1
|
Sun H, Qiu J, Qiu J. Epigenetic regulation of innate lymphoid cells. Eur J Immunol 2024:e2350379. [PMID: 38824666 DOI: 10.1002/eji.202350379] [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: 08/31/2023] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/04/2024]
Abstract
Innate lymphoid cells (ILCs) lack antigen-specific receptors and are considered the innate arm of the immune system, phenotypically and functionally mirroring CD4+ helper T cells. ILCs are categorized into groups 1, 2, and 3 based on transcription factors and cytokine expression. ILCs predominantly reside in mucosal tissues and play important roles in regional immune responses. The development and function of ILC subsets are controlled by both transcriptional and epigenetic mechanisms, which have been extensively studied in recent years. Epigenetic regulation refers to inheritable changes in gene expression that occur without affecting DNA sequences. This mainly includes chromatin status, histone modifications, and DNA methylation. In this review, we summarize recent discoveries on epigenetic mechanisms regulating ILC development and function, and how these regulations affect disease progression under pathological conditions. Although the ablation of specific epigenetic regulators can cause global changes in corresponding epigenetic modifications to the chromatin, only partial genes with altered epigenetic modifications change their mRNA expression, resulting in specific outcomes in cell differentiation and function. Therefore, elucidating epigenetic mechanisms underlying the regulation of ILCs will provide potential targets for the diagnosis and treatment of inflammatory diseases.
Collapse
Affiliation(s)
- Hanxiao Sun
- Department of Laboratory Medicine, Department of Blood Transfusion, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinxin Qiu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ju Qiu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
2
|
Ferreira ACF, Szeto ACH, Clark PA, Crisp A, Kozik P, Jolin HE, McKenzie ANJ. Neuroprotective protein ADNP-dependent histone remodeling complex promotes T helper 2 immune cell differentiation. Immunity 2023; 56:1468-1484.e7. [PMID: 37285842 PMCID: PMC10501989 DOI: 10.1016/j.immuni.2023.05.010] [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: 11/16/2022] [Revised: 03/31/2023] [Accepted: 05/12/2023] [Indexed: 06/09/2023]
Abstract
Type 2 immune responses are critical in tissue homeostasis, anti-helminth immunity, and allergy. T helper 2 (Th2) cells produce interleukin-4 (IL-4), IL-5, and IL-13 from the type 2 gene cluster under regulation by transcription factors (TFs) including GATA3. To better understand transcriptional regulation of Th2 cell differentiation, we performed CRISPR-Cas9 screens targeting 1,131 TFs. We discovered that activity-dependent neuroprotector homeobox protein (ADNP) was indispensable for immune reactions to allergen. Mechanistically, ADNP performed a previously unappreciated role in gene activation, forming a critical bridge in the transition from pioneer TFs to chromatin remodeling by recruiting the helicase CHD4 and ATPase BRG1. Although GATA3 and AP-1 bound the type 2 cytokine locus in the absence of ADNP, they were unable to initiate histone acetylation or DNA accessibility, resulting in highly impaired type 2 cytokine expression. Our results demonstrate an important role for ADNP in promoting immune cell specialization.
Collapse
Affiliation(s)
| | | | - Paula A Clark
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Alastair Crisp
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Patrycja Kozik
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Helen E Jolin
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | |
Collapse
|
3
|
Epigenetic regulation of T cell lineages in skin and blood following hematopoietic stem cell transplantation. Clin Immunol 2023; 248:109245. [PMID: 36702179 DOI: 10.1016/j.clim.2023.109245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/15/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023]
Abstract
Allogeneic hematopoietic stem-cell transplantation (HSCT) seeks to reconstitute the host's immune system from donor stem cells. The success of HSCT is threatened by complications including leukemia relapse or graft-versus-host-disease (GvHD). To investigate the underlying regulatory processes in central and peripheral T cell recovery, we performed sequential multi-omics analysis of T cells of the skin and blood during HSCT. We detected rapid effector T cell reconstitution, while emergence of regulatory T cells was delayed. Epigenetic and gene-regulatory programs were associated with recovering T cells and diverged greatly between skin and blood T cells. The BRG1/BRM-associated factor chromatin remodeling complex and histone deacetylases (HDACs) were epigenetic regulators involved in restoration of T cell homeostasis after transplantation. In isolated T cells of patients after HSCT, we observed class I HDAC-inhibitors to modulate their dysbalance. The present study highlights the importance of epigenetic regulation in the recovery of T cells following HSCT.
Collapse
|
4
|
UTX maintains the functional integrity of the murine hematopoietic system by globally regulating aging-associated genes. Blood 2021; 137:908-922. [PMID: 33174606 DOI: 10.1182/blood.2019001044] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/18/2020] [Indexed: 02/07/2023] Open
Abstract
Epigenetic regulation is essential for the maintenance of the hematopoietic system, and its deregulation is implicated in hematopoietic disorders. In this study, UTX, a demethylase for lysine 27 on histone H3 (H3K27) and a component of COMPASS-like and SWI/SNF complexes, played an essential role in the hematopoietic system by globally regulating aging-associated genes. Utx-deficient (UtxΔ/Δ) mice exhibited myeloid skewing with dysplasia, extramedullary hematopoiesis, impaired hematopoietic reconstituting ability, and increased susceptibility to leukemia, which are the hallmarks of hematopoietic aging. RNA-sequencing (RNA-seq) analysis revealed that Utx deficiency converted the gene expression profiles of young hematopoietic stem-progenitor cells (HSPCs) to those of aged HSPCs. Utx expression in hematopoietic stem cells declined with age, and UtxΔ/Δ HSPCs exhibited increased expression of an aging-associated marker, accumulation of reactive oxygen species, and impaired repair of DNA double-strand breaks. Pathway and chromatin immunoprecipitation analyses coupled with RNA-seq data indicated that UTX contributed to hematopoietic homeostasis mainly by maintaining the expression of genes downregulated with aging via demethylase-dependent and -independent epigenetic programming. Of note, comparison of pathway changes in UtxΔ/Δ HSPCs, aged muscle stem cells, aged fibroblasts, and aged induced neurons showed substantial overlap, strongly suggesting common aging mechanisms among different tissue stem cells.
Collapse
|
5
|
Tafessu A, Banaszynski LA. Establishment and function of chromatin modification at enhancers. Open Biol 2020; 10:200255. [PMID: 33050790 PMCID: PMC7653351 DOI: 10.1098/rsob.200255] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
How a single genome can give rise to distinct cell types remains a fundamental question in biology. Mammals are able to specify and maintain hundreds of cell fates by selectively activating unique subsets of their genome. This is achieved, in part, by enhancers-genetic elements that can increase transcription of both nearby and distal genes. Enhancers can be identified by their unique chromatin signature, including transcription factor binding and the enrichment of specific histone post-translational modifications, histone variants, and chromatin-associated cofactors. How each of these chromatin features contributes to enhancer function remains an area of intense study. In this review, we provide an overview of enhancer-associated chromatin states, and the proteins and enzymes involved in their establishment. We discuss recent insights into the effects of the enhancer chromatin state on ongoing transcription versus their role in the establishment of new transcription programmes, such as those that occur developmentally. Finally, we highlight the role of enhancer chromatin in new conceptual advances in gene regulation such as condensate formation.
Collapse
Affiliation(s)
| | - Laura A. Banaszynski
- UT Southwestern Medical Center, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, Hamon Center for Regenerative Science and Medicine, Dallas, TX 75390-8511, USA
| |
Collapse
|
6
|
Li N, Liu S, Zhang Y, Yu L, Hu Y, Wu T, Fang M, Xu Y. Transcriptional Activation of Matricellular Protein Spondin2 (SPON2) by BRG1 in Vascular Endothelial Cells Promotes Macrophage Chemotaxis. Front Cell Dev Biol 2020; 8:794. [PMID: 32974343 PMCID: PMC7461951 DOI: 10.3389/fcell.2020.00794] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 07/28/2020] [Indexed: 12/18/2022] Open
Abstract
The matricellular protein SPON2 plays diverse roles in the development of cardiovascular diseases. SPON2 is expressed in endothelial cells, but its transcription regulation in the context of atherogenesis remains incompletely appreciated. Here we report that SPON2 expression was up-regulated by pro-atherogenic stimuli (oxLDL and TNF-α) in vascular endothelia cells. In addition, endothelial SPON2 was elevated in Apoe–/– mice fed on a Western diet compared to the control mice. Induction of SPON2 in endothelial cells by pro-atherogenic stimuli was mediated by BRG1, a chromatin remodeling protein, both in vitro and in vivo. Further analysis revealed that BRG1 interacted with the sequence-specific transcription factor Egr-1 to activate SPON2 transcription. BRG1 contributed to SPON2 trans-activation by modulating chromatin structure surrounding the SPON2 promoter. Functionally, activation of SPON2 transcription by the Egr-1/BRG1 complex provided chemoattractive cues for macrophage trafficking. SPON2 depletion abrogated the ability of BRG1 or Egr-1 to stimulate endothelial derived chemoattractive cue for macrophage migration. On the contrary, recombinant SPON2 rescued endothelial chemo-attractability in the absence of BRG1 or Egr-1. In conclusion, our data have identified a novel transcriptional cascade in endothelial cells that may potentially promote macrophage recruitment and vascular inflammation leading to atherogenesis.
