1
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Sadria M, Layton A, Goyal S, Bader GD. Fatecode enables cell fate regulator prediction using classification-supervised autoencoder perturbation. CELL REPORTS METHODS 2024:100819. [PMID: 38986613 DOI: 10.1016/j.crmeth.2024.100819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 11/20/2023] [Accepted: 06/18/2024] [Indexed: 07/12/2024]
Abstract
Cell reprogramming, which guides the conversion between cell states, is a promising technology for tissue repair and regeneration, with the ultimate goal of accelerating recovery from diseases or injuries. To accomplish this, regulators must be identified and manipulated to control cell fate. We propose Fatecode, a computational method that predicts cell fate regulators based only on single-cell RNA sequencing (scRNA-seq) data. Fatecode learns a latent representation of the scRNA-seq data using a deep learning-based classification-supervised autoencoder and then performs in silico perturbation experiments on the latent representation to predict genes that, when perturbed, would alter the original cell type distribution to increase or decrease the population size of a cell type of interest. We assessed Fatecode's performance using simulations from a mechanistic gene-regulatory network model and scRNA-seq data mapping blood and brain development of different organisms. Our results suggest that Fatecode can detect known cell fate regulators from single-cell transcriptomics datasets.
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Affiliation(s)
- Mehrshad Sadria
- Department of Applied Mathematics, University of Waterloo, Waterloo, ON, Canada.
| | - Anita Layton
- Department of Applied Mathematics, University of Waterloo, Waterloo, ON, Canada; Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, Canada; Department of Biology, University of Waterloo, Waterloo, ON, Canada; School of Pharmacy, University of Waterloo, Waterloo, ON, Canada
| | - Sidhartha Goyal
- Department of Physics, University of Toronto, Toronto, ON, Canada
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; The Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; The Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Canadian Institute for Advanced Research (CIFAR), Toronto, ON, Canada
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2
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Jiménez JM, Contreras-Riquelme JS, Vidal PM, Prado C, Bastías M, Meneses C, Martín AJM, Perez-Acle T, Pacheco R. Identification of master regulator genes controlling pathogenic CD4 + T cell fate in inflammatory bowel disease through transcriptional network analysis. Sci Rep 2024; 14:10553. [PMID: 38719901 PMCID: PMC11078927 DOI: 10.1038/s41598-024-61158-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
Inflammatory bowel diseases (IBD) are a group of chronic inflammatory conditions of the gastrointestinal tract associated with multiple pathogenic factors, including dysregulation of the immune response. Effector CD4+ T cells and regulatory CD4+ T cells (Treg) are central players in maintaining the balance between tolerance and inflammation. Interestingly, genetic modifications in these cells have been implicated in regulating the commitment of specific phenotypes and immune functions. However, the transcriptional program controlling the pathogenic behavior of T helper cells in IBD progression is still unknown. In this study, we aimed to find master transcription regulators controlling the pathogenic behavior of effector CD4+ T cells upon gut inflammation. To achieve this goal, we used an animal model of IBD induced by the transfer of naïve CD4+ T cells into recombination-activating gene 1 (Rag1) deficient mice, which are devoid of lymphocytes. As a control, a group of Rag1-/- mice received the transfer of the whole CD4+ T cells population, which includes both effector T cells and Treg. When gut inflammation progressed, we isolated CD4+ T cells from the colonic lamina propria and spleen tissue, and performed bulk RNA-seq. We identified differentially up- and down-regulated genes by comparing samples from both experimental groups. We found 532 differentially expressed genes (DEGs) in the colon and 30 DEGs in the spleen, mostly related to Th1 response, leukocyte migration, and response to cytokines in lamina propria T-cells. We integrated these data into Gene Regulatory Networks to identify Master Regulators, identifying four up-regulated master gene regulators (Lef1, Dnmt1, Mybl2, and Jup) and only one down-regulated master regulator (Foxo3). The altered expression of master regulators observed in the transcriptomic analysis was confirmed by qRT-PCR analysis and found an up-regulation of Lef1 and Mybl2, but without differences on Dnmt1, Jup, and Foxo3. These two master regulators have been involved in T cells function and cell cycle progression, respectively. We identified two master regulator genes associated with the pathogenic behavior of effector CD4+ T cells in an animal model of IBD. These findings provide two new potential molecular targets for treating IBD.
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Affiliation(s)
- José M Jiménez
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile
| | | | - Pía M Vidal
- Biomedical Science Research Laboratory, Neuroimmunology and Regeneration of the Central Nervous System Unit, Basic Sciences Department, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Carolina Prado
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, 7510156, Providencia, Santiago, Chile
| | - Macarena Bastías
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudio Meneses
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Facultad de Agronomía y Sistemas Naturales, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alberto J M Martín
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile
- Escuela de Ingeniería, Facultad de Ingeniería Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Tomás Perez-Acle
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile
- Escuela de Ingeniería, Facultad de Ingeniería Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Rodrigo Pacheco
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile.
- Facultad de Medicina y Ciencia, Universidad San Sebastián, 7510156, Providencia, Santiago, Chile.
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3
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Chen W, Zhong W, Yu L, Lin X, Xie J, Liu Z. A Drosophila Model Reveals the Potential Role for mtt in Retinal Disease. Int J Mol Sci 2024; 25:899. [PMID: 38255972 PMCID: PMC10815649 DOI: 10.3390/ijms25020899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/03/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Congenital stationary night blindness (CSNB) is a genetically heterogeneous inherited retinal disorder, caused by over 300 mutations in 17 different genes. While there are numerous fly models available for simulating ocular diseases, most are focused on mimicking retinitis pigmentosa (RP), with animal models specifically addressing CSNB limited to mammals. Here, we present a CSNB fly model associated with the mtt gene, utilizing RNA interference (RNAi) to silence the mtt gene in fly eyes (homologous to the mammalian GRM6 gene) and construct a CSNB model. Through this approach, we observed significant defects in the eye structure and function upon reducing mtt expression in fly eyes. This manifested as disruptions in the compound eye lens structure and reduced sensitivity to light responses. These results suggest a critical role for mtt in the function of fly adult eyes. Interestingly, we found that the mtt gene is not expressed in the photoreceptor neurons of adult flies but is localized to the inner lamina neurons. In summary, these results underscore the crucial involvement of mtt in fly retinal function, providing a framework for understanding the pathogenic mechanisms of CSNB and facilitating research into potential therapeutic interventions.
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Affiliation(s)
- Wenfeng Chen
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Wenmiao Zhong
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Lingqi Yu
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Xiang Lin
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Jiayu Xie
- School of Medicine, Chongqing University, Chongqing 400044, China;
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Zhenxing Liu
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
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4
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Schwarz D, Lourido S. The multifaceted roles of Myb domain-containing proteins in apicomplexan parasites. Curr Opin Microbiol 2023; 76:102395. [PMID: 37866202 PMCID: PMC10872578 DOI: 10.1016/j.mib.2023.102395] [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: 07/26/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023]
Abstract
Apicomplexan parasites are a large and diverse clade of protists responsible for significant diseases of humans and animals. Central to the ability of these parasites to colonize their host and evade immune responses is an expanded repertoire of gene-expression programs that requires the coordinated action of complex transcriptional networks. DNA-binding proteins and chromatin regulators are essential orchestrators of apicomplexan gene expression that often act in concert. Although apicomplexan genomes encode various families of putative DNA-binding proteins, most remain functionally and mechanistically unexplored. This review highlights the versatile role of myeloblastosis (Myb) domain-containing proteins in apicomplexan parasites as transcription factors and chromatin regulators. We explore the diversity of Myb domain structure and use phylogenetic analysis to identify common features across the phylum. This provides a framework to discuss functional heterogeneity and regulation of Myb domain-containing proteins particularly emphasizing their role in parasite differentiation.
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Affiliation(s)
- Dominic Schwarz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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5
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Kholodenko BN, Kolch W, Rukhlenko OS. Reversing pathological cell states: the road less travelled can extend the therapeutic horizon. Trends Cell Biol 2023; 33:913-923. [PMID: 37263821 PMCID: PMC10593090 DOI: 10.1016/j.tcb.2023.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 06/03/2023]
Abstract
Acquisition of omics data advances at a formidable pace. Yet, our ability to utilize these data to control cell phenotypes and design interventions that reverse pathological states lags behind. Here, we posit that cell states are determined by core networks that control cell-wide networks. To steer cell fate decisions, core networks connecting genotype to phenotype must be reconstructed and understood. A recent method, cell state transition assessment and regulation (cSTAR), applies perturbation biology to quantify causal connections and mechanistically models how core networks influence cell phenotypes. cSTAR models are akin to digital cell twins enabling us to purposefully convert pathological states back to physiologically normal states. While this capability has a range of applications, here we discuss reverting oncogenic transformation.
