1
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Wang Z, Tian W, Guo Y, Wang D, Zhang Y, Zhi Y, Li D, Li W, Li Z, Jiang R, Han R, Sun G, Li G, Tian Y, Li H, Kang X, Liu X. Dynamic alternations of three-dimensional chromatin architecture contribute to phenotypic characteristics of breast muscle in chicken. Commun Biol 2024; 7:910. [PMID: 39068219 PMCID: PMC11283561 DOI: 10.1038/s42003-024-06599-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 07/17/2024] [Indexed: 07/30/2024] Open
Abstract
Breast muscle growth rate and intramuscular fat (IMF) content show apparent differences between fast-growing broilers and slow-growing indigenous chickens. However, the underlying genetic basis of these phenotypic characteristics remains elusive. In this study, we investigate the dynamic alterations of three-dimensional genome architecture and chromatin accessibility in breast muscle across four key developmental stages from embryo to starter chick in Arbor Acres (AA) broilers and Yufen (YF) indigenous chickens. The limited breed-specifically up-regulated genes (Bup-DEGs) are embedded in breed-specific A compartment, while a majority of the Bup-DEGs involving myogenesis and adipogenesis are regulated by the breed-specific TAD reprogramming. Chromatin loops allow distal accessible regions to interact with myogenic genes, and those loops share an extremely low similarity between chicken with different growth rate. Moreover, AA-specific loop interactions promote the expression of 40 Bup-DEGs, such as IGF1, which contributes to myofiber hypertrophy. YF-specific loop interactions or distal accessible regions lead to increased expression of 5 Bup-DEGs, including PIGO, PEMT, DHCR7, TMEM38B, and DHDH, which contribute to IMF deposition. These results help elucidate the regulation of breast muscle growth and IMF deposition in chickens.
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Affiliation(s)
- Zhang Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Weihua Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yulong Guo
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dandan Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yanyan Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yihao Zhi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Donghua Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research, Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research, Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research, Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research, Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research, Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research, Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research, Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research, Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China.
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China.
- International Joint Research, Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China.
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China.
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China.
- International Joint Research, Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China.
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China.
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China.
- International Joint Research, Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China.
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2
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Wang B, Bian Q. Regulation of 3D genome organization during T cell activation. FEBS J 2024. [PMID: 38944686 DOI: 10.1111/febs.17211] [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: 01/04/2024] [Revised: 04/23/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024]
Abstract
Within the three-dimensional (3D) nuclear space, the genome organizes into a series of orderly structures that impose important influences on gene regulation. T lymphocytes, crucial players in adaptive immune responses, undergo intricate transcriptional remodeling upon activation, leading to differentiation into specific effector and memory T cell subsets. Recent evidence suggests that T cell activation is accompanied by dynamic changes in genome architecture at multiple levels, providing a unique biological context to explore the functional relevance and molecular mechanisms of 3D genome organization. Here, we summarize recent advances that link the reorganization of genome architecture to the remodeling of transcriptional programs and conversion of cell fates during T cell activation and differentiation. We further discuss how various chromatin architecture regulators, including CCCTC-binding factor and several transcription factors, collectively modulate the genome architecture during this process.
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Affiliation(s)
- Bao Wang
- Shanghai lnstitute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
| | - Qian Bian
- Shanghai lnstitute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
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3
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Banerjee S, Sanyal S, Hodawadekar S, Naiyer S, Bano N, Banerjee A, Rhoades J, Dong D, Allman D, Atchison ML. Unusual lineage plasticity revealed by YY1 knockout in pro-B cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586298. [PMID: 38586061 PMCID: PMC10996465 DOI: 10.1101/2024.03.22.586298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
During B cell development, cells progress through multiple developmental stages with the pro-B cell stage defining commitment to the B cell lineage. YY1 is a ubiquitous transcription factor that is capable of both activation and repression functions. We find here that knockout of YY1 at the pro-B cell stage eliminates B lineage commitment. YY1 knockout pro-B cells can generate T lineage cells in vitro using the OP9- DL4 feeder system, as well as in vivo after injection into sub-lethally irradiated Rag1 -/- mice. These T lineage-like cells lose their B lineage transcript profile and gain a T cell lineage profile. Single cell-RNA-seq experiments showed that as YY1 knockout pro-B cells transition into T lineage cells, various cell clusters adopt transcript profiles representing a multiplicity of hematopoietic lineages indicating unusual lineage plasticity. Given the ubiquitous nature of YY1 and its dual activation and repression functions, YY1 likely regulates commitment in multiple cell lineages.