Collapse
Affiliation(s)
- Nan Li
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Shuai Liu
- Hainan Provincial Key Laboratory for Tropical Cardiovascular Diseases Research and Key Laboratory of Emergency and Trauma of Ministry of Education, Institute of Cardiovascular Research of the First Affiliated Hospital, Hainan Medical University, Haikou, China.,Department of Cardiology, Kaifeng People's Hospital, Kaifeng, China
| | - Yuanyuan Zhang
- Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Liming Yu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Yanjiang Hu
- Department of Cardiothoracic Surgery, Liyang People's Hospital, Liyang, China
| | - Teng Wu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Mingming Fang
- Department of Clinical Medicine and Laboratory Center for Experimental Medicine, Jiangsu Health Vocational Institute, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Yong Xu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| |
Collapse
|
7
|
In situ conversion of defective Treg into SuperTreg cells to treat advanced IPEX-like disorders in mice. Nat Commun 2020; 11:2781. [PMID: 32493900 PMCID: PMC7271236 DOI: 10.1038/s41467-020-15836-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Mutations disrupting regulatory T (Treg) cell function can cause IPEX and IPEX-related disorders, but whether established disease can be reversed by correcting these mutations is unclear. Treg-specific deletion of the chromatin remodeling factor Brg1 impairs Treg cell activation and causes fatal autoimmunity in mice. Here, we show with a reversible knockout model that re-expression of Brg1, in conjunction with the severe endogenous proinflammatory environment, can convert defective Treg cells into powerful, super-activated Treg cells (SuperTreg cells) that can resolve advanced autoimmunity, with Brg1 re-expression in a minor fraction of Treg cells sufficient for the resolution in some cases. SuperTreg cells have enhanced trafficking and regulatory capabilities, but become deactivated as the inflammation subsides, thus avoiding excessive immune suppression. We propose a simple, robust yet safe gene-editing-based therapy for IPEX and IPEX-related disorders that exploits the defective Treg cells and the inflammatory environment pre-existing in the patients. Mutations that affect Treg cell function can cause lethal autoimmunity, but whether correcting these mutations can reverse established disease is unclear. Here, the authors correct Treg cell-specific Brg1 mutation in a minor fraction of Treg cells, which supercharges these cells to rescue mice from otherwise fatal IPEX-like autoimmunity.
Collapse
|
8
|
Mirlekar B. Co-expression of master transcription factors determines CD4 + T cell plasticity and functions in auto-inflammatory diseases. Immunol Lett 2020; 222:58-66. [PMID: 32220615 DOI: 10.1016/j.imlet.2020.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/05/2020] [Accepted: 03/18/2020] [Indexed: 02/08/2023]
Abstract
Master CD4+ T cell lineage determined transcription factors are found to be dysregulated in pathogenesis of autoimmune and inflammatory diseases. CD4+ T cells categorized into different lineages based on their functions, cell surface markers and master transcription factors those required for expression of lineage specific cytokines. T-bet, GATA3, RORγt and Foxp3 are major transcription regulators of Th1, Th2, Th17 and Treg cells respectively. Significant progress has been made in understanding expression of lineage specific master regulators that drives CD4+ T cell differentiation. It is known that each CD4+ T cell lineage express precise determined transcription factor and due to cross regulation between these factors the CD4+ T cells able to maintain thier specific phenotype. However, recent studies shows that the lineage specifying transcription factors frequently co-expressed. There is an emerging area of research revealing that the co-expression of lineage-specifying transcription factors alters the potential function and flexibility of subsets of CD4+ T cell, this in turn favors the autoimmune pathology. Here, we discuss similarities and differences between mutually co-expressed transcription factors in CD4+ T cell subsets and then recapitulates on cell type specific and dynamic balance between the lineage restricted transcription factors in determining plasticity of CD4+ T cell subsets. Furthermore, we discuss abnormal regulation of such transcription factors that establishes a pathogenic CD4+ T cell phenotype in autoimmune diseases and how this understanding will provide further insight into potential therapeutic development.
Collapse
Affiliation(s)
- Bhalchandra Mirlekar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, Chapel Hill, NC, 27514, USA.
| |
Collapse
|
9
|
Regulation of KDM2B and Brg1 on Inflammatory Response of Nasal Mucosa in CRSwNP. Inflammation 2019; 42:1389-1400. [DOI: 10.1007/s10753-019-01000-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
10
|
Henriksson J, Chen X, Gomes T, Ullah U, Meyer KB, Miragaia R, Duddy G, Pramanik J, Yusa K, Lahesmaa R, Teichmann SA. Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation. Cell 2019; 176:882-896.e18. [PMID: 30639098 PMCID: PMC6370901 DOI: 10.1016/j.cell.2018.11.044] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 09/19/2018] [Accepted: 11/28/2018] [Indexed: 12/24/2022]
Abstract
T helper type 2 (Th2) cells are important regulators of mammalian adaptive immunity and have relevance for infection, autoimmunity, and tumor immunology. Using a newly developed, genome-wide retroviral CRISPR knockout (KO) library, combined with RNA-seq, ATAC-seq, and ChIP-seq, we have dissected the regulatory circuitry governing activation and differentiation of these cells. Our experiments distinguish cell activation versus differentiation in a quantitative framework. We demonstrate that these two processes are tightly coupled and are jointly controlled by many transcription factors, metabolic genes, and cytokine/receptor pairs. There are only a small number of genes regulating differentiation without any role in activation. By combining biochemical and genetic data, we provide an atlas for Th2 differentiation, validating known regulators and identifying factors, such as Pparg and Bhlhe40, as part of the core regulatory network governing Th2 helper cell fates.
Collapse
Affiliation(s)
- Johan Henriksson
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
| | - Xi Chen
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tomás Gomes
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ubaid Ullah
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6 FI-20520, Turku, Finland
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ricardo Miragaia
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Graham Duddy
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jhuma Pramanik
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kosuke Yusa
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6 FI-20520, Turku, Finland
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, UK.
| |
Collapse
|
11
|
The Role of Nucleosomes in Epigenetic Gene Regulation. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
|
12
|
Moon JS, Lee HJ, Ho CC, Shin JS, Ghosh S, Kim JH, Lee SK. Immuno-suppressive function of nucleus-transducible BAF57-ΔPH in T cell activation via degradation of endogenous BAF57. Int J Hematol 2018; 108:375-383. [PMID: 29978433 DOI: 10.1007/s12185-018-2491-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/26/2018] [Accepted: 06/26/2018] [Indexed: 11/28/2022]
Abstract
The BAF57 subunit, an indispensable member of the BAF complex, is functionally implicated in apoptosis, cell cycle, and T cell development through chromosomal remodeling. However, the precise roles of BAF57 in the T cell receptor (TcR)-mediated signaling pathway have not been elucidated. In this study, a nucleus-transducible form of BAF57, absent the proline-rich and HMG domains (ntBAF57-ΔPH), was generated to interfere with the interaction between BAF57 and its binding protein, BAF155. ntBAF57-ΔPH was effectively delivered into mouse CD4+ T cells in a dose- and time-dependent manner, without cellular toxicity. Inhibition of T cell activation by ntBAF57-ΔPH was mediated by its disruption of the interaction between BAF155 and BAF57, leading to the degradation of endogenous BAF57 and BAF155. This phenomenon led to alterations in gene expression similar to those associated with Ciclosporin A treatment. In vivo administration of ntBAF57-ΔPH enhanced survival rate of sepsis-induced mice and reduced the LPS-induced secretion of pro-inflammatory cytokines and the expression of endogenous BAF57. These results reveal a novel function of BAF57 as an essential regulator of T cell activation. ntBAF57-ΔPH represents a novel immune-suppressive drug candidate with potential uses in the treatment of autoimmunity and graft rejection.