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Affiliation(s)
- Boris N Kholodenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland; Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - Oleksii S Rukhlenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
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6
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Vicencio E, Nuñez-Belmar J, Cardenas JP, Cortés BI, Martin AJM, Maracaja-Coutinho V, Rojas A, Cafferata EA, González-Osuna L, Vernal R, Cortez C. Transcriptional Signatures and Network-Based Approaches Identified Master Regulators Transcription Factors Involved in Experimental Periodontitis Pathogenesis. Int J Mol Sci 2023; 24:14835. [PMID: 37834287 PMCID: PMC10573220 DOI: 10.3390/ijms241914835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Periodontitis is a chronic inflammatory disease characterized by the progressive and irreversible destruction of the periodontium. Its aetiopathogenesis lies in the constant challenge of the dysbiotic biofilm, which triggers a deregulated immune response responsible for the disease phenotype. Although the molecular mechanisms underlying periodontitis have been extensively studied, the regulatory mechanisms at the transcriptional level remain unclear. To generate transcriptomic data, we performed RNA shotgun sequencing of the oral mucosa of periodontitis-affected mice. Since genes are not expressed in isolation during pathological processes, we disclose here the complete repertoire of differentially expressed genes (DEG) and co-expressed modules to build Gene Regulatory Networks (GRNs) and identify the Master Transcriptional Regulators of periodontitis. The transcriptional changes revealed 366 protein-coding genes and 42 non-coding genes differentially expressed and enriched in the immune response. Furthermore, we found 13 co-expression modules with different representation degrees and gene expression levels. Our GRN comprises genes from 12 gene clusters, 166 nodes, of which 33 encode Transcription Factors, and 201 connections. Finally, using these strategies, 26 master regulators of periodontitis were identified. In conclusion, combining the transcriptomic analyses with the regulatory network construction represents a powerful and efficient strategy for identifying potential periodontitis-therapeutic targets.
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Affiliation(s)
- Emiliano Vicencio
- Escuela de Tecnología Médica, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile;
| | - Josefa Nuñez-Belmar
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile; (J.N.-B.); (J.P.C.)
| | - Juan P. Cardenas
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile; (J.N.-B.); (J.P.C.)
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
| | - Bastian I. Cortés
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alberto J. M. Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago 7780272, Chile;
- Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago 8420524, Chile
| | - Vinicius Maracaja-Coutinho
- Centro de Modelamiento Molecular, Biofísica y Bioinformática, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380492, Chile; (V.M.-C.); (A.R.)
- Advanced Center for Chronic Diseases—ACCDiS, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380492, Chile
| | - Adolfo Rojas
- Centro de Modelamiento Molecular, Biofísica y Bioinformática, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380492, Chile; (V.M.-C.); (A.R.)
| | - Emilio A. Cafferata
- Laboratorio de Biología Periodontal, Facultad de Odontología, Universidad de Chile, Santiago 8380492, Chile; (E.A.C.); (L.G.-O.); (R.V.)
| | - Luis González-Osuna
- Laboratorio de Biología Periodontal, Facultad de Odontología, Universidad de Chile, Santiago 8380492, Chile; (E.A.C.); (L.G.-O.); (R.V.)
| | - Rolando Vernal
- Laboratorio de Biología Periodontal, Facultad de Odontología, Universidad de Chile, Santiago 8380492, Chile; (E.A.C.); (L.G.-O.); (R.V.)
| | - Cristian Cortez
- Escuela de Tecnología Médica, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile;
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7
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Arancibia-Opazo S, Contreras-Riquelme JS, Sánchez M, Cisternas-Olmedo M, Vidal RL, Martin AJM, Sáez MA. Transcriptional and Histone Acetylation Changes Associated with CRE Elements Expose Key Factors Governing the Regulatory Circuit in the Early Stage of Huntington's Disease Models. Int J Mol Sci 2023; 24:10848. [PMID: 37446028 DOI: 10.3390/ijms241310848] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Huntington's disease (HD) is a disorder caused by an abnormal expansion of trinucleotide CAG repeats within the huntingtin (Htt) gene. Under normal conditions, the CREB Binding Protein interacts with CREB elements and acetylates Lysine 27 of Histone 3 to direct the expression of several genes. However, mutant Htt causes depletion of CBP, which in turn induces altered histone acetylation patterns and transcriptional deregulation. Here, we have studied a differential expression analysis and H3K27ac variation in 4- and 6-week-old R6/2 mice as a model of juvenile HD. The analysis of differential gene expression and acetylation levels were integrated into Gene Regulatory Networks revealing key regulators involved in the altered transcription cascade. Our results show changes in acetylation and gene expression levels that are related to impaired neuronal development, and key regulators clearly defined in 6-week-old mice are proposed to drive the downstream regulatory cascade in HD. Here, we describe the first approach to determine the relationship among epigenetic changes in the early stages of HD. We determined the existence of changes in pre-symptomatic stages of HD as a starting point for early onset indicators of the progression of this disease.
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Affiliation(s)
- Sandra Arancibia-Opazo
- Chromatin, Epigenetic, and Neuroscience Laboratory, Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
- Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago 8580745, Chile
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Universidad San Sebastián, Santiago 8580704, Chile
| | - J Sebastián Contreras-Riquelme
- Plant Genome Regulation Lab, Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
| | - Mario Sánchez
- Chromatin, Epigenetic, and Neuroscience Laboratory, Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
| | - Marisol Cisternas-Olmedo
- Centro de Biología Integrativa, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Biomedical Neuroscience Institute, University of Chile, Santiago 8380455, Chile
- Center for Geroscience, Brain Health, and Metabolism, Santiago 8380453, Chile
| | - René L Vidal
- Centro de Biología Integrativa, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Biomedical Neuroscience Institute, University of Chile, Santiago 8380455, Chile
- Center for Geroscience, Brain Health, and Metabolism, Santiago 8380453, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - Alberto J M Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Universidad San Sebastián, Santiago 8580704, Chile
- Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago 7500000, Chile
| | - Mauricio A Sáez
- Chromatin, Epigenetic, and Neuroscience Laboratory, Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
- Centro de Oncología de Precisión, Facultad de Medicina Universidad Mayor, Santiago 7560908, Chile
- Laboratorio de Investigación en Salud de Precisión, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Temuco 4813302, Chile
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8
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Licon MH, Giuliano CJ, Chan AW, Chakladar S, Eberhard JN, Shallberg LA, Chandrasekaran S, Waldman BS, Koshy AA, Hunter CA, Lourido S. A positive feedback loop controls Toxoplasma chronic differentiation. Nat Microbiol 2023; 8:889-904. [PMID: 37081202 PMCID: PMC10520893 DOI: 10.1038/s41564-023-01358-2] [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: 04/26/2022] [Accepted: 03/07/2023] [Indexed: 04/22/2023]
Abstract
Successful infection strategies must balance pathogen amplification and persistence. In the obligate intracellular parasite Toxoplasma gondii this is accomplished through differentiation into dedicated cyst-forming chronic stages that avoid clearance by the host immune system. The transcription factor BFD1 is both necessary and sufficient for stage conversion; however, its regulation is not understood. In this study we examine five factors that are transcriptionally activated by BFD1. One of these is a cytosolic RNA-binding protein of the CCCH-type zinc-finger family, which we name bradyzoite formation deficient 2 (BFD2). Parasites lacking BFD2 fail to induce BFD1 and are consequently unable to fully differentiate in culture or in mice. BFD2 interacts with the BFD1 transcript under stress, and deletion of BFD2 reduces BFD1 protein levels but not messenger RNA abundance. The reciprocal effects on BFD2 transcription and BFD1 translation outline a positive feedback loop that enforces the chronic-stage gene-expression programme. Thus, our findings help explain how parasites both initiate and commit to chronic differentiation. This work provides new mechanistic insight into the regulation of T. gondii persistence, and can be exploited in the design of strategies to prevent and treat these key reservoirs of human infection.
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Affiliation(s)
| | - Christopher J Giuliano
- Whitehead Institute, Cambridge, MA, USA
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex W Chan
- Whitehead Institute, Cambridge, MA, USA
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sundeep Chakladar
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Julia N Eberhard
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lindsey A Shallberg
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Benjamin S Waldman
- Whitehead Institute, Cambridge, MA, USA
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Anita A Koshy
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
- Department of Neurology, Department of Immunobiology, University of Arizona, Tucson, AZ, USA
| | - Christopher A Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sebastian Lourido
- Whitehead Institute, Cambridge, MA, USA.
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, USA.
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9
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Krup AL, Winchester SAB, Ranade SS, Agrawal A, Devine WP, Sinha T, Choudhary K, Dominguez MH, Thomas R, Black BL, Srivastava D, Bruneau BG. A Mesp1-dependent developmental breakpoint in transcriptional and epigenomic specification of early cardiac precursors. Development 2023; 150:dev201229. [PMID: 36994838 PMCID: PMC10259516 DOI: 10.1242/dev.201229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 03/21/2023] [Indexed: 03/31/2023]
Abstract
Transcriptional networks governing cardiac precursor cell (CPC) specification are incompletely understood owing, in part, to limitations in distinguishing CPCs from non-cardiac mesoderm in early gastrulation. We leveraged detection of early cardiac lineage transgenes within a granular single-cell transcriptomic time course of mouse embryos to identify emerging CPCs and describe their transcriptional profiles. Mesp1, a transiently expressed mesodermal transcription factor, is canonically described as an early regulator of cardiac specification. However, we observed perdurance of CPC transgene-expressing cells in Mesp1 mutants, albeit mislocalized, prompting us to investigate the scope of the role of Mesp1 in CPC emergence and differentiation. Mesp1 mutant CPCs failed to robustly activate markers of cardiomyocyte maturity and crucial cardiac transcription factors, yet they exhibited transcriptional profiles resembling cardiac mesoderm progressing towards cardiomyocyte fates. Single-cell chromatin accessibility analysis defined a Mesp1-dependent developmental breakpoint in cardiac lineage progression at a shift from mesendoderm transcriptional networks to those necessary for cardiac patterning and morphogenesis. These results reveal Mesp1-independent aspects of early CPC specification and underscore a Mesp1-dependent regulatory landscape required for progression through cardiogenesis.
