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Patierno BM, Emerson MM. Enhanced Plasmid-Based Transcriptional Activation in Developing Mouse Photoreceptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597220. [PMID: 38895286 PMCID: PMC11185626 DOI: 10.1101/2024.06.06.597220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Rod photoreceptor formation in the postnatal mouse is a widely used model system for studying mammalian photoreceptor development. This experimental paradigm provides opportunities for both gain and loss-of-function studies which can be accomplished through in vivo plasmid delivery and electroporation. However, the cis-regulatory elements used to implement this approach have not been fully evaluated or optimized for the unique transcriptional environment of photoreceptors. Here we report that the use of a photoreceptor cis-regulatory element from the Crx gene in combination with broadly active promoter elements can increase the targeting of developing rod photoreceptors in the mouse. This can lead to greater reporter expression, as well as enhanced misexpression and loss-of-function phenotypes in these cells. This study also highlights the importance of identifying and testing relevant cis-regulatory elements when planning cell subtype specific experiments. The use of the specific hybrid elements in this study will provide a more efficacious gene delivery system to study mammalian photoreceptor formation.
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Affiliation(s)
- Brendon M. Patierno
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, 10031
| | - Mark M. Emerson
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, 10031
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031
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2
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Zheng Y, Stormo GD, Chen S. Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584677. [PMID: 38559186 PMCID: PMC10979960 DOI: 10.1101/2024.03.12.584677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Paired-class homeodomain transcription factors (HD TFs) play essential roles in vertebrate development, and their mutations are linked to human diseases. One unique feature of paired-class HD is cooperative dimerization on specific palindrome DNA sequences. Yet, the functional significance of HD cooperative dimerization in animal development and its dysregulation in diseases remain elusive. Using the retinal TF Cone-rod Homeobox (CRX) as a model, we have studied how blindness-causing mutations in the paired HD, p.E80A and p.K88N, alter CRX's cooperative dimerization, lead to gene misexpression and photoreceptor developmental deficits in dominant manners. CRXE80A maintains binding at monomeric WT CRX motifs but is deficient in cooperative binding at dimeric motifs. CRXE80A's cooperativity defect impacts the exponential increase of photoreceptor gene expression in terminal differentiation and produces immature, non-functional photoreceptors in the CrxE80A retinas. CRXK88N is highly cooperative and localizes to ectopic genomic sites with strong enrichment of dimeric HD motifs. CRXK88N's altered biochemical properties disrupt CRX's ability to direct dynamic chromatin remodeling during development to activate photoreceptor differentiation programs and silence progenitor programs. Our study here provides in vitro and in vivo molecular evidence that paired-class HD cooperative dimerization regulates neuronal development and dysregulation of cooperative binding contributes to severe dominant blinding retinopathies.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
| | - Gary D. Stormo
- Department of Genetics, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
- Department of Developmental Biology, Washington University in St Louis, Saint Louis, Missouri, 63110, USA
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3
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Zheng Y, Chen S. Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research. Front Cell Neurosci 2024; 18:1347436. [PMID: 38414750 PMCID: PMC10896975 DOI: 10.3389/fncel.2024.1347436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
The vertebrate retina is made up of six specialized neuronal cell types and one glia that are generated from a common retinal progenitor. The development of these distinct cell types is programmed by transcription factors that regulate the expression of specific genes essential for cell fate specification and differentiation. Because of the complex nature of transcriptional regulation, understanding transcription factor functions in development and disease is challenging. Research on the Cone-rod homeobox transcription factor CRX provides an excellent model to address these challenges. In this review, we reflect on 25 years of mammalian CRX research and discuss recent progress in elucidating the distinct pathogenic mechanisms of four CRX coding variant classes. We highlight how in vitro biochemical studies of CRX protein functions facilitate understanding CRX regulatory principles in animal models. We conclude with a brief discussion of the emerging systems biology approaches that could accelerate precision medicine for CRX-linked diseases and beyond.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
| | - Shiming Chen
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, Saint Louis, MO, United States
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4
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Javed A, Santos-França PL, Mattar P, Cui A, Kassem F, Cayouette M. Ikaros family proteins redundantly regulate temporal patterning in the developing mouse retina. Development 2023; 150:286611. [PMID: 36537580 DOI: 10.1242/dev.200436] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/06/2022] [Indexed: 12/24/2022]
Abstract
Temporal identity factors regulate competence of neural progenitors to generate specific cell types in a time-dependent manner, but how they operate remains poorly defined. In the developing mouse retina, the Ikaros zinc-finger transcription factor Ikzf1 regulates production of early-born cell types, except cone photoreceptors. In this study we show that, during early stages of retinal development, another Ikaros family protein, Ikzf4, functions redundantly with Ikzf1 to regulate cone photoreceptor production. Using CUT&RUN and functional assays, we show that Ikzf4 binds and represses genes involved in late-born rod photoreceptor specification, hence favoring cone production. At late stages, when Ikzf1 is no longer expressed in progenitors, we show that Ikzf4 re-localizes to target genes involved in gliogenesis and is required for Müller glia production. We report that Ikzf4 regulates Notch signaling genes and is sufficient to activate the Hes1 promoter through two Ikzf GGAA-binding motifs, suggesting a mechanism by which Ikzf4 may influence gliogenesis. These results uncover a combinatorial role for Ikaros family members during nervous system development and provide mechanistic insights on how they temporally regulate cell fate output.