Collapse
Affiliation(s)
- Jae-Seung Moon
- Department of Biotechnology, Yonsei University College of Life Science and Biotechnology, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
| | - Hong-Jai Lee
- Department of Biotechnology, Yonsei University College of Life Science and Biotechnology, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
| | - Chun-Chang Ho
- Department of Biotechnology, Yonsei University College of Life Science and Biotechnology, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
| | - Jin-Su Shin
- Department of Biotechnology, Yonsei University College of Life Science and Biotechnology, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
| | - Sankar Ghosh
- Department of Microbiology and Immunology, Columbia University, College of Physicians and Surgeons, New York, NY, USA
| | - Jung-Ho Kim
- Good T cells, Inc, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
| | - Sang-Kyou Lee
- Department of Biotechnology, Yonsei University College of Life Science and Biotechnology, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea. .,Good T cells, Inc, 50 Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea.
| |
Collapse
|
13
|
Brg1 promotes liver fibrosis via activation of hepatic stellate cells. Exp Cell Res 2018; 364:191-197. [DOI: 10.1016/j.yexcr.2018.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 02/02/2018] [Accepted: 02/05/2018] [Indexed: 01/21/2023]
|
14
|
Poterlowicz K, Yarker JL, Malashchuk I, Lajoie BR, Mardaryev AN, Gdula MR, Sharov AA, Kohwi-Shigematsu T, Botchkarev VA, Fessing MY. 5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells. PLoS Genet 2017; 13:e1006966. [PMID: 28863138 PMCID: PMC5599062 DOI: 10.1371/journal.pgen.1006966] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 09/14/2017] [Accepted: 08/08/2017] [Indexed: 02/07/2023] Open
Abstract
Mammalian genomes contain several dozens of large (>0.5 Mbp) lineage-specific gene loci harbouring functionally related genes. However, spatial chromatin folding, organization of the enhancer-promoter networks and their relevance to Topologically Associating Domains (TADs) in these loci remain poorly understood. TADs are principle units of the genome folding and represents the DNA regions within which DNA interacts more frequently and less frequently across the TAD boundary. Here, we used Chromatin Conformation Capture Carbon Copy (5C) technology to characterize spatial chromatin interaction network in the 3.1 Mb Epidermal Differentiation Complex (EDC) locus harbouring 61 functionally related genes that show lineage-specific activation during terminal keratinocyte differentiation in the epidermis. 5C data validated by 3D-FISH demonstrate that the EDC locus is organized into several TADs showing distinct lineage-specific chromatin interaction networks based on their transcription activity and the gene-rich or gene-poor status. Correlation of the 5C results with genome-wide studies for enhancer-specific histone modifications (H3K4me1 and H3K27ac) revealed that the majority of spatial chromatin interactions that involves the gene-rich TADs at the EDC locus in keratinocytes include both intra- and inter-TAD interaction networks, connecting gene promoters and enhancers. Compared to thymocytes in which the EDC locus is mostly transcriptionally inactive, these interactions were found to be keratinocyte-specific. In keratinocytes, the promoter-enhancer anchoring regions in the gene-rich transcriptionally active TADs are enriched for the binding of chromatin architectural proteins CTCF, Rad21 and chromatin remodeler Brg1. In contrast to gene-rich TADs, gene-poor TADs show preferential spatial contacts with each other, do not contain active enhancers and show decreased binding of CTCF, Rad21 and Brg1 in keratinocytes. Thus, spatial interactions between gene promoters and enhancers at the multi-TAD EDC locus in skin epithelial cells are cell type-specific and involve extensive contacts within TADs as well as between different gene-rich TADs, forming the framework for lineage-specific transcription.
Collapse
Affiliation(s)
- Krzysztof Poterlowicz
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, United Kingdom
| | - Joanne L. Yarker
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, United Kingdom
| | - Igor Malashchuk
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, United Kingdom
| | - Brian R. Lajoie
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Andrei N. Mardaryev
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, United Kingdom
| | - Michal R. Gdula
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Andrey A. Sharov
- Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Terumi Kohwi-Shigematsu
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, California, United States of America
| | - Vladimir A. Botchkarev
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, United Kingdom
- Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail: (MYF); , (VAB)
| | - Michael Y. Fessing
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, United Kingdom
- * E-mail: (MYF); , (VAB)
| |
Collapse
|
15
|
Archacki R, Yatusevich R, Buszewicz D, Krzyczmonik K, Patryn J, Iwanicka-Nowicka R, Biecek P, Wilczynski B, Koblowska M, Jerzmanowski A, Swiezewski S. Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression. Nucleic Acids Res 2017; 45:3116-3129. [PMID: 27994035 PMCID: PMC5389626 DOI: 10.1093/nar/gkw1273] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/08/2016] [Indexed: 12/23/2022] Open
Abstract
ATP-dependent chromatin remodeling complexes are important regulators of gene expression in Eukaryotes. In plants, SWI/SNF-type complexes have been shown critical for transcriptional control of key developmental processes, growth and stress responses. To gain insight into mechanisms underlying these roles, we performed whole genome mapping of the SWI/SNF catalytic subunit BRM in Arabidopsis thaliana, combined with transcript profiling experiments. Our data show that BRM occupies thousands of sites in Arabidopsis genome, most of which located within or close to genes. Among identified direct BRM transcriptional targets almost equal numbers were up- and downregulated upon BRM depletion, suggesting that BRM can act as both activator and repressor of gene expression. Interestingly, in addition to genes showing canonical pattern of BRM enrichment near transcription start site, many other genes showed a transcription termination site-centred BRM occupancy profile. We found that BRM-bound 3΄ gene regions have promoter-like features, including presence of TATA boxes and high H3K4me3 levels, and possess high antisense transcriptional activity which is subjected to both activation and repression by SWI/SNF complex. Our data suggest that binding to gene terminators and controlling transcription of non-coding RNAs is another way through which SWI/SNF complex regulates expression of its targets.
Collapse
Affiliation(s)
- Rafal Archacki
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Ruslan Yatusevich
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Daniel Buszewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Katarzyna Krzyczmonik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Jacek Patryn
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.,College of Inter-FacultyIndividual Studies in Mathematics and Natural Sciences, Warsaw 02-089, Poland
| | - Roksana Iwanicka-Nowicka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Przemyslaw Biecek
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics,University of Warsaw, Warsaw 02-097, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw 00-662, Poland
| | - Bartek Wilczynski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics,University of Warsaw, Warsaw 02-097, Poland
| | - Marta Koblowska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Andrzej Jerzmanowski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Szymon Swiezewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| |
Collapse
|
16
|
Zhang H, Sun Z, Yu L, Sun J. MiR-139-5p inhibits proliferation and promoted apoptosis of human airway smooth muscle cells by downregulating the Brg1 gene. Respir Physiol Neurobiol 2017; 246:9-16. [PMID: 28711603 DOI: 10.1016/j.resp.2017.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/06/2017] [Accepted: 07/06/2017] [Indexed: 12/27/2022]
Abstract
MicroRNAs have emerged as critical regulators in the pathogenesis of asthma. However, the role of microRNAs in asthma needs to be further elucidated. In this study, we found that miR-139-5p was greatly decreased in airway smooth muscle (ASM) cells from asthmatic humans as well as ASM cells stimulated with cytokines. Overexpression of miR-139-5p markedly suppressed ASM cell proliferation and promoted cell apoptosis, whereas knockdown of miR-139-5p had the opposite effect. Further study verified that Brg1, a chromatin remodeling factor, was upregulated in ASM cells treated with cytokines and acted as a direct target of miR-139-5p. Ectopic expression of Brg1 partially reversed the effect of miR-139-5p on cell proliferation and apoptosis. Moreover, overexpression of Brg1 restored miR-139-5p-induced downregulation of Akt and p70S6K phosphorylation. Together, these data indicate that miR-139-5p may function as a key regulator of ASM cell proliferation and apoptosis, potentially by targeting the Brg1 gene, and thus suggesting a potential role of miR-139-5p in the pathogenesis of asthma.
Collapse
Affiliation(s)
- Huanying Zhang
- Department of Respiration, Affiliated Hospital of Shandong Medical College, Linyi, 276000, China
| | - Zhongmei Sun
- Department of Respiration, Chinese Medicine Hospital of Rizhao City, Rizhao, 276800, China
| | - Lianfeng Yu
- Department of Anatomy, Shandong Medical College, No. 6 Jucai Road, Lanshan District, Linyi, 276000, China.
| | - Jie Sun
- Department of Traditional Chinese Medicine, Shandong Medical College, Linyi, 276000, China
| |
Collapse
|
17
|
Xu W, Xu H, Fang M, Wu X, Xu Y. MKL1 links epigenetic activation of MMP2 to ovarian cancer cell migration and invasion. Biochem Biophys Res Commun 2017; 487:500-508. [PMID: 28385531 DOI: 10.1016/j.bbrc.2017.04.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 04/02/2017] [Indexed: 11/15/2022]
Abstract
Responding to pro-metastatic cues such as low oxygen tension, cancer cells develop several different strategies to facilitate migration and invasion. During this process, expression levels of matrix metalloproteinases (MMPs) are up-regulated so that cancer cells can more easily enter or exit the circulation. In this report we show that message levels of the transcriptional modulator MKL1 were elevated in malignant forms of ovarian cancer tissues in humans when compared to more benign forms accompanying a similar change in MMP2 expression. MKL1 silencing blocked hypoxia-induced migration and invasion of ovarian cancer cells (SKOV-3) in vitro. Over-expression of MKL1 activated while MKL1 depletion repressed MMP2 transcription in SKOV-3 cells. MKL1 was recruited to the MMP2 promoter by NF-κB in response to hypoxia. Mechanistically, MKL1 recruited a histone methyltransferase, SET1, and a chromatin remodeling protein, BRG1, and coordinated their interaction to alter the chromatin structure surrounding the MMP2 promoter leading to transcriptional activation. Both BRG1 and SET1 were essential for hypoxia-induced MMP2 trans-activation. Finally, expression levels of SET1 and BRG1 were positively correlated with ovarian cancer malignancies in humans. Together, our data suggest that MKL1 promotes ovarian cancer cell migration and invasion by epigenetically activating MMP2 transcription.
