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Dawson J, Bryant A, Jordan T, Bhikot S, Macon S, Walton B, Ajamu-Johnson A, Langridge PD, Malmi-Kakkada AN. Contact area and tissue growth dynamics shape synthetic juxtacrine signaling patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.12.548752. [PMID: 37503188 PMCID: PMC10370035 DOI: 10.1101/2023.07.12.548752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cell-cell communication through direct contact, or juxtacrine signaling, is important in development, disease, and many areas of physiology. Synthetic forms of juxtacrine signaling can be precisely controlled and operate orthogonally to native processes, making them a powerful reductionist tool with which to address fundamental questions in cell-cell communication in vivo. Here we investigate how cell-cell contact length and tissue growth dynamics affect juxtacrine signal responses through implementing a custom synthetic gene circuit in Drosophila wing imaginal discs alongside mathematical modeling to determine synthetic Notch (synNotch) activation patterns. We find that the area of contact between cells largely determines the extent of synNotch activation, leading to the prediction that the shape of the interface between signal-sending and signal-receiving cells will impact the magnitude of the synNotch response. Notably, synNotch outputs form a graded spatial profile that extends several cell diameters from the signal source, providing evidence that the response to juxtacrine signals can persist in cells as they proliferate away from source cells, or that cells remain able to communicate directly over several cell diameters. Our model suggests the former mechanism may be sufficient, since it predicts graded outputs without diffusion or long-range cell-cell communication. Overall, we identify that cell-cell contact area together with output synthesis and decay rates likely govern the pattern of synNotch outputs in both space and time during tissue growth, insights that may have broader implications for juxtacrine signaling in general.
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Murugan NJ, Cariba S, Abeygunawardena S, Rouleau N, Payne SL. Biophysical control of plasticity and patterning in regeneration and cancer. Cell Mol Life Sci 2023; 81:9. [PMID: 38099951 PMCID: PMC10724343 DOI: 10.1007/s00018-023-05054-6] [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: 08/18/2023] [Revised: 10/12/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
Cells and tissues display a remarkable range of plasticity and tissue-patterning activities that are emergent of complex signaling dynamics within their microenvironments. These properties, which when operating normally guide embryogenesis and regeneration, become highly disordered in diseases such as cancer. While morphogens and other molecular factors help determine the shapes of tissues and their patterned cellular organization, the parallel contributions of biophysical control mechanisms must be considered to accurately predict and model important processes such as growth, maturation, injury, repair, and senescence. We now know that mechanical, optical, electric, and electromagnetic signals are integral to cellular plasticity and tissue patterning. Because biophysical modalities underly interactions between cells and their extracellular matrices, including cell cycle, metabolism, migration, and differentiation, their applications as tuning dials for regenerative and anti-cancer therapies are being rapidly exploited. Despite this, the importance of cellular communication through biophysical signaling remains disproportionately underrepresented in the literature. Here, we provide a review of biophysical signaling modalities and known mechanisms that initiate, modulate, or inhibit plasticity and tissue patterning in models of regeneration and cancer. We also discuss current approaches in biomedical engineering that harness biophysical control mechanisms to model, characterize, diagnose, and treat disease states.
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Affiliation(s)
- Nirosha J Murugan
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada.
- Allen Discovery Center, Tufts University, Medford, MA, USA.
| | - Solsa Cariba
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | | | - Nicolas Rouleau
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
- Allen Discovery Center, Tufts University, Medford, MA, USA
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Samantha L Payne
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
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Manicka S, Pai VP, Levin M. Information integration during bioelectric regulation of morphogenesis of the embryonic frog brain. iScience 2023; 26:108398. [PMID: 38034358 PMCID: PMC10687303 DOI: 10.1016/j.isci.2023.108398] [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: 01/23/2023] [Revised: 07/18/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
Spatiotemporal patterns of cellular resting potential regulate several aspects of development. One key aspect of the bioelectric code is that transcriptional and morphogenetic states are determined not by local, single-cell, voltage levels but by specific distributions of voltage across cell sheets. We constructed and analyzed a minimal dynamical model of collective gene expression in cells based on inputs of multicellular voltage patterns. Causal integration analysis revealed a higher-order mechanism by which information about the voltage pattern was spatiotemporally integrated into gene activity, as well as a division of labor among and between the bioelectric and genetic components. We tested and confirmed predictions of this model in a system in which bioelectric control of morphogenesis regulates gene expression and organogenesis: the embryonic brain of the frog Xenopus laevis. This study demonstrates that machine learning and computational integration approaches can advance our understanding of the information-processing underlying morphogenetic decision-making, with a potential for other applications in developmental biology and regenerative medicine.