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4
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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.
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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
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5
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Salataj E, Spilianakis CG, Chaumeil J. Single-cell detection of primary transcripts, their genomic loci and nuclear factors by 3D immuno-RNA/DNA FISH in T cells. Front Immunol 2023; 14:1156077. [PMID: 37215121 PMCID: PMC10193148 DOI: 10.3389/fimmu.2023.1156077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Over the past decades, it has become increasingly clear that higher order chromatin folding and organization within the nucleus is involved in the regulation of genome activity and serves as an additional epigenetic mechanism that modulates cellular functions and gene expression programs in diverse biological processes. In particular, dynamic allelic interactions and nuclear locations can be of functional importance during the process of lymphoid differentiation and the regulation of immune responses. Analyses of the proximity between chromatin and/or nuclear regions can be performed on populations of cells with high-throughput sequencing approaches such as chromatin conformation capture ("3C"-based) or DNA adenine methyltransferase identification (DamID) methods, or, in individual cells, by the simultaneous visualization of genomic loci, their primary transcripts and nuclear compartments within the 3-dimensional nuclear space using Fluorescence In Situ Hybridization (FISH) and immunostaining. Here, we present a detailed protocol to simultaneously detect nascent RNA transcripts (3D RNA FISH), their genomic loci (3D DNA FISH) and/or their chromosome territories (CT paint DNA FISH) combined with the antibody-based detection of various nuclear factors (immunofluorescence). We delineate the application and effectiveness of this robust and reproducible protocol in several murine T lymphocyte subtypes (from differentiating thymic T cells, to activated splenic and peripheral T cells) as well as other murine cells, including embryonic stem cells, B cells, megakaryocytes and macrophages.
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Affiliation(s)
- Eralda Salataj
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Charalampos G. Spilianakis
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Julie Chaumeil
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
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6
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Michieletto MF, Tello-Cajiao JJ, Mowel WK, Chandra A, Yoon S, Joannas L, Clark ML, Jimenez MT, Wright JM, Lundgren P, Williams A, Thaiss CA, Vahedi G, Henao-Mejia J. Multiscale 3D genome organization underlies ILC2 ontogenesis and allergic airway inflammation. Nat Immunol 2023; 24:42-54. [PMID: 36050414 PMCID: PMC10134076 DOI: 10.1038/s41590-022-01295-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 07/18/2022] [Indexed: 01/06/2023]
Abstract
Innate lymphoid cells (ILCs) are well-characterized immune cells that play key roles in host defense and tissue homeostasis. Yet, how the three-dimensional (3D) genome organization underlies the development and functions of ILCs is unknown. Herein, we carried out an integrative analysis of the 3D genome structure, chromatin accessibility and gene expression in mature ILCs. Our results revealed that the local 3D configuration of the genome is rewired specifically at loci associated with ILC biology to promote their development and functional differentiation. Importantly, we demonstrated that the ontogenesis of ILC2s and the progression of allergic airway inflammation are determined by a unique local 3D configuration of the region containing the ILC-lineage-defining factor Id2, which is characterized by multiple interactions between the Id2 promoter and distal regulatory elements bound by the transcription factors GATA-3 and RORα, unveiling the mechanism whereby the Id2 expression is specifically controlled in group 2 ILCs.