Collapse
Affiliation(s)
- Wenping Xu
- Department of Pathophysiology, Jiangsu Jiankang Vocational College, Nanjing, China
| | - Huihui Xu
- Key Laboratory of Cardiovascular Disease, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Mingming Fang
- Department of Nursing, Jiangsu Jiankang Vocational College, Nanjing, China
| | - Xiaoyan Wu
- Key Laboratory of Cardiovascular Disease, Department of Pathophysiology, Nanjing Medical University, Nanjing, China.
| | - Yong Xu
- Key Laboratory of Cardiovascular Disease, Department of Pathophysiology, Nanjing Medical University, Nanjing, China.
| |
Collapse
|
18
|
The Role of Epigenetic Regulation in Transcriptional Memory in the Immune System. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 106:43-69. [DOI: 10.1016/bs.apcsb.2016.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
19
|
Liu Z, Lei Q, Wei W, Xiong L, Shi Y, Yan G, Gao C, Ye T, Wang N, Yu L. Synthesis and biological evaluation of (E)-4-(3-arylvinyl-1H-indazol-6-yl)pyrimidin-2-amine derivatives as PLK4 inhibitors for the treatment of breast cancer. RSC Adv 2017. [DOI: 10.1039/c7ra02518a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
SAR explorations identified (E)-4-(3-arylvinyl-1H-indazol-6-yl)pyrimidin-2-amine derivative14ias a potential PLK4 inhibitor with significant anti-breast cancer activityin vitroandin vivo.
Collapse
|
20
|
Abstract
Mutations in enhancer-associated chromatin-modifying components and genomic alterations in non-coding regions of the genome occur frequently in cancer, and other diseases pointing to the importance of enhancer fidelity to ensure proper tissue homeostasis. In this review, I will use specific examples to discuss how mutations in chromatin-modifying factors might affect enhancer activity of disease-relevant genes. I will then consider direct evidence from single nucleotide polymorphisms, small insertions, or deletions but also larger genomic rearrangements such as duplications, deletions, translocations, and inversions of specific enhancers to demonstrate how they have the ability to impact enhancer activity of disease genes including oncogenes and tumor suppressor genes. Considering that the scientific community only fairly recently has begun to focus its attention on "enhancer malfunction" in disease, I propose that multiple new enhancer-regulated and disease-relevant processes will be uncovered in the near future that will constitute the mechanistic basis for novel therapeutic avenues.
Collapse
Affiliation(s)
- Hans-Martin Herz
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| |
Collapse
|
21
|
The Swi3 protein plays a unique role in regulating respiration in eukaryotes. Biosci Rep 2016; 36:BSR20160083. [PMID: 27190130 PMCID: PMC5293592 DOI: 10.1042/bsr20160083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/17/2016] [Indexed: 01/08/2023] Open
Abstract
Recent experimental evidence increasingly shows that the dysregulation of cellular bioenergetics is associated with a wide array of common human diseases, including cancer, neurological diseases and diabetes. Respiration provides a vital source of cellular energy for most eukaryotic cells, particularly high energy demanding cells. However, the understanding of how respiration is globally regulated is very limited. Interestingly, recent evidence suggests that Swi3 is an important regulator of respiration genes in yeast. In this report, we performed an array of biochemical and genetic experiments and computational analysis to directly evaluate the function of Swi3 and its human homologues in regulating respiration. First, we showed, by computational analysis and measurements of oxygen consumption and promoter activities, that Swi3, not Swi2, regulates genes encoding functions involved in respiration and oxygen consumption. Biochemical analysis showed that the levels of mitochondrial respiratory chain complexes were substantially increased in Δswi3 cells, compared with the parent cells. Additionally, our data showed that Swi3 strongly affects haem/oxygen-dependent activation of respiration gene promoters whereas Swi2 affects only the basal, haem-independent activities of these promoters. We found that increased expression of aerobic expression genes is correlated with increased oxygen consumption and growth rates in Δswi3 cells in air. Furthermore, using computational analysis and RNAi knockdown, we showed that the mammalian Swi3 BAF155 and BAF170 regulate respiration in HeLa cells. Together, these experimental and computational data demonstrated that Swi3 and its mammalian homologues are key regulators in regulating respiration.
Collapse
|
22
|
Ohmura S, Mizuno S, Oishi H, Ku CJ, Hermann M, Hosoya T, Takahashi S, Engel JD. Lineage-affiliated transcription factors bind the Gata3 Tce1 enhancer to mediate lineage-specific programs. J Clin Invest 2016; 126:865-78. [PMID: 26808502 DOI: 10.1172/jci83894] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/10/2015] [Indexed: 01/09/2023] Open
Abstract
The transcription factor GATA3 is essential for the genesis and maturation of the T cell lineage, and GATA3 dysregulation has pathological consequences. Previous studies have shown that GATA3 function in T cell development is regulated by multiple signaling pathways and that the Notch nuclear effector, RBP-J, binds specifically to the Gata3 promoter. We previously identified a T cell-specific Gata3 enhancer (Tce1) lying 280 kb downstream from the structural gene and demonstrated in transgenic mice that Tce1 promoted T lymphocyte-specific transcription of reporter genes throughout T cell development; however, it was not clear if Tce1 is required for Gata3 transcription in vivo. Here, we determined that the canonical Gata3 promoter is insufficient for Gata3 transcriptional activation in T cells in vivo, precluding the possibility that promoter binding by a host of previously implicated transcription factors alone is responsible for Gata3 expression in T cells. Instead, we demonstrated that multiple lineage-affiliated transcription factors bind to Tce1 and that this enhancer confers T lymphocyte-specific Gata3 activation in vivo, as targeted deletion of Tce1 in a mouse model abrogated critical functions of this T cell-regulatory element. Together, our data show that Tce1 is both necessary and sufficient for critical aspects of Gata3 T cell-specific transcriptional activity.
Collapse
|
23
|
Laurette P, Strub T, Koludrovic D, Keime C, Le Gras S, Seberg H, Van Otterloo E, Imrichova H, Siddaway R, Aerts S, Cornell RA, Mengus G, Davidson I. Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells. eLife 2015; 4. [PMID: 25803486 PMCID: PMC4407272 DOI: 10.7554/elife.06857] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 03/24/2015] [Indexed: 12/17/2022] Open
Abstract
Microphthalmia-associated transcription factor (MITF) is the master regulator of the melanocyte lineage. To understand how MITF regulates transcription, we used tandem affinity purification and mass spectrometry to define a comprehensive MITF interactome identifying novel cofactors involved in transcription, DNA replication and repair, and chromatin organisation. We show that MITF interacts with a PBAF chromatin remodelling complex comprising BRG1 and CHD7. BRG1 is essential for melanoma cell proliferation in vitro and for normal melanocyte development in vivo. MITF and SOX10 actively recruit BRG1 to a set of MITF-associated regulatory elements (MAREs) at active enhancers. Combinations of MITF, SOX10, TFAP2A, and YY1 bind between two BRG1-occupied nucleosomes thus defining both a signature of transcription factors essential for the melanocyte lineage and a specific chromatin organisation of the regulatory elements they occupy. BRG1 also regulates the dynamics of MITF genomic occupancy. MITF-BRG1 interplay thus plays an essential role in transcription regulation in melanoma.
Collapse
Affiliation(s)
- Patrick Laurette
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Thomas Strub
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Dana Koludrovic
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Céline Keime
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Stéphanie Le Gras
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Hannah Seberg
- University of Iowa College of Medicine, Iowa City, United States
| | | | - Hana Imrichova
- Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, Leuven, Belgium
| | - Robert Siddaway
- Arthur and Sonia Labatt Brain Tumor Research Centre, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, Canada
| | - Stein Aerts
- Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, Leuven, Belgium
| | - Robert A Cornell
- University of Iowa College of Medicine, Iowa City, United States
| | - Gabrielle Mengus
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| |
Collapse
|
24
|
Carissimi C, Laudadio I, Cipolletta E, Gioiosa S, Mihailovich M, Bonaldi T, Macino G, Fulci V. ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites. Nucleic Acids Res 2015; 43:1498-512. [PMID: 25605800 PMCID: PMC4330357 DOI: 10.1093/nar/gku1387] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Argonaute (AGO) proteins have a well-established role in post-transcriptional regulation of gene expression as key component of the RNA silencing pathways. Recent evidence involves AGO proteins in mammalian nuclear processes such as transcription and splicing, though the mechanistic aspects of AGO nuclear functions remain largely elusive. Here, by SILAC-based interaction proteomics, we identify the chromatin-remodelling complex SWI/SNF as a novel AGO2 interactor in human cells. Moreover, we show that nuclear AGO2 is loaded with a novel class of Dicer-dependent short RNAs (sRNAs), that we called swiRNAs, which map nearby the Transcription Start Sites (TSSs) bound by SWI/SNF. The knock-down of AGO2 decreases nucleosome occupancy at the first nucleosome located downstream of TSSs in a swiRNA-dependent manner. Our findings indicate that in human cells AGO2 binds SWI/SNF and a novel class of sRNAs to establish nucleosome occupancy on target TSSs.