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Affiliation(s)
- Alexis Leigh Krup
- Biomedical Sciences Program, University of California, San Francisco, CA 94158, USA
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Sarah A. B. Winchester
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Sanjeev S. Ranade
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ayushi Agrawal
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - W. Patrick Devine
- Department of Pathology, University of California, San Francisco, CA 94158, USA
| | - Tanvi Sinha
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Krishna Choudhary
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Martin H. Dominguez
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
- Department of Medicine, Division of Cardiology, University of California, San Francisco, CA 94158, USA
- Cardiovascular Institute and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Reuben Thomas
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Brian L. Black
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Deepak Srivastava
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
- Department of Pediatrics, University of California, San Francisco, CA 94158, USA
- Roddenberry Center for Stem Cell Biology and Medicine, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Benoit G. Bruneau
- Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Pediatrics, University of California, San Francisco, CA 94158, USA
- Roddenberry Center for Stem Cell Biology and Medicine, Gladstone Institutes, San Francisco, CA 94158, USA
- Institute of Human Genetics, University of California, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94158, USA
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10
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Functional Resilience of Mutually Repressing Motifs Embedded in Larger Networks. Biomolecules 2022; 12:biom12121842. [PMID: 36551270 PMCID: PMC9775907 DOI: 10.3390/biom12121842] [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: 08/15/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Elucidating the design principles of regulatory networks driving cellular decision-making has important implications for understanding cell differentiation and guiding the design of synthetic circuits. Mutually repressing feedback loops between 'master regulators' of cell fates can exhibit multistable dynamics enabling "single-positive" phenotypes: (high A, low B) and (low A, high B) for a toggle switch, and (high A, low B, low C), (low A, high B, low C) and (low A, low B, high C) for a toggle triad. However, the dynamics of these two motifs have been interrogated in isolation in silico, but in vitro and in vivo, they often operate while embedded in larger regulatory networks. Here, we embed these motifs in complex larger networks of varying sizes and connectivity to identify hallmarks under which these motifs maintain their canonical dynamical behavior. We show that an increased number of incoming edges onto a motif leads to a decay in their canonical stand-alone behaviors. We also show that this decay can be exacerbated by adding self-inhibition but not self-activation loops on the 'master regulators'. These observations offer insights into the design principles of biological networks containing these motifs and can help devise optimal strategies for the integration of these motifs into larger synthetic networks.
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11
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Sierra-Pagan JE, Garry DJ. The regulatory role of pioneer factors during cardiovascular lineage specification – A mini review. Front Cardiovasc Med 2022; 9:972591. [PMID: 36082116 PMCID: PMC9445115 DOI: 10.3389/fcvm.2022.972591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/03/2022] [Indexed: 11/15/2022] Open
Abstract
Cardiovascular disease (CVD) remains the number one cause of death worldwide. Ischemic heart disease contributes to heart failure and has considerable morbidity and mortality. Therefore, alternative therapeutic strategies are urgently needed. One class of epigenetic regulators known as pioneer factors has emerged as an important tool for the development of regenerative therapies for the treatment of CVD. Pioneer factors bind closed chromatin and remodel it to drive lineage specification. Here, we review pioneer factors within the cardiovascular lineage, particularly during development and reprogramming and highlight the implications this field of research has for the future development of cardiac specific regenerative therapies.
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Affiliation(s)
- Javier E. Sierra-Pagan
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Daniel J. Garry
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, United States
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, United States
- *Correspondence: Daniel J. Garry
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12
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Regulation of Eye Determination and Regionalization in the Spider Parasteatoda tepidariorum. Cells 2022; 11:cells11040631. [PMID: 35203282 PMCID: PMC8870698 DOI: 10.3390/cells11040631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 11/17/2022] Open
Abstract
Animal visual systems are enormously diverse, but their development appears to be controlled by a set of conserved retinal determination genes (RDGs). Spiders are particular masters of visual system innovation, and offer an excellent opportunity to study the evolution of animal eyes. Several RDGs have been identified in spider eye primordia, but their interactions and regulation remain unclear. From our knowledge of RDG network regulation in Drosophila melanogaster, we hypothesize that orthologs of Pax6, eyegone, Wnt genes, hh, dpp, and atonal could play important roles in controlling eye development in spiders. We analyzed the expression of these genes in developing embryos of the spider Parasteatodatepidariorum, both independently and in relation to the eye primordia, marked using probes for the RDG sine oculis. Our results support conserved roles for Wnt genes in restricting the size and position of the eye field, as well as for atonal initiating photoreceptor differentiation. However, we found no strong evidence for an upstream role of Pax6 in eye development, despite its label as a master regulator of animal eye development; nor do eyg, hh or dpp compensate for the absence of Pax6. Conversely, our results indicate that hh may work with Wnt signaling to restrict eye growth, a role similar to that of Sonichedgehog (Shh) in vertebrates.
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13
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Levis NA, Ragsdale EJ. Linking Molecular Mechanisms and Evolutionary Consequences of Resource Polyphenism. Front Integr Neurosci 2022; 16:805061. [PMID: 35210995 PMCID: PMC8861301 DOI: 10.3389/fnint.2022.805061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Resource polyphenism—the occurrence of environmentally induced, discrete, and intraspecific morphs showing differential niche use—is taxonomically widespread and fundamental to the evolution of ecological function where it has arisen. Despite longstanding appreciation for the ecological and evolutionary significance of resource polyphenism, only recently have its proximate mechanisms begun to be uncovered. Polyphenism switches, especially those influencing and influenced by trophic interactions, offer a route to integrating proximate and ultimate causation in studies of plasticity, and its potential influence on evolution more generally. Here, we use the major events in generalized polyphenic development as a scaffold for linking the molecular mechanisms of polyphenic switching with potential evolutionary outcomes of polyphenism and for discussing challenges and opportunities at each step in this process. Not only does the study of resource polyphenism uncover interesting details of discrete plasticity, it also illuminates and informs general principles at the intersection of development, ecology, and evolution.
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14
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Weasner BM, Kumar JP. The timing of cell fate decisions is crucial for initiating pattern formation in the Drosophila eye. Development 2022; 149:274084. [PMID: 35072208 PMCID: PMC8917411 DOI: 10.1242/dev.199634] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 12/09/2021] [Indexed: 01/26/2023]
Abstract
The eye-antennal disc of Drosophila is composed of three cell layers: a columnar epithelium called the disc proper (DP); an overlying sheet of squamous cells called the peripodial epithelium (PE); and a strip of cuboidal cells that joins the other two cellular sheets to each other and comprises the outer margin (M) of the disc. The M cells play an important role in patterning the eye because it is here that the Hedgehog (Hh), Decapentaplegic (Dpp) and JAK/STAT pathways function to initiate pattern formation. Dpp signaling is lost from the margin of eyes absent (eya) mutant discs and, as a result, the initiation of retinal patterning is blocked. Based on these observations, Eya has been proposed to control the initiation of the morphogenetic furrow via regulation of Dpp signaling within the M. We show that the failure in pattern formation surprisingly results from M cells prematurely adopting a head epidermis fate. This switch in fate normally takes place during pupal development after the eye has been patterned. Our results suggest that the timing of cell fate decisions is essential for correct eye development.
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15
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Folkendt L, Lohmann I, Domsch K. An Evolutionary Perspective on Hox Binding Site Preferences in Two Different Tissues. J Dev Biol 2021; 9:jdb9040057. [PMID: 34940504 PMCID: PMC8705983 DOI: 10.3390/jdb9040057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/23/2021] [Accepted: 12/07/2021] [Indexed: 01/04/2023] Open
Abstract
Transcription factor (TF) networks define the precise development of multicellular organisms. While many studies focused on TFs expressed in specific cell types to elucidate their contribution to cell specification and differentiation, it is less understood how broadly expressed TFs perform their precise functions in the different cellular contexts. To uncover differences that could explain tissue-specific functions of such TFs, we analyzed here genomic chromatin interactions of the broadly expressed Drosophila Hox TF Ultrabithorax (Ubx) in the mesodermal and neuronal tissues using bioinformatics. Our investigations showed that Ubx preferentially interacts with multiple yet tissue-specific chromatin sites in putative regulatory regions of genes in both tissues. Importantly, we found the classical Hox/Ubx DNA binding motif to be enriched only among the neuronal Ubx chromatin interactions, whereas a novel Ubx-like motif with rather low predicted Hox affinities was identified among the regions bound by Ubx in the mesoderm. Finally, our analysis revealed that tissues-specific Ubx chromatin sites are also different with regards to the distribution of active and repressive histone marks. Based on our data, we propose that the tissue-related differences in Ubx binding behavior could be a result of the emergence of the mesoderm as a new germ layer in triploblastic animals, which might have required the Hox TFs to relax their binding specificity.
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Affiliation(s)
- Laura Folkendt
- Developmental Biology, Erlangen-Nürnberg University, 91058 Erlangen, Germany;
| | - Ingrid Lohmann
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
- Correspondence: (I.L.); (K.D.)
| | - Katrin Domsch
- Developmental Biology, Erlangen-Nürnberg University, 91058 Erlangen, Germany;
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
- Correspondence: (I.L.); (K.D.)
