single positive (SP4) and CD8 SP (SP8) thymocytes. Integration of chromatin accessibility with TF motifs genome-wide allowed us to infer stage-specific occupied TF binding sites within known and potentially novel regulatory elements. Our results provide genome-wide stage-specific T cell open chromatin profiles, and allow the identification of candidate TFs that drive thymocyte differentiation at each developmental stage.
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Affiliation(s)
- Tomonori Hosoya
- Department of Cell and Developmental Biology, Ann Arbor, USA
| | | | - John Hensley
- Department of Computational Medicine and Bioinformatics, Ann Arbor, USA
| | - Greggory Myers
- Department of Cell and Developmental Biology, Ann Arbor, USA
| | - Yasuhiro Kyono
- Department of Computational Medicine and Bioinformatics, Ann Arbor, USA.,Department of Human Genetics, University of Michigan, 3035 BSRB, 109 Zina Pitcher Place, Ann Arbor, Michigan, 48109-2200, USA
| | - Jacob Kitzman
- Department of Computational Medicine and Bioinformatics, Ann Arbor, USA.,Department of Human Genetics, University of Michigan, 3035 BSRB, 109 Zina Pitcher Place, Ann Arbor, Michigan, 48109-2200, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, Ann Arbor, USA.,Department of Human Genetics, University of Michigan, 3035 BSRB, 109 Zina Pitcher Place, Ann Arbor, Michigan, 48109-2200, USA
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Gata3 Hypomorphic Mutant Mice Rescued with a Yeast Artificial Chromosome Transgene Suffer a Glomerular Mesangial Cell Defect. Mol Cell Biol 2016; 36:2272-81. [PMID: 27296697 DOI: 10.1128/mcb.00173-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/06/2016] [Indexed: 12/24/2022] Open
Abstract
GATA3 is a zinc finger transcription factor that plays a crucial role in embryonic kidney development, while its precise functions in the adult kidney remain largely unexplored. Here, we demonstrate that GATA3 is specifically expressed in glomerular mesangial cells and plays a critical role in the maintenance of renal glomerular function. Newly generated Gata3 hypomorphic mutant mice exhibited neonatal lethality associated with severe renal hypoplasia. Normal kidney size was restored by breeding the hypomorphic mutant with a rescuing transgenic mouse line bearing a 662-kb Gata3 yeast artificial chromosome (YAC), and these animals (termed G3YR mice) survived to adulthood. However, most of the G3YR mice showed degenerative changes in glomerular mesangial cells, which deteriorated progressively during postnatal development. Consequently, the G3YR adult mice suffered severe renal failure. We found that the 662-kb Gata3 YAC transgene recapitulated Gata3 expression in the renal tubules but failed to direct sufficient GATA3 activity to mesangial cells. Renal glomeruli of the G3YR mice had significantly reduced amounts of platelet-derived growth factor receptor (PDGFR), which is known to participate in the development and maintenance of glomerular mesangial cells. These results demonstrate a critical role for GATA3 in the maintenance of mesangial cells and its absolute requirement for prevention of glomerular disease.
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Miano JM, Zhu QM, Lowenstein CJ. A CRISPR Path to Engineering New Genetic Mouse Models for Cardiovascular Research. Arterioscler Thromb Vasc Biol 2016; 36:1058-75. [PMID: 27102963 PMCID: PMC4882230 DOI: 10.1161/atvbaha.116.304790] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/06/2016] [Indexed: 12/26/2022]
Abstract
Previous efforts to target the mouse genome for the addition, subtraction, or substitution of biologically informative sequences required complex vector design and a series of arduous steps only a handful of laboratories could master. The facile and inexpensive clustered regularly interspaced short palindromic repeats (CRISPR) method has now superseded traditional means of genome modification such that virtually any laboratory can quickly assemble reagents for developing new mouse models for cardiovascular research. Here, we briefly review the history of CRISPR in prokaryotes, highlighting major discoveries leading to its formulation for genome modification in the animal kingdom. Core components of CRISPR technology are reviewed and updated. Practical pointers for 2-component and 3-component CRISPR editing are summarized with many applications in mice including frameshift mutations, deletion of enhancers and noncoding genes, nucleotide substitution of protein-coding and gene regulatory sequences, incorporation of loxP sites for conditional gene inactivation, and epitope tag integration. Genotyping strategies are presented and topics of genetic mosaicism and inadvertent targeting discussed. Finally, clinical applications and ethical considerations are addressed as the biomedical community eagerly embraces this astonishing innovation in genome editing to tackle previously intractable questions.
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Affiliation(s)
- Joseph M Miano
- From the Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY (J.M.M., Q.M.Z., C.J.L.); and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA (Q.M.Z.).
| | - Qiuyu Martin Zhu
- From the Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY (J.M.M., Q.M.Z., C.J.L.); and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA (Q.M.Z.)
| | - Charles J Lowenstein
- From the Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY (J.M.M., Q.M.Z., C.J.L.); and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA (Q.M.Z.)
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