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Affiliation(s)
- Santosh Manicka
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
| | - Vaibhav P. Pai
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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Mim MS, Knight C, Zartman JJ. Quantitative insights in tissue growth and morphogenesis with optogenetics. Phys Biol 2023; 20:061001. [PMID: 37678266 PMCID: PMC10594237 DOI: 10.1088/1478-3975/acf7a1] [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: 01/20/2023] [Revised: 08/15/2023] [Accepted: 09/07/2023] [Indexed: 09/09/2023]
Abstract
Cells communicate with each other to jointly regulate cellular processes during cellular differentiation and tissue morphogenesis. This multiscale coordination arises through the spatiotemporal activity of morphogens to pattern cell signaling and transcriptional factor activity. This coded information controls cell mechanics, proliferation, and differentiation to shape the growth and morphogenesis of organs. While many of the molecular components and physical interactions have been identified in key model developmental systems, there are still many unresolved questions related to the dynamics involved due to challenges in precisely perturbing and quantitatively measuring signaling dynamics. Recently, a broad range of synthetic optogenetic tools have been developed and employed to quantitatively define relationships between signal transduction and downstream cellular responses. These optogenetic tools can control intracellular activities at the single cell or whole tissue scale to direct subsequent biological processes. In this brief review, we highlight a selected set of studies that develop and implement optogenetic tools to unravel quantitative biophysical mechanisms for tissue growth and morphogenesis across a broad range of biological systems through the manipulation of morphogens, signal transduction cascades, and cell mechanics. More generally, we discuss how optogenetic tools have emerged as a powerful platform for probing and controlling multicellular development.
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Affiliation(s)
- Mayesha Sahir Mim
- Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - Caroline Knight
- Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - Jeremiah J Zartman
- Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, United States of America
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Pierini G, Dahmann C. Hedgehog morphogen gradient is robust towards variations in tissue morphology in Drosophila. Sci Rep 2023; 13:8454. [PMID: 37231029 DOI: 10.1038/s41598-023-34632-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/04/2023] [Indexed: 05/27/2023] Open
Abstract
During tissue development, gradients of secreted signaling molecules known as morphogens provide cells with positional information. The mechanisms underlying morphogen spreading have been widely studied, however, it remains largely unexplored whether the shape of morphogen gradients is influenced by tissue morphology. Here, we developed an analysis pipeline to quantify the distribution of proteins within a curved tissue. We applied it to the Hedgehog morphogen gradient in the Drosophila wing and eye-antennal imaginal discs, which are flat and curved tissues, respectively. Despite a different expression profile, the slope of the Hedgehog gradient was comparable between the two tissues. Moreover, inducing ectopic folds in wing imaginal discs did not affect the slope of the Hedgehog gradient. Suppressing curvature in the eye-antennal imaginal disc also did not alter the Hedgehog gradient slope but led to ectopic Hedgehog expression. In conclusion, through the development of an analysis pipeline that allows quantifying protein distribution in curved tissues, we show that the Hedgehog gradient is robust towards variations in tissue morphology.
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Affiliation(s)
- Giulia Pierini
- School of Science, Technische Universität Dresden, 01062, Dresden, Germany
| | - Christian Dahmann
- School of Science, Technische Universität Dresden, 01062, Dresden, Germany.
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062, Dresden, Germany.