Collapse
Affiliation(s)
- Claudia Carissimi
- Dipartimento di Biotecnologie Cellulari ed Ematologia, 'Sapienza' Università di Roma, Rome 00161, Italy
| | - Ilaria Laudadio
- Dipartimento di Biotecnologie Cellulari ed Ematologia, 'Sapienza' Università di Roma, Rome 00161, Italy
| | - Emanuela Cipolletta
- Dipartimento di Biotecnologie Cellulari ed Ematologia, 'Sapienza' Università di Roma, Rome 00161, Italy
| | - Silvia Gioiosa
- Dipartimento di Biotecnologie Cellulari ed Ematologia, 'Sapienza' Università di Roma, Rome 00161, Italy
| | - Marija Mihailovich
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy
| | - Giuseppe Macino
- Dipartimento di Biotecnologie Cellulari ed Ematologia, 'Sapienza' Università di Roma, Rome 00161, Italy
| | - Valerio Fulci
- Dipartimento di Biotecnologie Cellulari ed Ematologia, 'Sapienza' Università di Roma, Rome 00161, Italy
| |
Collapse
|
25
|
Lee GR. Transcriptional regulation of T helper type 2 differentiation. Immunology 2014; 141:498-505. [PMID: 24245687 DOI: 10.1111/imm.12216] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/29/2013] [Accepted: 11/13/2013] [Indexed: 12/20/2022] Open
Abstract
Considerable progress has been made in recent years towards our understanding of the molecular mechanisms of transcriptional regulation of T helper type 2 (Th2) cell differentiation. Additional transcription factors and chromatin-modifying factors were identified and shown to promote Th2 cell differentiation and inhibit differentiation into other subsets. Analyses of mice lacking several cis-regulatory elements have yielded more insight into the regulatory mechanism of Th2 cytokine genes. Gene deletion studies of several chromatin modifiers confirmed their impact on CD4 T-cell differentiation. In addition, recent genome-wide analyses of transcription factor binding and chromatin status revealed unexpected roles of these factors in Th2-cell differentiation. In this review, these recent findings and their implication are summarized.
Collapse
Affiliation(s)
- Gap Ryol Lee
- Department of Life Science, Sogang University, Seoul, Korea
| |
Collapse
|
26
|
Attanasio C, Nord AS, Zhu Y, Blow MJ, Biddie SC, Mendenhall EM, Dixon J, Wright C, Hosseini R, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Afzal V, Ren B, Bernstein BE, Rubin EM, Visel A, Pennacchio LA. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Res 2014; 24:920-9. [PMID: 24752179 PMCID: PMC4032856 DOI: 10.1101/gr.168930.113] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The SMARCA4 (also known as BRG1 in humans) chromatin remodeling factor is critical for establishing lineage-specific chromatin states during early mammalian development. However, the role of SMARCA4 in tissue-specific gene regulation during embryogenesis remains poorly defined. To investigate the genome-wide binding landscape of SMARCA4 in differentiating tissues, we engineered a Smarca4FLAG knock-in mouse line. Using ChIP-seq, we identified ∼51,000 SMARCA4-associated regions across six embryonic mouse tissues (forebrain, hindbrain, neural tube, heart, limb, and face) at mid-gestation (E11.5). The majority of these regions was distal from promoters and showed dynamic occupancy, with most distal SMARCA4 sites (73%) confined to a single or limited subset of tissues. To further characterize these regions, we profiled active and repressive histone marks in the same tissues and examined the intersection of informative chromatin states and SMARCA4 binding. This revealed distinct classes of distal SMARCA4-associated elements characterized by activating and repressive chromatin signatures that were associated with tissue-specific up- or down-regulation of gene expression and relevant active/repressed biological pathways. We further demonstrate the predicted active regulatory properties of SMARCA4-associated elements by retrospective analysis of tissue-specific enhancers and direct testing of SMARCA4-bound regions in transgenic mouse assays. Our results indicate a dual active/repressive function of SMARCA4 at distal regulatory sequences in vivo and support its role in tissue-specific gene regulation during embryonic development.
Collapse
Affiliation(s)
- Catia Attanasio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Alex S Nord
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Yiwen Zhu
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Matthew J Blow
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Simon C Biddie
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; Addenbrooke's Hospital, Cambridge University NHS Trust, Cambridge CB2 0QQ, United Kingdom
| | - Eric M Mendenhall
- HHMI and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Jesse Dixon
- Ludwig Institute for Cancer Research, UCSD School of Medicine, La Jolla, California 92093, USA
| | - Crystal Wright
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Roya Hosseini
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jennifer A Akiyama
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Amy Holt
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Ingrid Plajzer-Frick
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Malak Shoukry
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Veena Afzal
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, UCSD School of Medicine, La Jolla, California 92093, USA
| | - Bradley E Bernstein
- HHMI and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Edward M Rubin
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Axel Visel
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Len A Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| |
Collapse
|
27
|
Bhlhe40 controls cytokine production by T cells and is essential for pathogenicity in autoimmune neuroinflammation. Nat Commun 2014; 5:3551. [PMID: 24699451 PMCID: PMC4016562 DOI: 10.1038/ncomms4551] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 03/04/2014] [Indexed: 01/12/2023] Open
Abstract
TH1 and TH17 cells mediate neuroinflammation in experimental autoimmune encephalomyelitis (EAE), a mouse model of multiple sclerosis. Pathogenic TH cells in EAE must produce the pro-inflammatory cytokine granulocyte-macrophage colony stimulating factor (GM-CSF). TH cell pathogenicity in EAE is also regulated by cell-intrinsic production of the immunosuppressive cytokine interleukin 10 (IL-10). Here, we demonstrate that mice deficient for the basic helix-loop-helix (bHLH) transcription factor Bhlhe40 (Bhlhe40−/−) are resistant to the induction of EAE. Bhlhe40 is required in vivo in a T cell-intrinsic manner, where it positively regulates the production of GM-CSF and negatively regulates the production of IL-10. In vitro, GM-CSF secretion is selectively abrogated in polarized Bhlhe40−/− TH1 and TH17 cells, and these cells show increased production of IL-10. Blockade of IL-10 receptor in Bhlhe40−/− mice renders them susceptible to EAE. These findings identify Bhlhe40 as a critical regulator of autoreactive T cell pathogenicity.
Collapse
|
28
|
Mardaryev AN, Gdula MR, Yarker JL, Emelianov VU, Emelianov VN, Poterlowicz K, Sharov AA, Sharova TY, Scarpa JA, Joffe B, Solovei I, Chambon P, Botchkarev VA, Fessing MY. p63 and Brg1 control developmentally regulated higher-order chromatin remodelling at the epidermal differentiation complex locus in epidermal progenitor cells. Development 2014; 141:101-11. [PMID: 24346698 DOI: 10.1242/dev.103200] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chromatin structural states and their remodelling, including higher-order chromatin folding and three-dimensional (3D) genome organisation, play an important role in the control of gene expression. The role of 3D genome organisation in the control and execution of lineage-specific transcription programmes during the development and differentiation of multipotent stem cells into specialised cell types remains poorly understood. Here, we show that substantial remodelling of the higher-order chromatin structure of the epidermal differentiation complex (EDC), a keratinocyte lineage-specific gene locus on mouse chromosome 3, occurs during epidermal morphogenesis. During epidermal development, the locus relocates away from the nuclear periphery towards the nuclear interior into a compartment enriched in SC35-positive nuclear speckles. Relocation of the EDC locus occurs prior to the full activation of EDC genes involved in controlling terminal keratinocyte differentiation and is a lineage-specific, developmentally regulated event controlled by transcription factor p63, a master regulator of epidermal development. We also show that, in epidermal progenitor cells, p63 directly regulates the expression of the ATP-dependent chromatin remodeller Brg1, which binds to distinct domains within the EDC and is required for relocation of the EDC towards the nuclear interior. Furthermore, Brg1 also regulates gene expression within the EDC locus during epidermal morphogenesis. Thus, p63 and its direct target Brg1 play an essential role in remodelling the higher-order chromatin structure of the EDC and in the specific positioning of this locus within the landscape of the 3D nuclear space, as required for the efficient expression of EDC genes in epidermal progenitor cells during skin development.