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Affiliation(s)
- Michaël F Michieletto
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John J Tello-Cajiao
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Walter K Mowel
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aditi Chandra
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sora Yoon
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leonel Joannas
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Megan L Clark
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Monica T Jimenez
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jasmine M Wright
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrick Lundgren
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Adam Williams
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Christoph A Thaiss
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Golnaz Vahedi
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jorge Henao-Mejia
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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7
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Cuartero S, Stik G, Stadhouders R. Three-dimensional genome organization in immune cell fate and function. Nat Rev Immunol 2022; 23:206-221. [PMID: 36127477 DOI: 10.1038/s41577-022-00774-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Immune cell development and activation demand the precise and coordinated control of transcriptional programmes. Three-dimensional (3D) organization of the genome has emerged as an important regulator of chromatin state, transcriptional activity and cell identity by facilitating or impeding long-range genomic interactions among regulatory elements and genes. Chromatin folding thus enables cell type-specific and stimulus-specific transcriptional responses to extracellular signals, which are essential for the control of immune cell fate, for inflammatory responses and for generating a diverse repertoire of antigen receptor specificities. Here, we review recent findings connecting 3D genome organization to the control of immune cell differentiation and function, and discuss how alterations in genome folding may lead to immune dysfunction and malignancy.
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Affiliation(s)
- Sergi Cuartero
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain. .,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
| | - Grégoire Stik
- Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands. .,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
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8
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Azagra A, Meler A, de Barrios O, Tomás-Daza L, Collazo O, Monterde B, Obiols M, Rovirosa L, Vila-Casadesús M, Cabrera-Pasadas M, Gusi-Vives M, Graf T, Varela I, Sardina JL, Javierre BM, Parra M. The HDAC7-TET2 epigenetic axis is essential during early B lymphocyte development. Nucleic Acids Res 2022; 50:8471-8490. [PMID: 35904805 PMCID: PMC9410891 DOI: 10.1093/nar/gkac619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 06/23/2022] [Accepted: 07/05/2022] [Indexed: 12/02/2022] Open
Abstract
Correct B cell identity at each stage of cellular differentiation during B lymphocyte development is critically dependent on a tightly controlled epigenomic landscape. We previously identified HDAC7 as an essential regulator of early B cell development and its absence leads to a drastic block at the pro-B to pre-B cell transition. More recently, we demonstrated that HDAC7 loss in pro-B-ALL in infants associates with a worse prognosis. Here we delineate the molecular mechanisms by which HDAC7 modulates early B cell development. We find that HDAC7 deficiency drives global chromatin de-condensation, histone marks deposition and deregulates other epigenetic regulators and mobile elements. Specifically, the absence of HDAC7 induces TET2 expression, which promotes DNA 5-hydroxymethylation and chromatin de-condensation. HDAC7 deficiency also results in the aberrant expression of microRNAs and LINE-1 transposable elements. These findings shed light on the mechanisms by which HDAC7 loss or misregulation may lead to B cell–based hematological malignancies.
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Affiliation(s)
- Alba Azagra
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain.,Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
| | - Ainara Meler
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain.,Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
| | - Oriol de Barrios
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain.,Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
| | - Laureano Tomás-Daza
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain.,Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Olga Collazo
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain.,Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
| | - Beatriz Monterde
- Instituto de Biomedicina y Biotecnología de Cantabria. Universidad de Cantabria-CSIC. 39011 Santander, Spain
| | - Mireia Obiols
- Epigenetic Control of Haematopoiesis Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain
| | - Llorenç Rovirosa
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain
| | - Maria Vila-Casadesús
- Centre for Genomic Regulation (CRG), PRBB Building, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Mónica Cabrera-Pasadas
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain.,Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Mar Gusi-Vives
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation (CRG), PRBB Building, Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria. Universidad de Cantabria-CSIC. 39011 Santander, Spain
| | - José Luis Sardina
- Epigenetic Control of Haematopoiesis Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain
| | - Biola M Javierre
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain
| | - Maribel Parra
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain.,Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
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9
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Papadogkonas G, Papamatheakis DA, Spilianakis C. 3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells. Front Immunol 2022; 13:921375. [PMID: 35812421 PMCID: PMC9257000 DOI: 10.3389/fimmu.2022.921375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/26/2022] [Indexed: 12/12/2022] Open
Abstract
In the heart of innate and adaptive immunity lies the proper spatiotemporal development of several immune cell lineages. Multiple studies have highlighted the necessity of epigenetic and transcriptional regulation in cell lineage specification. This mode of regulation is mediated by transcription factors and chromatin remodelers, controlling developmentally essential gene sets. The core of transcription and epigenetic regulation is formulated by different epigenetic modifications determining gene expression. Apart from “classic” epigenetic modifications, 3D chromatin architecture is also purported to exert fundamental roles in gene regulation. Chromatin conformation both facilitates cell-specific factor binding at specified regions and is in turn modified as such, acting synergistically. The interplay between global and tissue-specific protein factors dictates the epigenetic landscape of T and innate lymphoid cell (ILC) lineages. The expression of global genome organizers such as CTCF, YY1, and the cohesin complexes, closely cooperate with tissue-specific factors to exert cell type-specific gene regulation. Special AT-rich binding protein 1 (SATB1) is an important tissue-specific genome organizer and regulator controlling both long- and short-range chromatin interactions. Recent indications point to SATB1’s cooperation with the aforementioned factors, linking global to tissue-specific gene regulation. Changes in 3D genome organization are of vital importance for proper cell development and function, while disruption of this mechanism can lead to severe immuno-developmental defects. Newly emerging data have inextricably linked chromatin architecture deregulation to tissue-specific pathophysiological phenotypes. The combination of these findings may shed light on the mechanisms behind pathological conditions.