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16
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Pichaud F, Casares F. Shaping an optical dome: The size and shape of the insect compound eye. Semin Cell Dev Biol 2021; 130:37-44. [PMID: 34810110 DOI: 10.1016/j.semcdb.2021.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 10/19/2022]
Abstract
The insect compound eye is the most abundant eye architecture on earth. It comes in a wide variety of shapes and sizes, which are exquisitely adapted to specific ecosystems. Here, we explore the organisational principles and pathways, from molecular to tissular, that underpin the building of this organ and highlight why it is an excellent model system to investigate the relationship between genes and tissue form. The compound eye offers wide fields of view, high sensitivity in motion detection and infinite depth of field. It is made of an array of visual units called ommatidia, which are precisely tiled in 3D to shape the retinal tissue as a dome-like structure. The eye starts off as a 2D epithelium, and it acquires its 3D organisation as ommatidia get into shape. Each ommatidium is made of a complement of retinal cells, including light-detecting photoreceptors and lens-secreting cells. The lens cells generate the typical hexagonal facet lens that lies atop the photoreceptors so that the eye surface consists of a quasi-crystalline array of these hexagonal facet-lenses. This array is curved to various degree, depending on the size and shape of the eye, and on the region of the retina. This curvature sets the resolution and visual field of the eye and is determined by i) the number and size of the facet lens - large ommatidial lenses can be used to generate flat, higher resolution areas, while smaller facets allow for stronger curvature of the eye, and ii) precise control of the inter facet-lens angle, which determines the optical axis of the each ommatidium. In this review we discuss how combinatorial variation in eye primordium shape, ommatidial number, facet lens size and inter facet-lens angle underpins the wide variety of insect eye shapes, and we explore what is known about the mechanisms that might control these parameters.
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Affiliation(s)
- Franck Pichaud
- MRC Laboratory for Molecular Cell Biology (LMCB), University College London, WC1E 6BT London, United Kingdom.
| | - Fernando Casares
- CABD-Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, ES-41013 Seville, Spain.
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17
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Raczkowski HL, DeKoter RP. Lineage-instructive functions of the E26-transformation-specific-family transcription factor Spi-C in immune cell development and disease. WIREs Mech Dis 2021; 13:e1519. [PMID: 34730294 DOI: 10.1002/wsbm.1519] [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: 11/04/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 11/10/2022]
Abstract
Cell fate decisions during hematopoiesis are the consequence of a complex mixture of inputs from cell-intrinsic and cell-extrinsic factors. In rare cases, expression of a single transcription factor, or a few key factors, may be sufficient to dictate lineage differentiation in a precursor cell. The E26-transformation-specific-family transcription factor Spi-C has emerged as an example of a lineage-instructive factor involved in the generation of mature, specialized subsets of both myeloid and lymphoid cells. Spi-C can instruct differentiation of splenic precursors into red pulp macrophages responsible for phagocytosing senescent red blood cells. In the B cell compartment, Spi-C acts as a key regulator of cell fate decisions at the pro-B to pre-B cell stage and for plasma cell differentiation. Spi-C regulates key genes including Nfkb1, Bach2, Syk, and Blnk to regulate cell cycle entry and B cell differentiation. Here, we review the biology of the lineage-instructive transcription factor Spi-C and its contribution to mechanisms of disease in macrophages and B cells. This article is categorized under: Cancer > Molecular and Cellular Physiology Immune System Diseases > Molecular and Cellular Physiology Infectious Diseases > Genetics/Genomics/Epigenetics.
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Affiliation(s)
- Hannah L Raczkowski
- Department of Microbiology & Immunology and the Center for Human Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada
| | - Rodney P DeKoter
- Department of Microbiology & Immunology and the Center for Human Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, Ontario, Canada
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18
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Aubert A, Stüder F, Colombo BM, Mendoza-Parra MA. A Core Transcription Regulatory Circuitry Defining Microglia Cell Identity Inferred from the Reanalysis of Multiple Human Microglia Differentiation Protocols. Brain Sci 2021; 11:brainsci11101338. [PMID: 34679401 PMCID: PMC8533937 DOI: 10.3390/brainsci11101338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 11/16/2022] Open
Abstract
Microglia, the immune cells in the brain involved in both homeostasis and injury/infection control, play a predominant role in neurodegenerative diseases. In vivo studies on microglia are limited due to the requirement of surgical intervention, which can lead to the destruction of the tissues. Over the last few years, multiple protocols-presenting a variety of strategies-have described microglia differentiation issued from human pluripotent stem cells. Herein, we have reanalyzed the transcriptomes released on six different microglia differentiation protocols and revealed a consensus core of master transcription regulatory circuitry defining microglia identity. Furthermore, we have discussed the major divergencies among the studied protocols and have provided suggestions to further enhance microglia differentiation assays.
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19
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In Silico Analysis to Explore Lineage-Independent and -Dependent Transcriptional Programs Associated with the Process of Endothelial and Neural Differentiation of Human Induced Pluripotent Stem Cells. J Clin Med 2021; 10:jcm10184161. [PMID: 34575270 PMCID: PMC8471316 DOI: 10.3390/jcm10184161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Despite a major interest in understanding how the endothelial cell phenotype is established, the underlying molecular basis of this process is not yet fully understood. We have previously reported the generation of induced pluripotent stem cells (iPS) from human umbilical vein endothelial cells and differentiation of the resulting HiPS back to endothelial cells (Ec-Diff), as well as neural (Nn-Diff) cell lineage that contained both neurons and astrocytes. Furthermore, the identities of these cell lineages were established by gene array analysis. Here, we explored the same arrays to gain insight into the gene alteration processes that accompany the establishment of endothelial vs. non-endothelial neural cell phenotypes. We compared the expression of genes that code for transcription factors and epigenetic regulators when HiPS is differentiated into these endothelial and non-endothelial lineages. Our in silico analyses have identified cohorts of genes that are similarly up- or downregulated in both lineages, as well as those that exhibit lineage-specific alterations. Based on these results, we propose that genes that are similarly altered in both lineages participate in priming the stem cell for differentiation in a lineage-independent manner, whereas those that are differentially altered in endothelial compared to neural cells participate in a lineage-specific differentiation process. Specific GATA family members and their cofactors and epigenetic regulators (DNMT3B, PRDM14, HELLS) with a major role in regulating DNA methylation were among participants in priming HiPS for lineage-independent differentiation. In addition, we identified distinct cohorts of transcription factors and epigenetic regulators whose alterations correlated specifically with the establishment of endothelial vs. non-endothelial neural lineages.
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20
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Salekeen R, Diaconeasa AG, Billah MM, Islam KMD. Energy Metabolism Focused Analysis of Sexual Dimorphism in Biological Aging and Hypothesized Sex-specificity in Sirtuin Dependency. Mitochondrion 2021; 60:85-100. [PMID: 34332101 DOI: 10.1016/j.mito.2021.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 07/09/2021] [Accepted: 07/26/2021] [Indexed: 01/09/2023]
Abstract
The process of biological aging or senescence refers to the gradual loss of homeostasis and subsequent loss of function - leading to higher chances of mortality. Many mechanisms and driving forces have been suggested to facilitate the evolution of a molecular circuit acting as a trade-off between survival and proliferation, resulting in senescence. A major observation on biological aging and longevity in humans and model organisms is the prevalence of significant sexual divergence in the onset, mechanisms and effects of aging associated processes. In the current account, we describe possible mechanisms by which aging, sex and reproduction are evolutionarily intertwined in order to maintain systemic energy homeostasis. We also interrogate existing literature on the sexual dimorphism of genetic, cellular, metabolic, endocrine and epigenetic processes driving cellular and systemic aging. Subsequently, based on available evidence, we propose a hypothetic model of sex-limited decoupling of female longevity from sirtuins, a major family of regulator proteins of the survival-proliferation trade-off. We also provide necessary considerations to be made in order to test the hypothesis and explore the physiological and therapeutic implications of this decoupling event in male and female longevity after reaching reproductive maturity. HYPOTHESIS STATEMENT: Sirtuins provide survival benefits in a sex-nonspecific manner but the dependency on sirtuins in driving metabolic networks after reaching reproductive maturity is evolutionarily decoupled from female longevity.
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Affiliation(s)
- Rahagir Salekeen
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh.
| | - Amalia Gabriela Diaconeasa
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania.
| | - Md Morsaline Billah
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh.
| | - Kazi Mohammed Didarul Islam
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh.
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21
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Garry DJ, Garry MG. Interspecies chimeras as a platform for exogenic organ production and transplantation. Exp Biol Med (Maywood) 2021; 246:1838-1844. [PMID: 34165344 DOI: 10.1177/15353702211024948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Chronic diseases are associated with considerable morbidity and mortality. Therefore, new therapeutic strategies are warranted. Here, we provide a brief review outlining the rationale and feasibility for the generation of intraspecies and interspecies chimeras, which one day may serve as a platform for organ transplantation. These strategies are further associated with consideration of scientific and ethical issues.