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Affiliation(s)
- Awais Javed
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
- Molecular Biology Program, Université de Montréal, Montreal H3T 1J4, Canada
| | - Pedro L Santos-França
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
- Molecular Biology Program, Université de Montréal, Montreal H3T 1J4, Canada
| | - Pierre Mattar
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
| | - Allie Cui
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
| | - Fatima Kassem
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
- Integrated Program in Neuroscience, McGill University, Montreal H3A 0G4, Canada
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montreal H2W 1R7, Canada
- Molecular Biology Program, Université de Montréal, Montreal H3T 1J4, Canada
- Integrated Program in Neuroscience, McGill University, Montreal H3A 0G4, Canada
- Department of Medicine, Université de Montréal, Montreal H3T 1J4, Canada
- Department of Anatomy and Cell Biology, Division of Experimental Medicine, McGill University, Montreal H3A 0G4, Canada
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5
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Olmos-Carreño CL, Figueres-Oñate M, Scicolone GE, López-Mascaraque L. Cell Fate of Retinal Progenitor Cells: In Ovo UbC-StarTrack Analysis. Int J Mol Sci 2022; 23:ijms232012388. [PMID: 36293245 PMCID: PMC9604099 DOI: 10.3390/ijms232012388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/28/2022] Open
Abstract
Clonal cell analysis outlines the ontogenic potential of single progenitor cells, allowing the elucidation of the neural heterogeneity among different cell types and their lineages. In this work, we analyze the potency of retinal stem/progenitor cells through development using the chick embryo as a model. We implemented in ovo the clonal genetic tracing strategy UbC-StarTrack for tracking retinal cell lineages derived from individual progenitors of the ciliary margin at E3.5 (HH21-22). The clonal assignment of the derived-cell progeny was performed in the neural retina at E11.5-12 (HH38) through the identification of sibling cells as cells expressing the same combination of fluorophores. Moreover, cell types were assessed based on their cellular morphology and laminar location. Ciliary margin derived-cell progenies are organized in columnar associations distributed along the peripheral retina with a limited tangential dispersion. The analysis revealed that, at the early stages of development, this region harbors multipotent and committed progenitor cells.
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Affiliation(s)
- Cindy L. Olmos-Carreño
- Instituto de Biología Celular y Neurociencias “Prof. E. De Robertis” (IBCN), CONICET and Departamento de Biología Celular, Histología, Embriología y Genética, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires 1121, Argentina
- Instituto Cajal-CSIC, Molecular, Cellular and Developmental Neurobiology Department, 28002 Madrid, Spain
| | - María Figueres-Oñate
- Instituto Cajal-CSIC, Molecular, Cellular and Developmental Neurobiology Department, 28002 Madrid, Spain
- Correspondence: (M.F.-O.); (L.L.-M.)
| | - Gabriel E. Scicolone
- Instituto de Biología Celular y Neurociencias “Prof. E. De Robertis” (IBCN), CONICET and Departamento de Biología Celular, Histología, Embriología y Genética, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires 1121, Argentina
| | - Laura López-Mascaraque
- Instituto Cajal-CSIC, Molecular, Cellular and Developmental Neurobiology Department, 28002 Madrid, Spain
- Correspondence: (M.F.-O.); (L.L.-M.)