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6
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Bornstein S, Shapiro I, Malyukov M, Züllig R, Luca E, Gelfgat E, Beuschlein F, Nölting S, Berruti A, Sigala S, Peitzsch M, Steenblock C, Ludwig B, Kugelmeier P, Hantel C. Innovative multidimensional models in a high-throughput-format for different cell types of endocrine origin. Cell Death Dis 2022; 13:648. [PMID: 35879289 PMCID: PMC9314441 DOI: 10.1038/s41419-022-05096-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 01/21/2023]
Abstract
The adrenal gland provides an important function by integrating neuronal, immune, vascular, metabolic and endocrine signals under a common organ capsule. It is the central organ of the stress response system and has been implicated in numerous stress-related disorders. While for other diseases, regeneration of healthy organ tissue has been aimed at such approaches are lacking for endocrine diseases - with the exception of type-I-diabetes. Moreover, adrenal tumor formation is very common, however, appropriate high-throughput applications reflecting the high heterogeneity and furthermore relevant 3D-structures in vitro are still widely lacking. Recently, we have initiated the development of standardized multidimensional models of a variety of endocrine cell/tissue sources in a new multiwell-format. Firstly, we confirmed common applicability for pancreatic pseudo-islets. Next, we translated applicability for spheroid establishment to adrenocortical cell lines as well as patient material to establish spheroids from malignant, but also benign adrenal tumors. We aimed furthermore at the development of bovine derived healthy adrenal organoids and were able to establish steroidogenic active organoids containing both, cells of cortical and medullary origin. Overall, we hope to open new avenues for basic research, endocrine cancer and adrenal tissue-replacement-therapies as we demonstrate potential for innovative mechanistic insights and personalized medicine in endocrine (tumor)-biology.
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Affiliation(s)
- Stefan Bornstein
- grid.412004.30000 0004 0478 9977Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Zurich, Switzerland ,grid.412282.f0000 0001 1091 2917Medizinische Klinik und Poliklinik III, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Igor Shapiro
- grid.412004.30000 0004 0478 9977Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Zurich, Switzerland
| | - Maria Malyukov
- grid.412282.f0000 0001 1091 2917Medizinische Klinik und Poliklinik III, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Richard Züllig
- grid.412004.30000 0004 0478 9977Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Zurich, Switzerland
| | - Edlira Luca
- grid.412004.30000 0004 0478 9977Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Zurich, Switzerland
| | - Evgeny Gelfgat
- grid.412282.f0000 0001 1091 2917Medizinische Klinik und Poliklinik III, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Felix Beuschlein
- grid.412004.30000 0004 0478 9977Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Zurich, Switzerland ,grid.411095.80000 0004 0477 2585Endocrine Research Unit, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, 80336 Munich, Germany
| | - Svenja Nölting
- grid.412004.30000 0004 0478 9977Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Zurich, Switzerland ,grid.411095.80000 0004 0477 2585Department of Medicine IV, University Hospital, LMU Munich, Ziemssenstraße 1, 80336 München, Germany
| | - Alfredo Berruti
- grid.7637.50000000417571846Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia at ASST Spedali Civili di Brescia, 25123 Brescia, Italy
| | - Sandra Sigala
- grid.7637.50000000417571846Section of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Mirko Peitzsch
- grid.412282.f0000 0001 1091 2917Medizinische Klinik und Poliklinik III, University Hospital Carl Gustav Carus Dresden, Dresden, Germany ,grid.412282.f0000 0001 1091 2917Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus at Technische Universität Dresden, Dresden, Germany
| | - Charlotte Steenblock
- grid.412282.f0000 0001 1091 2917Medizinische Klinik und Poliklinik III, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Barbara Ludwig
- grid.412004.30000 0004 0478 9977Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Zurich, Switzerland ,grid.412282.f0000 0001 1091 2917Medizinische Klinik und Poliklinik III, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | | | - Constanze Hantel
- grid.412004.30000 0004 0478 9977Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Zurich, Switzerland ,grid.412282.f0000 0001 1091 2917Medizinische Klinik und Poliklinik III, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