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Affiliation(s)
- Daniel J Garry
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA.,Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN 55455, USA.,NorthStar Genomics, LLC, Eagan, MN 55122, USA
| | - Mary G Garry
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA.,Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN 55455, USA.,NorthStar Genomics, LLC, Eagan, MN 55122, USA
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22
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Murgas L, Contreras-Riquelme S, Martínez-Hernandez JE, Villaman C, Santibáñez R, Martin AJM. Automated generation of context-specific gene regulatory networks with a weighted approach in Drosophila melanogaster. Interface Focus 2021; 11:20200076. [PMID: 34123358 PMCID: PMC8193463 DOI: 10.1098/rsfs.2020.0076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2021] [Indexed: 01/22/2023] Open
Abstract
The regulation of gene expression is a key factor in the development and maintenance of life in all organisms. Even so, little is known at whole genome scale for most genes and contexts. We propose a method, Tool for Weighted Epigenomic Networks in Drosophila melanogaster (Fly T-WEoN), to generate context-specific gene regulatory networks starting from a reference network that contains all known gene regulations in the fly. Unlikely regulations are removed by applying a series of knowledge-based filters. Each of these filters is implemented as an independent module that considers a type of experimental evidence, including DNA methylation, chromatin accessibility, histone modifications and gene expression. Fly T-WEoN is based on heuristic rules that reflect current knowledge on gene regulation in D. melanogaster obtained from the literature. Experimental data files can be generated with several standard procedures and used solely when and if available. Fly T-WEoN is available as a Cytoscape application that permits integration with other tools and facilitates downstream network analysis. In this work, we first demonstrate the reliability of our method to then provide a relevant application case of our tool: early development of D. melanogaster. Fly T-WEoN together with its step-by-step guide is available at https://weon.readthedocs.io.
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Affiliation(s)
- Leandro Murgas
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.,Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
| | - Sebastian Contreras-Riquelme
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.,Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370146, Chile
| | - J Eduardo Martínez-Hernandez
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.,Centro de Modelamiento Molecular, Biofísica y Bioinformática-CM2B2, Facultad de Ciencias Químicas y Farmaceuticas, Universidad de Chile, Santiago 8380492, Chile.,Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
| | - Camilo Villaman
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.,Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
| | - Rodrigo Santibáñez
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - Alberto J M Martin
- Laboratorio de Biología de Redes, Centro de Genónica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
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23
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Chen SW, Hung YS, Fuh JL, Chen NJ, Chu YS, Chen SC, Fann MJ, Wong YH. Efficient conversion of human induced pluripotent stem cells into microglia by defined transcription factors. Stem Cell Reports 2021; 16:1363-1380. [PMID: 33836143 PMCID: PMC8185376 DOI: 10.1016/j.stemcr.2021.03.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 12/14/2022] Open
Abstract
Microglia, the immune cells of the central nervous system, play critical roles in brain physiology and pathology. We report a novel approach that produces, within 10 days, the differentiation of human induced pluripotent stem cells (hiPSCs) into microglia (iMG) by forced expression of both SPI1 and CEBPA. High-level expression of the main microglial markers and the purity of the iMG cells were confirmed by RT-qPCR, immunostaining, and flow cytometry analyses. Whole-transcriptome analysis demonstrated that these iMGs resemble human fetal/adult microglia but not human monocytes. Moreover, these iMGs exhibited appropriate physiological functions, including various inflammatory responses, ADP/ATP-evoked migration, and phagocytic ability. When co-cultured with hiPSC-derived neurons, the iMGs respond and migrate toward injured neurons. This study has established a protocol for the rapid conversion of hiPSCs into functional iMGs, which should facilitate functional studies of human microglia using different disease models and also help with drug discovery. Efficient generation of human iMGs from iPSCs by forced expression of SPI1 and CEBPA The transcriptome profile of iMGs resembles that of human primary microglia The iMG cells possess appropriate physiological functioning An iN-iMG co-culture model is established for studying neuron-microglia interactions
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Affiliation(s)
- Shih-Wei Chen
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan (ROC); Department of Life Sciences and Institute of Genome Sciences, School of Life Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan (ROC)
| | - Yu-Sheng Hung
- Department of Life Sciences and Institute of Genome Sciences, School of Life Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan (ROC)
| | - Jong-Ling Fuh
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan (ROC); Division of General Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei 112, Taiwan (ROC)
| | - Nien-Jung Chen
- Institute of Microbiology and Immunology, School of Life Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan (ROC)
| | - Yeh-Shiu Chu
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan (ROC)
| | - Shu-Cian Chen
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan (ROC)
| | - Ming-Ji Fann
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan (ROC); Department of Life Sciences and Institute of Genome Sciences, School of Life Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan (ROC)
| | - Yu-Hui Wong
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan (ROC); Department of Life Sciences and Institute of Genome Sciences, School of Life Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan (ROC).
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24
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Krämer A. Master regulators as order parameters of gene expression states. Phys Rev E 2021; 103:012409. [PMID: 33601603 DOI: 10.1103/physreve.103.012409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/22/2020] [Indexed: 11/07/2022]
Abstract
Cell type-specific gene expression patterns are represented as memory states of a Hopfield neural network model. It is shown that order parameters of this model can be interpreted as concentrations of master transcription regulators that form concurrent positive feedback loops with a large number of downstream regulated genes. The order parameter free energy then defines an epigenetic landscape in which local minima correspond to stable cell states. The model is applied to gene expression data in the context of hematopoiesis.
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25
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Reeves WM, Shimai K, Winkley KM, Veeman MT. Brachyury controls Ciona notochord fate as part of a feed-forward network. Development 2021; 148:dev195230. [PMID: 33419874 PMCID: PMC7875503 DOI: 10.1242/dev.195230] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/18/2020] [Indexed: 12/22/2022]
Abstract
The notochord is a defining feature of the chordates. The transcription factor Brachyury (Bra) is a key regulator of notochord fate but here we show that it is not a unitary master regulator in the model chordate Ciona Ectopic Bra expression only partially reprograms other cell types to a notochord-like transcriptional profile and a subset of notochord-enriched genes is unaffected by CRISPR Bra disruption. We identify Foxa.a and Mnx as potential co-regulators, and find that combinatorial cocktails are more effective at reprogramming other cell types than Bra alone. We reassess the network relationships between Bra, Foxa.a and other components of the notochord gene regulatory network, and find that Foxa.a expression in the notochord is regulated by vegetal FGF signaling. It is a direct activator of Bra expression and has a binding motif that is significantly enriched in the regulatory regions of notochord-enriched genes. These and other results indicate that Bra and Foxa.a act together in a regulatory network dominated by positive feed-forward interactions, with neither being a classically defined master regulator.
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Affiliation(s)
- Wendy M Reeves
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Kotaro Shimai
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Konner M Winkley
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Michael T Veeman
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
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26
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Treveil A, Sudhakar P, Matthews ZJ, Wrzesiński T, Jones EJ, Brooks J, Ölbei M, Hautefort I, Hall LJ, Carding SR, Mayer U, Powell PP, Wileman T, Di Palma F, Haerty W, Korcsmáros T. Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches. Mol Omics 2021; 16:39-58. [PMID: 31819932 DOI: 10.1039/c9mo00130a] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The epithelial lining of the small intestine consists of multiple cell types, including Paneth cells and goblet cells, that work in cohort to maintain gut health. 3D in vitro cultures of human primary epithelial cells, called organoids, have become a key model to study the functions of Paneth cells and goblet cells in normal and diseased conditions. Advances in these models include the ability to skew differentiation to particular lineages, providing a useful tool to study cell type specific function/dysfunction in the context of the epithelium. Here, we use comprehensive profiling of mRNA, microRNA and long non-coding RNA expression to confirm that Paneth cell and goblet cell enrichment of murine small intestinal organoids (enteroids) establishes a physiologically accurate model. We employ network analysis to infer the regulatory landscape altered by skewing differentiation, and using knowledge of cell type specific markers, we predict key regulators of cell type specific functions: Cebpa, Jun, Nr1d1 and Rxra specific to Paneth cells, Gfi1b and Myc specific for goblet cells and Ets1, Nr3c1 and Vdr shared between them. Links identified between these regulators and cellular phenotypes of inflammatory bowel disease (IBD) suggest that global regulatory rewiring during or after differentiation of Paneth cells and goblet cells could contribute to IBD aetiology. Future application of cell type enriched enteroids combined with the presented computational workflow can be used to disentangle multifactorial mechanisms of these cell types and propose regulators whose pharmacological targeting could be advantageous in treating IBD patients with Crohn's disease or ulcerative colitis.
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Affiliation(s)
- A Treveil
- Earlham Institute, Norwich Research Park, Norwich, Norfolk NR4 7UZ, UK.
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27
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Quiquand M, Rimesso G, Qiao N, Suo S, Zhao C, Slattery M, White KP, Han JJ, Baker NE. New regulators of Drosophila eye development identified from temporal transcriptome changes. Genetics 2021; 217:6117222. [PMID: 33681970 DOI: 10.1093/genetics/iyab007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 12/28/2020] [Indexed: 11/12/2022] Open
Abstract
In the last larval instar, uncommitted progenitor cells in the Drosophila eye primordium start to adopt individual retinal cell fates, arrest their growth and proliferation, and initiate terminal differentiation into photoreceptor neurons and other retinal cell types. To explore the regulation of these processes, we have performed mRNA-Seq studies of the larval eye and antennal primordial at multiple developmental stages. A total of 10,893 fly genes were expressed during these stages and could be adaptively clustered into gene groups, some of whose expression increases or decreases in parallel with the cessation of proliferation and onset of differentiation. Using in situ hybridization of a sample of 98 genes to verify spatial and temporal expression patterns, we estimate that 534 genes or more are transcriptionally upregulated during retinal differentiation, and 1367 or more downregulated as progenitor cells differentiate. Each group of co-expressed genes is enriched for regulatory motifs recognized by co-expressed transcription factors, suggesting that they represent coherent transcriptional regulatory programs. Using available mutant strains, we describe novel roles for the transcription factors SoxNeuro (SoxN), H6-like homeobox (Hmx), CG10253, without children (woc), Structure specific recognition protein (Ssrp), and multisex combs (mxc).