Collapse
|
29
|
Prensner JR, Iyer MK, Sahu A, Asangani IA, Cao Q, Patel L, Vergara IA, Davicioni E, Erho N, Ghadessi M, Jenkins RB, Triche TJ, Malik R, Bedenis R, McGregor N, Ma T, Chen W, Han S, Jing X, Cao X, Wang X, Chandler B, Yan W, Siddiqui J, Kunju LP, Dhanasekaran SM, Pienta KJ, Feng FY, Chinnaiyan AM. The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet 2013; 45:1392-8. [PMID: 24076601 PMCID: PMC3812362 DOI: 10.1038/ng.2771] [Citation(s) in RCA: 521] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 08/30/2013] [Indexed: 12/25/2022]
Affiliation(s)
- John R Prensner
- 1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2]
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Lim PS, Li J, Holloway AF, Rao S. Epigenetic regulation of inducible gene expression in the immune system. Immunology 2013; 139:285-93. [PMID: 23521628 DOI: 10.1111/imm.12100] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/07/2013] [Accepted: 03/13/2013] [Indexed: 01/12/2023] Open
Abstract
T cells are exquisitely poised to respond rapidly to pathogens and have proved an instructive model for exploring the regulation of inducible genes. Individual genes respond to antigenic stimulation in different ways, and it has become clear that the interplay between transcription factors and the chromatin platform of individual genes governs these responses. Our understanding of the complexity of the chromatin platform and the epigenetic mechanisms that contribute to transcriptional control has expanded dramatically in recent years. These mechanisms include the presence/absence of histone modification marks, which form an epigenetic signature to mark active or inactive genes. These signatures are dynamically added or removed by epigenetic enzymes, comprising an array of histone-modifying enzymes, including the more recently recognized chromatin-associated signalling kinases. In addition, chromatin-remodelling complexes physically alter the chromatin structure to regulate chromatin accessibility to transcriptional regulatory factors. The advent of genome-wide technologies has enabled characterization of the chromatin landscape of T cells in terms of histone occupancy, histone modification patterns and transcription factor association with specific genomic regulatory regions, generating a picture of the T-cell epigenome. Here, we discuss the multi-layered regulation of inducible gene expression in the immune system, focusing on the interplay between transcription factors, and the T-cell epigenome, including the role played by chromatin remodellers and epigenetic enzymes. We will also use IL2, a key inducible cytokine gene in T cells, as an example of how the different layers of epigenetic mechanisms regulate immune responsive genes during T-cell activation.
Collapse
Affiliation(s)
- Pek Siew Lim
- Discipline of Biomedical Sciences, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, Australia.
| | | | | | | |
Collapse
|
31
|
Bao X, Tang J, Lopez-Pajares V, Tao S, Qu K, Crabtree GR, Khavari PA. ACTL6a enforces the epidermal progenitor state by suppressing SWI/SNF-dependent induction of KLF4. Cell Stem Cell 2013; 12:193-203. [PMID: 23395444 DOI: 10.1016/j.stem.2012.12.014] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 10/05/2012] [Accepted: 12/04/2012] [Indexed: 10/27/2022]
Abstract
Somatic progenitors suppress differentiation to maintain tissue self-renewal. The mammalian SWI/SNF chromatin-remodeling complex regulates nucleosome packaging to control differentiation in embryonic and adult stem cells. Catalytic Brg1 and Brm subunits are required for these processes; however, the roles of SWI/SNF regulatory subunits are not fully understood. Here, we show that ACTL6a/BAF53A modulates the SWI/SNF complex to suppress differentiation in epidermis. Conditional loss of ACTL6a resulted in terminal differentiation, cell-cycle exit, and hypoplasia, whereas ectopic expression of ACTL6a promoted the progenitor state. A significant portion of genes regulated by ACTL6a were found to also be targets of KLF4, a known activator of epidermal differentiation. Mechanistically, we show that ACTL6a prevents SWI/SNF complex binding to promoters of KLF4 and other differentiation genes and that SWI/SNF catalytic subunits are required for full induction of KLF4 targets. Thus, ACTL6a controls the epidermal progenitor state by sequestering SWI/SNF to prevent activation of differentiation programs.
Collapse
Affiliation(s)
- Xiaomin Bao
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | | | | | | | | |
Collapse
|
32
|
Cadet JL, Jayanthi S, McCoy MT, Ladenheim B, Saint-Preux F, Lehrmann E, De S, Becker KG, Brannock C. Genome-wide profiling identifies a subset of methamphetamine (METH)-induced genes associated with METH-induced increased H4K5Ac binding in the rat striatum. BMC Genomics 2013; 14:545. [PMID: 23937714 PMCID: PMC3751638 DOI: 10.1186/1471-2164-14-545] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 07/20/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND METH is an illicit drug of abuse that influences gene expression in the rat striatum. Histone modifications regulate gene transcription. METHODS We therefore used microarray analysis and genome-scale approaches to examine potential relationships between the effects of METH on gene expression and on DNA binding of histone H4 acetylated at lysine 4 (H4K5Ac) in the rat dorsal striatum of METH-naïve and METH-pretreated rats. RESULTS Acute and chronic METH administration caused differential changes in striatal gene expression. METH also increased H4K5Ac binding around the transcriptional start sites (TSSs) of genes in the rat striatum. In order to relate gene expression to histone acetylation, we binned genes of similar expression into groups of 100 genes and proceeded to relate gene expression to H4K5Ac binding. We found a positive correlation between gene expression and H4K5Ac binding in the striatum of control rats. Similar correlations were observed in METH-treated rats. Genes that showed acute METH-induced increased expression in saline-pretreated rats also showed METH-induced increased H4K5Ac binding. The acute METH injection caused similar increases in H4K5Ac binding in METH-pretreated rats, without affecting gene expression to the same degree. Finally, genes that showed METH-induced decreased expression exhibited either decreases or no changes in H4K5Ac binding. CONCLUSION Acute METH injections caused increased gene expression of genes that showed increased H4K5Ac binding near their transcription start sites.
Collapse
Affiliation(s)
- Jean Lud Cadet
- Molecular Neuropsychiatry Research Branch, DHHS/NIH/NIDA Intramural Research Program, 251 Bayview Boulevard, Baltimore, MD 21224, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Imbalzano AN, Imbalzano KM, Nickerson JA. BRG1, a SWI/SNF chromatin remodeling enzyme ATPase, is required for maintenance of nuclear shape and integrity. Commun Integr Biol 2013; 6:e25153. [PMID: 24228137 PMCID: PMC3821668 DOI: 10.4161/cib.25153] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 05/23/2013] [Indexed: 01/11/2023] Open
Abstract
We recently reported that reducing the levels of BRG1, the catalytic subunit of mammalian SWI/SNF chromatin remodeling enzymes, induces alterations in nuclear shape in a breast epithelial cell line. Immunostaining the BRG1 knockdown cells with nuclear lamina antibodies revealed a significantly increased frequency of grooves, or invaginations, in the nuclei. Disruption of each of the major cytoplasmic filament systems (actin, tubulin and cytokeratins) had no impact on the BRG1-dependent changes in nuclear shape, indicating that the observed changes in nuclear morphology are unlikely to be a result of alterations in the integrity of the nuclear-cytoplamic contacts in the cell. We propose that the BRG1-dependent nuclear shape changes reflect a role for the chromatin remodeling enzyme in maintaining the structural integrity of the nucleus via global regulation of chromatin structure and dynamics within the nucleus.
Collapse
Affiliation(s)
- Anthony N Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester, MA USA
| | | | | |
Collapse
|
34
|
Melamed A, Laydon DJ, Gillet NA, Tanaka Y, Taylor GP, Bangham CRM. Genome-wide determinants of proviral targeting, clonal abundance and expression in natural HTLV-1 infection. PLoS Pathog 2013; 9:e1003271. [PMID: 23555266 PMCID: PMC3605240 DOI: 10.1371/journal.ppat.1003271] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/10/2013] [Indexed: 12/20/2022] Open
Abstract
The regulation of proviral latency is a central problem in retrovirology. We postulate that the genomic integration site of human T lymphotropic virus type 1 (HTLV-1) determines the pattern of expression of the provirus, which in turn determines the abundance and pathogenic potential of infected T cell clones in vivo. We recently developed a high-throughput method for the genome-wide amplification, identification and quantification of proviral integration sites. Here, we used this protocol to test two hypotheses. First, that binding sites for transcription factors and chromatin remodelling factors in the genome flanking the proviral integration site of HTLV-1 are associated with integration targeting, spontaneous proviral expression, and in vivo clonal abundance. Second, that the transcriptional orientation of the HTLV-1 provirus relative to that of the nearest host gene determines spontaneous proviral expression and in vivo clonal abundance. Integration targeting was strongly associated with the presence of a binding site for specific host transcription factors, especially STAT1 and p53. The presence of the chromatin remodelling factors BRG1 and INI1 and certain host transcription factors either upstream or downstream of the provirus was associated respectively with silencing or spontaneous expression of the provirus. Cells expressing HTLV-1 Tax protein were significantly more frequent in clones of low abundance in vivo. We conclude that transcriptional interference and chromatin remodelling are critical determinants of proviral latency in natural HTLV-1 infection.