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Kumar N, Huizar FJ, Farfán-Pira KJ, Brodskiy PA, Soundarrajan DK, Nahmad M, Zartman JJ. MAPPER: An Open-Source, High-Dimensional Image Analysis Pipeline Unmasks Differential Regulation of Drosophila Wing Features. Front Genet 2022; 13:869719. [PMID: 35480325 PMCID: PMC9035675 DOI: 10.3389/fgene.2022.869719] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Phenomics requires quantification of large volumes of image data, necessitating high throughput image processing approaches. Existing image processing pipelines for Drosophila wings, a powerful genetic model for studying the underlying genetics for a broad range of cellular and developmental processes, are limited in speed, precision, and functional versatility. To expand on the utility of the wing as a phenotypic screening system, we developed MAPPER, an automated machine learning-based pipeline that quantifies high-dimensional phenotypic signatures, with each dimension quantifying a unique morphological feature of the Drosophila wing. MAPPER magnifies the power of Drosophila phenomics by rapidly quantifying subtle phenotypic differences in sample populations. We benchmarked MAPPER’s accuracy and precision in replicating manual measurements to demonstrate its widespread utility. The morphological features extracted using MAPPER reveal variable sexual dimorphism across Drosophila species and unique underlying sex-specific differences in morphogen signaling in male and female wings. Moreover, the length of the proximal-distal axis across the species and sexes shows a conserved scaling relationship with respect to the wing size. In sum, MAPPER is an open-source tool for rapid, high-dimensional analysis of large imaging datasets. These high-content phenomic capabilities enable rigorous and systematic identification of genotype-to-phenotype relationships in a broad range of screening and drug testing applications and amplify the potential power of multimodal genomic approaches.
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Affiliation(s)
- Nilay Kumar
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, United States
| | - Francisco J. Huizar
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, United States
| | - Keity J. Farfán-Pira
- Department of Physiology, Biophysics, and Neurosciences, Center for Research and Advanced Studies of the National Polytechnical Institute (Cinvestav), Mexico City, Mexico
| | - Pavel A. Brodskiy
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, United States
| | - Dharsan K. Soundarrajan
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, United States
| | - Marcos Nahmad
- Department of Physiology, Biophysics, and Neurosciences, Center for Research and Advanced Studies of the National Polytechnical Institute (Cinvestav), Mexico City, Mexico
| | - Jeremiah J. Zartman
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, United States
- *Correspondence: Jeremiah J. Zartman,
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Gómez-Gálvez P, Anbari S, Escudero LM, Buceta J. Mechanics and self-organization in tissue development. Semin Cell Dev Biol 2021; 120:147-159. [PMID: 34417092 DOI: 10.1016/j.semcdb.2021.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 01/01/2023]
Abstract
Self-organization is an all-important feature of living systems that provides the means to achieve specialization and functionality at distinct spatio-temporal scales. Herein, we review this concept by addressing the packing organization of cells, the sorting/compartmentalization phenomenon of cell populations, and the propagation of organizing cues at the tissue level through traveling waves. We elaborate on how different theoretical models and tools from Topology, Physics, and Dynamical Systems have improved the understanding of self-organization by shedding light on the role played by mechanics as a driver of morphogenesis. Altogether, by providing a historical perspective, we show how ideas and hypotheses in the field have been revisited, developed, and/or rejected and what are the open questions that need to be tackled by future research.
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Affiliation(s)
- Pedro Gómez-Gálvez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla and Departamento de Biologia Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
| | - Samira Anbari
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Luis M Escudero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla and Departamento de Biologia Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio), CSIC-UV, Paterna, 46980 Valencia, Spain.