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Affiliation(s)
- Manon Quiquand
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gerard Rimesso
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nan Qiao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shengbao Suo
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chunyu Zhao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Matthew Slattery
- Institute for Genomics & Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Kevin P White
- Institute for Genomics & Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jackie J Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nicholas E Baker
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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28
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Domsch K, Schröder J, Janeschik M, Schaub C, Lohmann I. The Hox Transcription Factor Ubx Ensures Somatic Myogenesis by Suppressing the Mesodermal Master Regulator Twist. Cell Rep 2021; 34:108577. [PMID: 33406430 DOI: 10.1016/j.celrep.2020.108577] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 10/25/2020] [Accepted: 12/08/2020] [Indexed: 02/03/2023] Open
Abstract
Early lineage-specific master regulators are essential for the specification of cell types. However, once cells are committed to a specific fate, it is critical to restrict the activity of such factors to enable differentiation. To date, it remains unclear how these factors are silenced. Using the Drosophila mesoderm as a model and a comparative genomic approach, we identify the Hox transcription factor Ultrabithorax (Ubx) to be critical for the repression of the master regulator Twist. Mesoderm-specific Ubx loss-of-function experiments using CRISPR-Cas9 and overexpression studies demonstrate that Ubx majorly impacts twist transcription. A mechanistic analysis reveals that Ubx requires the NK-homeodomain protein Tinman to bind to the twist promoter. Furthermore, we find these factor interactions to be critical for silencing by recruiting the Polycomb DNA binding protein Pleiohomeotic. Altogether, our data reveal that Ubx is a critical player in mediating the silencing of Twist, which is crucial for coordinated muscle differentiation.
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Affiliation(s)
- Katrin Domsch
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, 69120 Heidelberg, Germany.
| | - Julia Schröder
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, 69120 Heidelberg, Germany
| | - Matthias Janeschik
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, 69120 Heidelberg, Germany
| | - Christoph Schaub
- Erlangen-Nürnberg University, Developmental Biology, 91058 Erlangen, Germany
| | - Ingrid Lohmann
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, 69120 Heidelberg, Germany
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29
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Scale free topology as an effective feedback system. PLoS Comput Biol 2020; 16:e1007825. [PMID: 32392249 PMCID: PMC7241857 DOI: 10.1371/journal.pcbi.1007825] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 05/21/2020] [Accepted: 03/26/2020] [Indexed: 12/13/2022] Open
Abstract
Biological networks are often heterogeneous in their connectivity pattern, with degree distributions featuring a heavy tail of highly connected hubs. The implications of this heterogeneity on dynamical properties are a topic of much interest. Here we show that interpreting topology as a feedback circuit can provide novel insights on dynamics. Based on the observation that in finite networks a small number of hubs have a disproportionate effect on the entire system, we construct an approximation by lumping these nodes into a single effective hub, which acts as a feedback loop with the rest of the nodes. We use this approximation to study dynamics of networks with scale-free degree distributions, focusing on their probability of convergence to fixed points. We find that the approximation preserves convergence statistics over a wide range of settings. Our mapping provides a parametrization of scale free topology which is predictive at the ensemble level and also retains properties of individual realizations. Specifically, outgoing hubs have an organizing role that can drive the network to convergence, in analogy to suppression of chaos by an external drive. In contrast, incoming hubs have no such property, resulting in a marked difference between the behavior of networks with outgoing vs. incoming scale free degree distribution. Combining feedback analysis with mean field theory predicts a transition between convergent and divergent dynamics which is corroborated by numerical simulations. Furthermore, they highlight the effect of a handful of outlying hubs, rather than of the connectivity distribution law as a whole, on network dynamics. Nature abounds with complex networks of interacting elements—from the proteins in our cells, through neural networks in our brains, to species interacting in ecosystems. In all of these fields, the relation between network structure and dynamics is an important research question. A recurring feature of natural networks is their heterogeneous structure: individual elements exhibit a huge diversity of connectivity patterns, which complicates the understanding of network dynamics. To address this problem, we devised a simplified approximation for complex structured networks which captures their dynamical properties. Separating out the largest “hubs”—a small number of nodes with disproportionately high connectivity—we represent them by a single node linked to the rest of the network. This enables us to borrow concepts from control theory, where a system’s output is linked back to itself forming a feedback loop. In this analogy, hubs in heterogeneous networks implement a feedback circuit with the rest of the network. The analogy reveals how these hubs can coordinate the network and drive it more easily towards stable states. Our approach enables analyzing dynamical properties of heterogeneous networks, which is difficult to achieve with existing techniques. It is potentially applicable to many fields where heterogeneous networks are important.
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30
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Creed TM, Baldeosingh R, Eberly CL, Schlee CS, Kim M, Cutler JA, Pandey A, Civin CI, Fossett NG, Kingsbury TJ. The PAX-SIX-EYA-DACH network modulates GATA-FOG function in fly hematopoiesis and human erythropoiesis. Development 2020; 147:dev.177022. [PMID: 31806659 DOI: 10.1242/dev.177022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 11/25/2019] [Indexed: 12/15/2022]
Abstract
The GATA and PAX-SIX-EYA-DACH transcriptional networks (PSEDNs) are essential for proper development across taxa. Here, we demonstrate novel PSEDN roles in vivo in Drosophila hematopoiesis and in human erythropoiesis in vitro Using Drosophila genetics, we show that PSEDN members function with GATA to block lamellocyte differentiation and maintain the prohemocyte pool. Overexpression of human SIX1 stimulated erythroid differentiation of human erythroleukemia TF1 cells and primary hematopoietic stem-progenitor cells. Conversely, SIX1 knockout impaired erythropoiesis in both cell types. SIX1 stimulation of erythropoiesis required GATA1, as SIX1 overexpression failed to drive erythroid phenotypes and gene expression patterns in GATA1 knockout cells. SIX1 can associate with GATA1 and stimulate GATA1-mediated gene transcription, suggesting that SIX1-GATA1 physical interactions contribute to the observed functional interactions. In addition, both fly and human SIX proteins regulated GATA protein levels. Collectively, our findings demonstrate that SIX proteins enhance GATA function at multiple levels, and reveal evolutionarily conserved cooperation between the GATA and PSEDN networks that may regulate developmental processes beyond hematopoiesis.
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Affiliation(s)
- T Michael Creed
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Rajkumar Baldeosingh
- Center for Vascular and Inflammatory Diseases University of Maryland School of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Christian L Eberly
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Caroline S Schlee
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - MinJung Kim
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jevon A Cutler
- McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Oncology and Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Oncology and Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Curt I Civin
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Nancy G Fossett
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA .,Center for Vascular and Inflammatory Diseases University of Maryland School of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tami J Kingsbury
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA .,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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31
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Loubiere V, Papadopoulos GL, Szabo Q, Martinez AM, Cavalli G. Widespread activation of developmental gene expression characterized by PRC1-dependent chromatin looping. SCIENCE ADVANCES 2020; 6:eaax4001. [PMID: 31950077 PMCID: PMC6954061 DOI: 10.1126/sciadv.aax4001] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 11/06/2019] [Indexed: 05/21/2023]
Abstract
Polycomb repressive complexes 1 and 2 have been historically described as transcriptional repressors, but recent reports suggest that PRC1 might also support activation, although the underlying mechanisms remain elusive. Here, we show that stage-specific PRC1 binding at a subset of active promoters and enhancers during Drosophila development coincides with the formation of three-dimensional (3D) loops, an increase in expression during development and repression in PRC1 mutants. Dissection of the dachshund locus indicates that PRC1-anchored loops are versatile architectural platforms that persist when surrounding genes are transcriptionally active and fine-tune their expression. The analysis of RING1B binding profiles and 3D contacts during neural differentiation in mice suggests that this role is conserved in mammals.
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Affiliation(s)
- V. Loubiere
- Institute of Human Genetics, UMR 9002, CNRS–University of Montpellier, 34396 Montpellier, France
| | - G. L. Papadopoulos
- Institute of Human Genetics, UMR 9002, CNRS–University of Montpellier, 34396 Montpellier, France
| | - Q. Szabo
- Institute of Human Genetics, UMR 9002, CNRS–University of Montpellier, 34396 Montpellier, France
| | - A-M. Martinez
- Institute of Human Genetics, UMR 9002, CNRS–University of Montpellier, 34396 Montpellier, France
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32
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The β-oxidation pathway is downregulated during diapause termination in Calanus copepods. Sci Rep 2019; 9:16686. [PMID: 31723179 PMCID: PMC6853931 DOI: 10.1038/s41598-019-53032-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/28/2019] [Indexed: 12/22/2022] Open
Abstract
Calanus copepods are keystone species in marine ecosystems, mainly due to their high lipid content, which is a nutritious food source for e.g. juvenile fish. Accumulated lipids are catabolized to meet energy requirements during dormancy (diapause), which occurs during the last copepodite stage (C5). The current knowledge of lipid degradation pathways during diapause termination is limited. We characterized changes in lipid fullness and generated transcriptional profiles in C5s during termination of diapause and progression towards adulthood. Lipid fullness of C5s declined linearly during developmental progression, but more β-oxidation genes were upregulated in early C5s compared to late C5s and adults. We identified four possible master regulators of energy metabolism, which all were generally upregulated in early C5s, compared to late C5s and adults. We discovered that one of two enzymes in the carnitine shuttle is absent from the calanoid copepod lineage. Based on the geographical location of the sampling site, the field-samples were initially presumed to consist of C. finmarchicus. However, the identification of C. glacialis in some samples underlines the need for performing molecular analyses to reliably identify Calanus species. Our findings contributes to a better understanding of molecular events occurring during diapause and diapause termination in calanoid copepods.