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Affiliation(s)
- George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
- *Correspondence: Charalampos Spilianakis,
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10
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Miura H, Hiratani I. Cell cycle dynamics and developmental dynamics of the 3D genome: toward linking the two timescales. Curr Opin Genet Dev 2022; 73:101898. [PMID: 35026526 DOI: 10.1016/j.gde.2021.101898] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/11/2021] [Accepted: 12/15/2021] [Indexed: 11/03/2022]
Abstract
In the mammalian cell nucleus, chromosomes are folded differently in interphase and mitosis. Interphase chromosomes are relatively decondensed and display at least two unique layers of higher-order organization: topologically associating domains (TADs) and cell-type-specific A/B compartments, which correlate well with early/late DNA replication timing (RT). In mitosis, these structures rapidly disappear but are gradually reconstructed during G1 phase, coincident with the establishment of the RT program. However, these structures also change dynamically during cell differentiation and reprogramming, and yet we are surprisingly ignorant about the relationship between their cell cycle dynamics and developmental dynamics. In this review, we summarize the recent findings on this topic, discuss how these two processes might be coordinated with each other and its potential significance.
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Affiliation(s)
- Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047 Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047 Japan.
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11
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Kodali S, Meyer-Nava S, Landry S, Chakraborty A, Rivera-Mulia JC, Feng W. Epigenomic signatures associated with spontaneous and replication stress-induced DNA double strand breaks. Front Genet 2022; 13:907547. [PMID: 36506300 PMCID: PMC9730818 DOI: 10.3389/fgene.2022.907547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Common fragile sites (CFSs) are specific regions of all individuals' genome that are predisposed to DNA double strand breaks (DSBs) and undergo subsequent rearrangements. CFS formation can be induced in vitro by mild level of DNA replication stress, such as DNA polymerase inhibition or nucleotide pool disturbance. The mechanisms of CFS formation have been linked to DNA replication timing control, transcription activities, as well as chromatin organization. However, it is unclear what specific cis- or trans-factors regulate the interplay between replication and transcription that determine CFS formation. We recently reported genome-wide mapping of DNA DSBs under replication stress induced by aphidicolin in human lymphoblastoids for the first time. Here, we systematically compared these DSBs with regards to nearby epigenomic features mapped in the same cell line from published studies. We demonstrate that aphidicolin-induced DSBs are strongly correlated with histone 3 lysine 36 trimethylation, a marker for active transcription. We further demonstrate that this DSB signature is a composite effect by the dual treatment of aphidicolin and its solvent, dimethylsulfoxide, the latter of which potently induces transcription on its own. We also present complementing evidence for the association between DSBs and 3D chromosome architectural domains with high density gene cluster and active transcription. Additionally, we show that while DSBs were detected at all but one of the fourteen finely mapped CFSs, they were not enriched in the CFS core sequences and rather demarcated the CFS core region. Related to this point, DSB density was not higher in large genes of greater than 300 kb, contrary to reported enrichment of CFS sites at these large genes. Finally, replication timing analyses demonstrate that the CFS core region contain initiation events, suggesting that altered replication dynamics are responsible for CFS formation in relatively higher level of replication stress.