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Genetic Network Architecture and Environmental Cues Drive Spatial Organization of Phenotypic Division of Labor in Streptomyces coelicolor. mBio 2021; 12:mBio.00794-21. [PMID: 34006658 PMCID: PMC8262882 DOI: 10.1128/mbio.00794-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A number of bacteria are known to differentiate into cells with distinct phenotypic traits during processes such as biofilm formation or the development of reproductive structures. These cell types, by virtue of their specialized functions, embody a division of labor. However, how bacteria build spatial patterns of differentiated cells is not well understood. Here, we examine the factors that drive spatial patterns in divisions of labor in colonies of Streptomyces coelicolor, a multicellular bacterium capable of synthesizing an array of antibiotics and forming complex reproductive structures (e.g., aerial hyphae and spores). Using fluorescent reporters, we demonstrate that the pathways for antibiotic biosynthesis and aerial hypha formation are activated in distinct waves of gene expression that radiate outwards in S. coelicolor colonies. We also show that the spatiotemporal separation of these cell types depends on a key activator in the developmental pathway, AdpA. Importantly, when we manipulated local gradients by growing competing microbes nearby, or through physical disruption, expression in these pathways could be decoupled and/or disordered, respectively. Finally, the normal spatial organization of these cell types was partially restored with the addition of a siderophore, a public good made by these organisms, to the growth medium. Together, these results indicate that spatial divisions of labor in S. coelicolor colonies are determined by a combination of physiological gradients and regulatory network architecture, key factors that also drive patterns of cellular differentiation in multicellular eukaryotic organisms.
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Ali S, Arif I, Iqbal A, Hussain I, Abrar M, Khan MR, Shubin N, Abbasi AA. Comparative genomic analysis of human GLI2 locus using slowly evolving fish revealed the ancestral gnathostome set of early developmental enhancers. Dev Dyn 2021; 250:669-683. [PMID: 33381902 PMCID: PMC9292287 DOI: 10.1002/dvdy.291] [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: 04/21/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 12/03/2022] Open
Abstract
Background The zinc finger‐containing transcription factor Gli2, is a key mediator of Hedgehog (Hh) signaling and participates in embryonic patterning of various organs including the central nervous system (CNS) and limbs. Abnormal expression of Gli2 can impede the transcription of Hh target genes through disruption of proper balance between Gli2 and Gli3 functions. Therefore, delineation of enhancers that are required for complementary roles of Glis would allow the interrogation of those pathogenic variants that cause gene dysregulation, and a corresponding abnormal phenotype. Previously, we reported tissue‐specific enhancers for Gli family including Gli2 through direct tetrapod‐teleost comparisons. Results Here, we employed the sequence alignments of slowly evolving spotted gar and elephant shark and have identified six novel conserved noncoding elements in human GLI2 containing locus. Zebrafish‐based transgenic assays revealed that combined action of these autonomous CNEs reflects many aspects of Gli2 specific endogenous transcriptional activity, including CNS and pectoral fins. Conclusion Taken together with our previous findings, this study suggests that Hh‐signaling controlled deployment of Gli2 activity in embryonic patterning arose in the common ancestor of gnathostomes. These GLI2 specific cis‐regulatory modules will help to identify DNA variants that probably reside outside of coding intervals and are associated with congenital anomalies. We performed a phylogenetic footprint analyses of human GLI2 containing locus by incorporating relatively slowly evolving gar and elephant shark genomes and have identified multiple novel conserved non‐coding elements (CNEs) that were not predicted by direct human‐teleostcomparisons. Comparative analyses suggest that majority of the GLI2 associated CNEs identified in the present data and reported previously arose in the common ancestor of gnathostomes but lost in teleosts, presumably because of fast teleost sequence evolution. Functional testing of GLI2 associated CNEs by employing zebrafish based transgenic reporter assays revealed their tissue specific cis‐regulatory potential that corresponds with the results based on whole‐mount in situ hybridization analysis of gli2 mRNA in zebrafish. The delineated set of GLI2 associated enhancers can be further interrogated to determine their role in canonical Hh signaling, gene dysregulation, and a corresponding congenital anomaly.
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Affiliation(s)
- Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Irum Arif
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Ayesha Iqbal
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Islamabad, Pakistan
| | - Neil Shubin
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, USA
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
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