Collapse
Affiliation(s)
- Anat Melamed
- Department of Immunology, Wright-Fleming Institute, Imperial College London, London, United Kingdom
| | - Daniel J. Laydon
- Department of Immunology, Wright-Fleming Institute, Imperial College London, London, United Kingdom
| | - Nicolas A. Gillet
- Department of Immunology, Wright-Fleming Institute, Imperial College London, London, United Kingdom
- Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics (GIGA) of University of Liège (ULg), Liège, Belgium
| | - Yuetsu Tanaka
- Graduate School and Faculty of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Graham P. Taylor
- Department of Genitourinary Medicine and Communicable Diseases, Wright-Fleming Institute, Imperial College London, London, United Kingdom
| | - Charles R. M. Bangham
- Department of Immunology, Wright-Fleming Institute, Imperial College London, London, United Kingdom
- * E-mail:
| |
Collapse
|
35
|
Calo E, Wysocka J. Modification of enhancer chromatin: what, how, and why? Mol Cell 2013; 49:825-37. [PMID: 23473601 PMCID: PMC3857148 DOI: 10.1016/j.molcel.2013.01.038] [Citation(s) in RCA: 998] [Impact Index Per Article: 90.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/28/2013] [Accepted: 01/30/2013] [Indexed: 01/01/2023]
Abstract
Emergence of form and function during embryogenesis arises in large part through cell-type- and cell-state-specific variation in gene expression patterns, mediated by specialized cis-regulatory elements called enhancers. Recent large-scale epigenomic mapping revealed unexpected complexity and dynamics of enhancer utilization patterns, with 400,000 putative human enhancers annotated by the ENCODE project alone. These large-scale efforts were largely enabled through the understanding that enhancers share certain stereotypical chromatin features. However, an important question still lingers: what is the functional significance of enhancer chromatin modification? Here we give an overview of enhancer-associated modifications of histones and DNA and discuss enzymatic activities involved in their dynamic deposition and removal. We describe potential downstream effectors of these marks and propose models for exploring functions of chromatin modification in regulating enhancer activity during development.
Collapse
Affiliation(s)
- Eliezer Calo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | |
Collapse
|
36
|
Chaiyachati BH, Jani A, Wan Y, Huang H, Flavell R, Chi T. BRG1-mediated immune tolerance: facilitation of Treg activation and partial independence of chromatin remodelling. EMBO J 2013; 32:395-408. [PMID: 23321680 DOI: 10.1038/emboj.2012.350] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 12/05/2012] [Indexed: 02/02/2023] Open
Abstract
Treg activation in response to environmental cues is necessary for regulatory T cells (Tregs) to suppress inflammation, but little is known about the transcription mechanisms controlling Treg activation. We report that despite the known proinflammatory role of the chromatin-remodelling factor BRG1 in CD4 cells, deleting Brg1 in all αβ T cell lineages led to fatal inflammation, which reflected essential roles of BRG1 in Tregs. Brg1 deletion impaired Treg activation, concomitant with the onset of the inflammation. Remarkably, as the inflammation progressed, Tregs became increasingly activated, but the activation levels could not catch up with the severity of inflammation. In vitro assays indicate that BRG1 regulates a subset of TCR target genes including multiple chemokine receptor genes. Finally, using a method that can create littermates bearing either a tissue-specific point mutation or deletion, we found the BRG1 ATPase activity partially dispensable for BRG1 function. Collectively, these data suggest that BRG1 acts in part via remodelling-independent functions to sensitize Tregs to inflammatory cues, thus allowing Tregs to promptly and effectively suppress autoimmunity.
Collapse
Affiliation(s)
- Barbara H Chaiyachati
- Department of Immunobiology, Yale University Medical School, New Haven, CT 06520, USA
| | | | | | | | | | | |
Collapse
|
37
|
Abstract
Different cell types within a single organism are generally distinguished by strikingly different patterns of gene expression, which are dynamic throughout development and adult life. Distal enhancer elements are key drivers of spatiotemporal specificity in gene regulation. Often located tens of kilobases from their target promoters and functioning in an orientation-independent manner, the identification of bona fide enhancers has proved a formidable challenge. With the development of ChIP-seq, global cataloging of putative enhancers has become feasible. Here, we review the current understanding of the chromatin landscape at enhancers and how these chromatin features enable robust identification of tissue-specific enhancers.
Collapse
Affiliation(s)
- Gabriel E Zentner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | | |
Collapse
|
38
|
Euskirchen G, Auerbach RK, Snyder M. SWI/SNF chromatin-remodeling factors: multiscale analyses and diverse functions. J Biol Chem 2012; 287:30897-905. [PMID: 22952240 PMCID: PMC3438922 DOI: 10.1074/jbc.r111.309302] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromatin-remodeling enzymes play essential roles in many biological processes, including gene expression, DNA replication and repair, and cell division. Although one such complex, SWI/SNF, has been extensively studied, new discoveries are still being made. Here, we review SWI/SNF biochemistry; highlight recent genomic and proteomic advances; and address the role of SWI/SNF in human diseases, including cancer and viral infections. These studies have greatly increased our understanding of complex nuclear processes.
Collapse
Affiliation(s)
- Ghia Euskirchen
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA
| | | | | |
Collapse
|
39
|
|
40
|
Chung CW. Small molecule bromodomain inhibitors: extending the druggable genome. PROGRESS IN MEDICINAL CHEMISTRY 2012; 51:1-55. [PMID: 22520470 DOI: 10.1016/b978-0-12-396493-9.00001-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chun-Wa Chung
- Computational and Structural Sciences, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
| |
Collapse
|
41
|
Maston GA, Landt SG, Snyder M, Green MR. Characterization of enhancer function from genome-wide analyses. Annu Rev Genomics Hum Genet 2012; 13:29-57. [PMID: 22703170 DOI: 10.1146/annurev-genom-090711-163723] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There has been a recent surge in the use of genome-wide methodologies to identify and annotate the transcriptional regulatory elements in the human genome. Here we review some of these methodologies and the conceptual insights about transcription regulation that have been gained from the use of genome-wide studies. It has become clear that the binding of transcription factors is itself a highly regulated process, and binding does not always appear to have functional consequences. Numerous properties have now been associated with regulatory elements that may be useful in their identification. Several aspects of enhancer function have been shown to be more widespread than was previously appreciated, including the highly combinatorial nature of transcription factor binding, the postinitiation regulation of many target genes, and the binding of enhancers at early stages to maintain their competence during development. Going forward, the integration of multiple genome-wide data sets should become a standard approach to elucidate higher-order regulatory interactions.
Collapse
Affiliation(s)
- Glenn A Maston
- Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | | | | | | |
Collapse
|
42
|
Immediate-early gene activation by the MAPK pathways: what do and don't we know? Biochem Soc Trans 2012; 40:58-66. [PMID: 22260666 DOI: 10.1042/bst20110636] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The study of IE (immediate-early) gene activation mechanisms has provided numerous paradigms for how transcription is controlled in response to extracellular signalling. Many of the findings have been derived from investigating one of the IE genes, FOS, and the models extrapolated to regulatory mechanisms for other IE genes. However, whereas the overall principles of activation appear similar, recent evidence suggests that the underlying mechanistic details may differ depending on cell type, cellular stimulus and IE gene under investigation. In the present paper, we review recent advances in our understanding of IE gene transcription, chiefly focusing on FOS and its activation by ERK (extracellular-signal-regulated kinase) MAPK (mitogen-activated protein kinase) pathway signalling. We highlight important fundamental regulatory principles, but also illustrate the gaps in our current knowledge and the potential danger in making assumptions based on extrapolation from disparate studies.
Collapse
|
43
|
Romero OA, Setien F, John S, Gimenez-Xavier P, Gómez-López G, Pisano D, Condom E, Villanueva A, Hager GL, Sanchez-Cespedes M. The tumour suppressor and chromatin-remodelling factor BRG1 antagonizes Myc activity and promotes cell differentiation in human cancer. EMBO Mol Med 2012; 4:603-16. [PMID: 22407764 PMCID: PMC3407948 DOI: 10.1002/emmm.201200236] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 02/27/2012] [Accepted: 02/29/2012] [Indexed: 12/30/2022] Open
Abstract
BRG1, a member of the SWI/SNF complex, is mutated in cancer, but it is unclear how it promotes tumourigenesis. We report that re-expression of BRG1 in lung cancer cells up-regulates lung-specific transcripts, restoring the gene expression signature of normal lung. Using cell lines from several cancer types we found that those lacking BRG1 do not respond to retinoic acid (RA) or glucocorticoids (GC), while restoration of BRG1 restores sensitivity. Conversely, in SH-SY5Y cells, a paradigm of RA-dependent differentiation, abrogation of BRG1 prevented the response to RA. Further, our data suggest an antagonistic functional connection between BRG1 and MYC, whereby, refractoriness to RA and GC by BRG1 inactivation involves deregulation of MYC activity. Mechanistically, some of these effects are mediated by BRG1 binding to MYC and MYC-target promoters. The BRG1-MYC antagonism was also evident in primary tumours. Finally, BRG1 restoration significantly dampened invasion and progression and decreased MYC in lung cancer cells orthotopically implanted in nude mice. Thus, BRG1 inactivation enables cancer cells to sustain undifferentiated gene expression programs and prevent its response to environmental stimuli.