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Affiliation(s)
- Sravan Kodali
- Department of Biochemistry and Molecular Biology, Upstate Medical University, Syracuse, NY, United States
| | - Silvia Meyer-Nava
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Stephen Landry
- Department of Biochemistry and Molecular Biology, Upstate Medical University, Syracuse, NY, United States
| | - Arijita Chakraborty
- Department of Biochemistry and Molecular Biology, Upstate Medical University, Syracuse, NY, United States
| | - Juan Carlos Rivera-Mulia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Wenyi Feng
- Department of Biochemistry and Molecular Biology, Upstate Medical University, Syracuse, NY, United States
- *Correspondence: Wenyi Feng,
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12
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Scourzic L, Salataj E, Apostolou E. Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies. Front Immunol 2021; 12:669881. [PMID: 34054841 PMCID: PMC8160312 DOI: 10.3389/fimmu.2021.669881] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Proper lymphopoiesis and immune responses depend on the spatiotemporal control of multiple processes, including gene expression, DNA recombination and cell fate decisions. High-order 3D chromatin organization is increasingly appreciated as an important regulator of these processes and dysregulation of genomic architecture has been linked to various immune disorders, including lymphoid malignancies. In this review, we present the general principles of the 3D chromatin topology and its dynamic reorganization during various steps of B and T lymphocyte development and activation. We also discuss functional interconnections between architectural, epigenetic and transcriptional changes and introduce major key players of genomic organization in B/T lymphocytes. Finally, we present how alterations in architectural factors and/or 3D genome organization are linked to dysregulation of the lymphopoietic transcriptional program and ultimately to hematological malignancies.
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Affiliation(s)
| | | | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
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13
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Devenish LP, Mhlanga MM, Negishi Y. Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses. Front Immunol 2021; 12:662565. [PMID: 34046034 PMCID: PMC8144502 DOI: 10.3389/fimmu.2021.662565] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 12/27/2022] Open
Abstract
Mammals face and overcome an onslaught of endogenous and exogenous challenges in order to survive. Typical immune cells and barrier cells, such as epithelia, must respond rapidly and effectively to encountered pathogens and aberrant cells to prevent invasion and eliminate pathogenic species before they become overgrown and cause harm. On the other hand, inappropriate initiation and failed termination of immune cell effector function in the absence of pathogens or aberrant tissue gives rise to a number of chronic, auto-immune, and neoplastic diseases. Therefore, the fine control of immune effector functions to provide for a rapid, robust response to challenge is essential. Importantly, immune cells are heterogeneous due to various factors relating to cytokine exposure and cell-cell interaction. For instance, tissue-resident macrophages and T cells are phenotypically, transcriptionally, and functionally distinct from their circulating counterparts. Indeed, even the same cell types in the same environment show distinct transcription patterns at the single cell level due to cellular noise, despite being robust in concert. Additionally, immune cells must remain quiescent in a naive state to avoid autoimmunity or chronic inflammatory states but must respond robustly upon activation regardless of their microenvironment or cellular noise. In recent years, accruing evidence from next-generation sequencing, chromatin capture techniques, and high-resolution imaging has shown that local- and long-range genome architecture plays an important role in coordinating rapid and robust transcriptional responses. Here, we discuss the local- and long-range genome architecture of immune cells and the resultant changes upon pathogen or antigen exposure. Furthermore, we argue that genome structures contribute functionally to rapid and robust responses under noisy and distinct cellular environments and propose a model to explain this phenomenon.
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Affiliation(s)
- Liam P Devenish
- Division of Chemical, Systems, and Synthetic Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Musa M Mhlanga
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Yutaka Negishi
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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14
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Noordermeer D. 3D genome organization: setting the stage and introducing its players. Brief Funct Genomics 2020; 19:69-70. [PMID: 32239212 DOI: 10.1093/bfgp/elaa006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daan Noordermeer
- Chromatin Dynamics Group, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
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