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33
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Chrystal PW, Walter MA. Aniridia and Axenfeld-Rieger Syndrome: Clinical presentations, molecular genetics and current/emerging therapies. Exp Eye Res 2019; 189:107815. [PMID: 31560925 DOI: 10.1016/j.exer.2019.107815] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/11/2019] [Accepted: 09/23/2019] [Indexed: 12/20/2022]
Abstract
Aniridia and Axenfeld-Rieger Syndrome are related, human ocular disorders that are typically inherited in an autosomal dominant manner. Both result from incorrect development of the eye and have, as their most serious consequences, elevated risk to develop the blinding condition glaucoma. This review will focus on describing the clinical presentations of Aniridia and Axenfeld-Rieger Syndrome as well as the molecular genetics and current and emerging therapies used to treat patients.
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Affiliation(s)
- Paul W Chrystal
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Michael A Walter
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada.
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34
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Contreras EG, Sierralta J, Oliva C. Novel Strategies for the Generation of Neuronal Diversity: Lessons From the Fly Visual System. Front Mol Neurosci 2019; 12:140. [PMID: 31213980 PMCID: PMC6554424 DOI: 10.3389/fnmol.2019.00140] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/13/2019] [Indexed: 12/17/2022] Open
Abstract
Among all organs of an adult animal, the central nervous system stands out because of its vast complexity and morphological diversity. During early development, the entire central nervous system develops from an apparently homogenous group of progenitors that differentiate into all neural cell types. Therefore, understanding the molecular and genetic mechanisms that give rise to the cellular and anatomical diversity of the brain is a key goal of the developmental neurobiology field. With this aim in mind, the development of the central nervous system of model organisms has been extensively studied. From more than a century, the mechanisms of neurogenesis have been studied in the fruit fly Drosophila melanogaster. The visual system comprises one of the major structures of the Drosophila brain. The visual information is collected by the eye-retina photoreceptors and then processed by the four optic lobe ganglia: the lamina, medulla, lobula and lobula plate. The molecular mechanisms that originate neuronal diversity in the optic lobe have been unveiled in the past decade. In this article, we describe the early development and differentiation of the lobula plate ganglion, from the formation of the optic placode and the inner proliferation center to the specification of motion detection neurons. We focused specifically on how the precise combination of signaling pathways and cell-specific transcription factors patterns the pool of neural stem cells that generates the different neurons of the motion detection system.
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Affiliation(s)
- Esteban G Contreras
- Department of Neuroscience and Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Jimena Sierralta
- Department of Neuroscience and Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Carlos Oliva
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
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35
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Tian K, Henderson RE, Parker R, Brown A, Johnson JE, Bateman JR. Two modes of transvection at the eyes absent gene of Drosophila demonstrate plasticity in transcriptional regulatory interactions in cis and in trans. PLoS Genet 2019; 15:e1008152. [PMID: 31075100 PMCID: PMC6530868 DOI: 10.1371/journal.pgen.1008152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/22/2019] [Accepted: 04/23/2019] [Indexed: 01/10/2023] Open
Abstract
For many genes, proper gene expression requires coordinated and dynamic interactions between multiple regulatory elements, each of which can either promote or silence transcription. In Drosophila, the complexity of the regulatory landscape is further complicated by the tight physical pairing of homologous chromosomes, which can permit regulatory elements to interact in trans, a phenomenon known as transvection. To better understand how gene expression can be programmed through cis- and trans-regulatory interactions, we analyzed transvection effects for a collection of alleles of the eyes absent (eya) gene. We find that trans-activation of a promoter by the eya eye-specific enhancers is broadly supported in many allelic backgrounds, and that the availability of an enhancer to act in trans can be predicted based on the molecular lesion of an eya allele. Furthermore, by manipulating promoter availability in cis and in trans, we demonstrate that the eye-specific enhancers of eya show plasticity in their promoter preference between two different transcriptional start sites, which depends on promoter competition between the two potential targets. Finally, we show that certain alleles of eya demonstrate pairing-sensitive silencing resulting from trans-interactions between Polycomb Response Elements (PREs), and genetic and genomic data support a general role for PcG proteins in mediating transcriptional silencing at eya. Overall, our data highlight how eya gene regulation relies upon a complex but plastic interplay between multiple enhancers, promoters, and PREs. Gene regulation requires interactions between regions of DNA known as regulatory elements, which, in combination, determine where and when a gene will be active or silenced. Some genes use just a few regulatory elements, whereas others rely on highly complex interactions between many different elements that are poorly understood. While we typically imagine regulatory elements interacting with one another along the length of a single chromosome, in a curious phenomenon called transvection, elements can communicate between two different chromosomes that are held in close proximity. Here, we use the study of transvection to better understand how different regulatory elements contribute to the expression of eyes absent (eya), a gene required for proper eye development in Drosophila. Our data show that a class of elements that initiate eya gene expression, called promoters, will compete with one another for activation by eya’s enhancers, a second class of regulatory element, with the promoter that is closest to the enhancers being the favored target for activation. Furthermore, our study of transvection uncovers an important role for a silencing element, called a PRE, in opposing eya gene expression. Overall, our study sheds new light on how different elements combine to produce patterned expression of eya.
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Affiliation(s)
- Katherine Tian
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Rachel E. Henderson
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Reyna Parker
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Alexia Brown
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Justine E. Johnson
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Jack R. Bateman
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
- * E-mail:
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36
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Lehmann M, Knust E, Hebbar S. Drosophila melanogaster: A Valuable Genetic Model Organism to Elucidate the Biology of Retinitis Pigmentosa. Methods Mol Biol 2019; 1834:221-249. [PMID: 30324448 DOI: 10.1007/978-1-4939-8669-9_16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Retinitis pigmentosa (RP) is a complex inherited disease. It is associated with mutations in a wide variety of genes with many different functions. These mutations impact the integrity of rod photoreceptors and ultimately result in the progressive degeneration of rods and cone photoreceptors in the retina, leading to complete blindness. A hallmark of this disease is the variable degree to which symptoms are manifest in patients. This is indicative of the influence of the environment, and/or of the distinct genetic makeup of the individual.The fruit fly, Drosophila melanogaster, has effectively proven to be a great model system to better understand interconnected genetic networks. Unraveling genetic interactions and thereby different cellular processes is relatively easy because more than a century of research on flies has enabled the creation of sophisticated genetic tools to perturb gene function. A remarkable conservation of disease genes across evolution and the similarity of the general organization of the fly and vertebrate photoreceptor cell had prompted research on fly retinal degeneration. To date six fly models for RP, including RP4, RP11, RP12, RP14, RP25, and RP26, have been established, and have provided useful information on RP disease biology. In this chapter, an outline of approaches and experimental specifications are described to enable utilizing or developing new fly models of RP.
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Affiliation(s)
- Malte Lehmann
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Elisabeth Knust
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - Sarita Hebbar
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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Jiao X, Li Z, Wang M, Katiyar S, Di Sante G, Farshchian M, South AP, Cocola C, Colombo D, Reinbold R, Zucchi I, Wu K, Tabas I, Spike BT, Pestell RG. Dachshund Depletion Disrupts Mammary Gland Development and Diverts the Composition of the Mammary Gland Progenitor Pool. Stem Cell Reports 2018; 12:135-151. [PMID: 30554919 PMCID: PMC6335505 DOI: 10.1016/j.stemcr.2018.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 12/31/2022] Open
Abstract
DACH1 abundance is reduced in human malignancies, including breast cancer. Herein DACH1 was detected among multipotent fetal mammary stem cells in the embryo, among mixed lineage precursors, and in adult basal cells and (ERα+) luminal progenitors. Dach1 gene deletion at 6 weeks in transgenic mice reduced ductal branching, reduced the proportion of mammary basal cells (Lin− CD24med CD29high) and reduced abundance of basal cytokeratin 5, whereas DACH1 overexpression induced ductal branching, increased Gata3 and Notch1, and expanded mammosphere formation in LA-7 breast cells. Mammary gland-transforming growth factor β (TGF-β) activity, known to reduce ductal branching and to reduce the basal cell population, increased upon Dach1 deletion, associated with increased SMAD phosphorylation. Association of the scaffold protein Smad anchor for receptor activation with Smad2/3, which facilitates TGF-β activation, was reduced by endogenous DACH1. DACH1 increases basal cells, enhances ductal formation and restrains TGF-β activity in vivo. Dach1 is expressed in mammary gland fetal stem cells and adult luminal cells Dach1 expands mammary gland basal/myoepithelial cells Dach1 induces post-natal mammary gland ductal formation Dach1 retrains TGF-β activity in the mammary gland in vivo
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Affiliation(s)
- Xuanmao Jiao
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA 18902, USA
| | - Zhiping Li
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA 18902, USA
| | - Min Wang
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA 18902, USA
| | - Sanjay Katiyar
- Department of Cancer Biology, Thomas Jefferson University, Bluemle Life Sciences Building, 233 South 10(th) Street, Philadelphia, PA 19107, USA
| | - Gabriele Di Sante
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA 18902, USA
| | - Mehdi Farshchian
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Bluemle Life Sciences Building, 233 South 10(th) Street, Philadelphia, PA 19107, USA
| | - Andrew P South
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Bluemle Life Sciences Building, 233 South 10(th) Street, Philadelphia, PA 19107, USA
| | - Cinzia Cocola
- Istituto Tecnologie Biomediche, Consiglio Nazionale Delle Ricerche, Via Cervi 93, Segrate, 20090 Milano, Italy
| | - Daniele Colombo
- Istituto Tecnologie Biomediche, Consiglio Nazionale Delle Ricerche, Via Cervi 93, Segrate, 20090 Milano, Italy
| | - Rolland Reinbold
- Istituto Tecnologie Biomediche, Consiglio Nazionale Delle Ricerche, Via Cervi 93, Segrate, 20090 Milano, Italy
| | - Ileana Zucchi
- Istituto Tecnologie Biomediche, Consiglio Nazionale Delle Ricerche, Via Cervi 93, Segrate, 20090 Milano, Italy
| | - Kongming Wu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
| | - Ira Tabas
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin T Spike
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Room 2505, Salt Lake City, UT 84112, USA
| | - Richard G Pestell
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA 18902, USA; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 637551, Singapore.