Collapse
Affiliation(s)
- Octavio A Romero
- Genes and Cancer Group, Cancer Epigenetics and Biology Program-PEBC, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
Gene-distal cis-regulatory sequences, such as enhancers, are key contributors of tissue-specific gene expression. In particular, enhancers can be located up to hundreds of kilobases from the promoters that they control, making their identification challenging. Thanks to the recent technological advances to map histone modifications and chromatin-associated factors genome-wide, several studies have begun to characterize chromatin signatures of active enhancers. Here, we discuss some of these results and how they provide new insights into the tissue-specific organization of enhancer repertoires.
Collapse
|
45
|
Ottaviani D, Lever E, Mao S, Christova R, Ogunkolade BW, Jones TA, Szary J, Aarum J, Mumin MA, Pieri CA, Krawetz SA, Sheer D. CTCF binds to sites in the major histocompatibility complex that are rapidly reconfigured in response to interferon-gamma. Nucleic Acids Res 2012; 40:5262-70. [PMID: 22367884 PMCID: PMC3384298 DOI: 10.1093/nar/gks158] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Activation of the major histocompatibility complex (MHC) by interferon-gamma (IFN−γ) is a fundamental step in the adaptive immune response to pathogens. Here, we show that reorganization of chromatin loop domains in the MHC is evident within the first 30 min of IFN−γ treatment of fibroblasts, and that further dynamic alterations occur up to 6 h. These very rapid changes occur at genomic sites which are occupied by CTCF and are close to IFN−γ-inducible MHC genes. Early responses to IFN−γ are thus initiated independently of CIITA, the master regulator of MHC class II genes and prepare the MHC for subsequent induction of transcription.
Collapse
Affiliation(s)
- Diego Ottaviani
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Newark St, London E1 2AT, UK
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Wurster AL, Precht P, Becker KG, Wood WH, Zhang Y, Wang Z, Pazin MJ. IL-10 transcription is negatively regulated by BAF180, a component of the SWI/SNF chromatin remodeling enzyme. BMC Immunol 2012; 13:9. [PMID: 22336179 PMCID: PMC3313858 DOI: 10.1186/1471-2172-13-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 02/15/2012] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND SWI/SNF chromatin remodeling enzymes play a critical role in the development of T helper lymphocytes, including Th2 cells, and directly program chromatin structure at Th2 cytokine genes. Different versions of SWI/SNF complexes, including BAF and PBAF, have been described based on unique subunit composition. However, the relative role of BAF and PBAF in Th cell function and cytokine expression has not been reported. RESULTS Here we examine the role of the PBAF SWI/SNF complex in Th cell development and gene expression using mice deficient for a PBAF-specific component, BAF180. We find that T cell development in the thymus and lymphoid periphery is largely normal when the BAF180 gene is deleted late in thymic development. However, BAF180-deficient Th2 cells express high levels of the immunoregulatory cytokine IL-10. BAF180 binds directly to regulatory elements in the Il-10 locus but is replaced by BAF250 BAF complexes in the absence of BAF180, resulting in increased histone acetylation and CBP recruitment to the IL-10 locus. CONCLUSIONS These results demonstrate that BAF180 is a repressor of IL-10 transcription in Th2 cells and suggest that the differential recruitment of different SWI/SNF subtypes can have direct consequences on chromatin structure and gene transcription.
Collapse
Affiliation(s)
- Andrea L Wurster
- Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, USA
| | | | | | | | | | | | | |
Collapse
|
47
|
Abstract
One of the best studied systems for mammalian chromatin remodeling is transcriptional regulation during T cell development. The variety of these studies have led to important findings in T cell gene regulation and cell fate determination. Importantly, these findings have also advanced our knowledge of the function of remodeling enzymes in mammalian gene regulation. First we briefly present biochemical and cell-free analysis of 3 types of ATP dependent remodeling enzymes (SWI/SNF, Mi2, and ISWI) to construct an intellectual framework to understand how these enzymes might be working. Second, we compare and contrast the function of these enzymes during early (thymic) and late (peripheral) T cell development. Finally, we examine some of the gaps in our present understanding.
Collapse
Affiliation(s)
- Andrea L. Wurster
- Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, USA
| | - Michael J. Pazin
- Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, USA
| |
Collapse
|
48
|
Potts RC, Zhang P, Wurster AL, Precht P, Mughal MR, Wood WH, Zhang Y, Becker KG, Mattson MP, Pazin MJ. CHD5, a brain-specific paralog of Mi2 chromatin remodeling enzymes, regulates expression of neuronal genes. PLoS One 2011; 6:e24515. [PMID: 21931736 PMCID: PMC3172237 DOI: 10.1371/journal.pone.0024515] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 08/12/2011] [Indexed: 11/19/2022] Open
Abstract
CHD5 is frequently deleted in neuroblastoma and is a tumor suppressor gene. However, little is known about the role of CHD5 other than it is homologous to chromatin remodeling ATPases. We found CHD5 mRNA was restricted to the brain; by contrast, most remodeling ATPases were broadly expressed. CHD5 protein isolated from mouse brain was associated with HDAC2, p66ß, MTA3 and RbAp46 in a megadalton complex. CHD5 protein was detected in several rat brain regions and appeared to be enriched in neurons. CHD5 protein was predominantly nuclear in primary rat neurons and brain sections. Microarray analysis revealed genes that were upregulated and downregulated when CHD5 was depleted from primary neurons. CHD5 depletion altered expression of neuronal genes, transcription factors, and brain-specific subunits of the SWI/SNF remodeling enzyme. Expression of gene sets linked to aging and Alzheimer's disease were strongly altered by CHD5 depletion from primary neurons. Chromatin immunoprecipitation revealed CHD5 bound to these genes, suggesting the regulation was direct. Together, these results indicate that CHD5 protein is found in a NuRD-like multi-protein complex. CHD5 expression is restricted to the brain, unlike the closely related family members CHD3 and CHD4. CHD5 regulates expression of neuronal genes, cell cycle genes and remodeling genes. CHD5 is linked to regulation of genes implicated in aging and Alzheimer's disease.
Collapse
Affiliation(s)
- Rebecca Casaday Potts
- Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Peisu Zhang
- Laboratory of Neuroscience, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Andrea L. Wurster
- Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Patricia Precht
- Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Mohamed R. Mughal
- Laboratory of Neuroscience, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States of America
| | - William H. Wood
- Research Resources Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Yonqing Zhang
- Research Resources Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Kevin G. Becker
- Research Resources Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Mark P. Mattson
- Laboratory of Neuroscience, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Michael J. Pazin
- Laboratory of Molecular Biology and Immunology, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|
49
|
Application of ChIP-Seq and related techniques to the study of immune function. Immunity 2011; 34:830-42. [PMID: 21703538 DOI: 10.1016/j.immuni.2011.06.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Indexed: 01/02/2023]
Abstract
Behaviors observed at the cellular level such as development and acquisition of effector functions by immune cells result from transcriptional changes. The biochemical mediators of transcription are sequence-specific transcription factors (TFs), chromatin modifying enzymes, and chromatin, the complex of DNA and histone proteins. Covalent modification of DNA and histones, also termed epigenetic modification, influences the accessibility of target sequences for transcription factors on chromatin and the expression of linked genes required for immune functions. Genome-wide techniques such as ChIP-Seq have described the entire "cistrome" of transcription factors involved in specific developmental steps of B and T cells and started to define specific immune responses in terms of the binding profiles of critical effectors and epigenetic modification patterns. Current data suggest that both promoters and enhancers are prepared for action at different stages of activation by epigenetic modification through distinct transcription factors in different cells.
Collapse
|
50
|
Abstract
Signal transducer and activator of transcription (STAT) proteins are critical mediators of cytokine signaling. Among the seven STAT proteins, STAT6 is activated by IL-4 and IL-13 and plays a predominant role in the immune system. However, there is increasing evidence that STAT6 may function in other tissues and organ systems. IL-4, IL-13, and STAT6 promote humoral immunity, clearance of helminthic parasites as well as the pathogenesis of allergic disorders like asthma, food allergies, and atopic dermatitis. In this review, we will describe our current understanding of the biological functions of STAT6 and summarize recent advances in understanding the molecular mechanisms by which STAT6 regulates transcription.
Collapse
Affiliation(s)
- Shreevrat Goenka
- HB Wells Center of Pediatric Research, Department of Pediatrics, Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, 46202, USA.
| | | |
Collapse
|