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Gaspar P, Almudi I, Nunes MDS, McGregor AP. Human eye conditions: insights from the fly eye. Hum Genet 2018; 138:973-991. [PMID: 30386938 DOI: 10.1007/s00439-018-1948-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 10/20/2018] [Indexed: 12/22/2022]
Abstract
The fruit fly Drosophila melanogaster has served as an excellent model to study and understand the genetics of many human diseases from cancer to neurodegeneration. Studying the regulation of growth, determination and differentiation of the compound eyes of this fly, in particular, have provided key insights into a wide range of diseases. Here we review the regulation of the development of fly eyes in light of shared aspects with human eye development. We also show how understanding conserved regulatory pathways in eye development together with the application of tools for genetic screening and functional analyses makes Drosophila a powerful model to diagnose and characterize the genetics underlying many human eye conditions, such as aniridia and retinitis pigmentosa. This further emphasizes the importance and vast potential of basic research to underpin applied research including identifying and treating the genetic basis of human diseases.
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Affiliation(s)
- Pedro Gaspar
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Isabel Almudi
- Centro Andaluz de Biología del Desarrollo, CSIC/ Universidad Pablo de Olavide, Carretera de Utrera Km1, 41013, Sevilla, Spain
| | - Maria D S Nunes
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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Morrison CA, Chen H, Cook T, Brown S, Treisman JE. Glass promotes the differentiation of neuronal and non-neuronal cell types in the Drosophila eye. PLoS Genet 2018; 14:e1007173. [PMID: 29324767 PMCID: PMC5783423 DOI: 10.1371/journal.pgen.1007173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 01/24/2018] [Accepted: 12/29/2017] [Indexed: 11/18/2022] Open
Abstract
Transcriptional regulators can specify different cell types from a pool of equivalent progenitors by activating distinct developmental programs. The Glass transcription factor is expressed in all progenitors in the developing Drosophila eye, and is maintained in both neuronal and non-neuronal cell types. Glass is required for neuronal progenitors to differentiate as photoreceptors, but its role in non-neuronal cone and pigment cells is unknown. To determine whether Glass activity is limited to neuronal lineages, we compared the effects of misexpressing it in neuroblasts of the larval brain and in epithelial cells of the wing disc. Glass activated overlapping but distinct sets of genes in these neuronal and non-neuronal contexts, including markers of photoreceptors, cone cells and pigment cells. Coexpression of other transcription factors such as Pax2, Eyes absent, Lozenge and Escargot enabled Glass to induce additional genes characteristic of the non-neuronal cell types. Cell type-specific glass mutations generated in cone or pigment cells using somatic CRISPR revealed autonomous developmental defects, and expressing Glass specifically in these cells partially rescued glass mutant phenotypes. These results indicate that Glass is a determinant of organ identity that acts in both neuronal and non-neuronal cells to promote their differentiation into functional components of the eye.
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Affiliation(s)
- Carolyn A. Morrison
- Skirball Institute for Biomolecular Medicine and Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
| | - Hao Chen
- Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
| | - Tiffany Cook
- Center of Molecular Medicine and Genomics and Department of Ophthalmology, Wayne State University School of Medicine, Detroit, MI, United States of America
| | - Stuart Brown
- Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
| | - Jessica E. Treisman
- Skirball Institute for Biomolecular Medicine and Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
- * E-mail:
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Davis TL, Rebay I. Pleiotropy in Drosophila organogenesis: Mechanistic insights from Combgap and the retinal determination gene network. Fly (Austin) 2018; 12:62-70. [PMID: 29125381 DOI: 10.1080/19336934.2017.1402994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Master regulatory transcription factors cooperate in networks to shepherd cells through organogenesis. In the Drosophila eye, a collection of master control proteins known as the retinal determination gene network (RDGN) switches the direction and targets of its output to choreograph developmental transitions, but the molecular partners that enable such regulatory flexibility are not known. We recently showed that two RDGN members, Eyes absent (Eya) and Sine oculis (So), promote exit from the terminal cell cycle known as the second mitotic wave (SMW) to permit differentiation. A search for co-factors identified the ubiquitously expressed Combgap (Cg) as a novel transcriptional partner that impedes cell cycle exit and interferes with Eya-So activity specifically in this context. Here, we argue that Cg acts as a flexible transcriptional platform that contributes to numerous gene expression outcomes by a variety of mechanisms. For example, Cg provides repressive activities that dampen Eya-So output, but not by recruiting Polycomb chromatin-remodeling complexes as it does in other contexts. We propose that master regulators depend on both specifically expressed co-factors that assemble the combinatorial code and broadly expressed partners like Cg that recruit the diverse molecular activities needed to appropriately regulate their target enhancers.
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Affiliation(s)
- Trevor L Davis
- a Committee on Development, Regeneration, and Stem Cell Biology , University of Chicago , Chicago , IL , USA
| | - Ilaria Rebay
- a Committee on Development, Regeneration, and Stem Cell Biology , University of Chicago , Chicago , IL , USA.,b Ben May Department for Cancer Research , University of Chicago , Chicago , IL , USA
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Abstract
Transcription factors that trigger major developmental decisions in plants and animals are termed "master regulators". Such master regulators are classically seen as acting on the top of a regulatory hierarchy that determines a complete developmental program, and they usually encode transcription factors. Here, we introduce master regulators of flowering time and flower development as examples to show how analysis of molecular interactions and gene-regulatory networks in plants has changed our view on the molecular mechanisms by which these factors control developmental processes. A picture has emerged that emphasizes a complex combinatorial interplay in determining cell-type transcriptional programs, and a high level of feedback control. The expression of master regulators themselves is usually regulated by multiple factors integrating environmental and endogenous spatiotemporal cues. Master regulatory transcription factors regulate gene expression by different mechanisms, including modifications in chromatin status in the bound regions. A poorly understood phenomenon is how developmental master regulators exert functions in different cell- and organ types. This is especially relevant for those factors that have important functions in several developmental processes.
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The rewiring of transcription circuits in evolution. Curr Opin Genet Dev 2017; 47:121-127. [PMID: 29120735 DOI: 10.1016/j.gde.2017.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 12/24/2022]
Abstract
The binding of transcription regulators to cis-regulatory sequences is a key step through which all cells regulate expression of their genes. Due to gains and losses of cis-regulatory sequences and changes in the transcription regulators themselves, the binding connections between regulators and their target genes rapidly change over evolutionary time and constitute a major source of biological novelty. This review covers recent work, carried out in a wide range of species, that addresses the overall extent of these evolutionary changes, their consequences, and some of the molecular mechanisms that lie behind them.
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Mutations that impair Eyes absent tyrosine phosphatase activity in vitro reduce robustness of retinal determination gene network output in Drosophila. PLoS One 2017; 12:e0187546. [PMID: 29108015 PMCID: PMC5673202 DOI: 10.1371/journal.pone.0187546] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/20/2017] [Indexed: 12/01/2022] Open
Abstract
A limited collection of signaling networks and transcriptional effectors directs the full spectrum of cellular behaviors that comprise development. One mechanism to diversify regulatory potential is to combine multiple biochemical activities into the same protein. Exemplifying this principle of modularity, Eyes absent (Eya), originally identified as a transcriptional co-activator within the retinal determination gene network (RDGN), also harbors tyrosine and threonine phosphatase activities. Although mounting evidence argues for the importance of Eya’s phosphatase activities to mammalian biology, genetic rescue experiments in Drosophila have shown that the tyrosine phosphatase function is dispensable for normal development. In this study, we repeated these rescue experiments in genetically sensitized backgrounds in which the dose of one or more RDGN factor was reduced. Heterozygosity for sine oculis or dachshund, both core RDGN members, compromised the ability of phosphatase-dead eya, but not of the control wild type eya transgene, to rescue the retinal defects and reduced viability associated with eya loss. We speculate that Eya’s tyrosine phosphatase activity, although non-essential, confers robustness to RDGN output.
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