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6
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Bachu VS, Kandoi S, Park KU, Kaufman ML, Schwanke M, Lamba DA, Brzezinski JA. An enhancer located in a Pde6c intron drives transient expression in the cone photoreceptors of developing mouse and human retinas. Dev Biol 2022; 488:131-150. [PMID: 35644251 PMCID: PMC10676565 DOI: 10.1016/j.ydbio.2022.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/29/2022] [Accepted: 05/19/2022] [Indexed: 02/04/2023]
Abstract
How cone photoreceptors are formed during retinal development is only partially known. This is in part because we do not fully understand the gene regulatory network responsible for cone genesis. We reasoned that cis-regulatory elements (enhancers) active in nascent cones would be regulated by the same upstream network that controls cone formation. To dissect this network, we searched for enhancers active in developing cones. By electroporating enhancer-driven fluorescent reporter plasmids, we observed that a sequence within an intron of the cone-specific Pde6c gene acted as an enhancer in developing mouse cones. Similar fluorescent reporter plasmids were used to generate stable transgenic human induced pluripotent stem cells that were then grown into three-dimensional human retinal organoids. These organoids contained fluorescently labeled cones, demonstrating that the Pde6c enhancer was also active in human cones. We observed that enhancer activity was transient and labeled a minor population of developing rod photoreceptors in both mouse and human systems. This cone-enriched pattern argues that the Pde6c enhancer is activated in cells poised between rod and cone fates. Additionally, it suggests that the Pde6c enhancer is activated by the same regulatory network that selects or stabilizes cone fate choice. To further understand this regulatory network, we identified essential enhancer sequence regions through a series of mutagenesis experiments. This suggested that the Pde6c enhancer was regulated by transcription factor binding at five or more locations. Binding site predictions implicated transcription factor families known to control photoreceptor formation and families not previously associated with cone development. These results provide a framework for deciphering the gene regulatory network that controls cone genesis in both human and mouse systems. Our new transgenic human stem cell lines provide a tool for determining which cone developmental mechanisms are shared and distinct between mice and humans.
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Affiliation(s)
- Vismaya S Bachu
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sangeetha Kandoi
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michael L Kaufman
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michael Schwanke
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Deepak A Lamba
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Joseph A Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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7
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Honnell V, Norrie JL, Patel AG, Ramirez C, Zhang J, Lai YH, Wan S, Dyer MA. Identification of a modular super-enhancer in murine retinal development. Nat Commun 2022; 13:253. [PMID: 35017532 PMCID: PMC8752785 DOI: 10.1038/s41467-021-27924-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 12/20/2021] [Indexed: 11/23/2022] Open
Abstract
Super-enhancers are expansive regions of genomic DNA comprised of multiple putative enhancers that contribute to the dynamic gene expression patterns during development. This is particularly important in neurogenesis because many essential transcription factors have complex developmental stage- and cell-type specific expression patterns across the central nervous system. In the developing retina, Vsx2 is expressed in retinal progenitor cells and is maintained in differentiated bipolar neurons and Müller glia. A single super-enhancer controls this complex and dynamic pattern of expression. Here we show that deletion of one region disrupts retinal progenitor cell proliferation but does not affect cell fate specification. The deletion of another region has no effect on retinal progenitor cell proliferation but instead leads to a complete loss of bipolar neurons. This prototypical super-enhancer may serve as a model for dissecting the complex gene expression patterns for neurogenic transcription factors during development. Moreover, it provides a unique opportunity to alter expression of individual transcription factors in particular cell types at specific stages of development. This provides a deeper understanding of function that cannot be achieved with traditional knockout mouse approaches.
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Affiliation(s)
- Victoria Honnell
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jackie L Norrie
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Anand G Patel
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Cody Ramirez
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jiakun Zhang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yu-Hsuan Lai
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shibiao Wan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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8
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Chen X, Emerson MM. Notch signaling represses cone photoreceptor formation through the regulation of retinal progenitor cell states. Sci Rep 2021; 11:14525. [PMID: 34267251 PMCID: PMC8282820 DOI: 10.1038/s41598-021-93692-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/25/2021] [Indexed: 11/29/2022] Open
Abstract
Notch signaling is required to repress the formation of vertebrate cone photoreceptors and to maintain the proliferative potential of multipotent retinal progenitor cells. However, the mechanism by which Notch signaling controls these processes is unknown. Recently, restricted retinal progenitor cells with limited proliferation capacity and that preferentially generate cone photoreceptors have been identified. Thus, there are several potential steps during cone genesis that Notch signaling could act. Here we use cell type specific cis-regulatory elements to localize the primary role of Notch signaling in cone genesis to the formation of restricted retinal progenitor cells from multipotent retinal progenitor cells. Localized inhibition of Notch signaling in restricted progenitor cells does not alter the number of cones derived from these cells. Cell cycle promotion is not a primary effect of Notch signaling but an indirect effect on progenitor cell state transitions that leads to depletion of the multipotent progenitor cell population. Taken together, this suggests that the role of Notch signaling in cone photoreceptor formation and proliferation are both mediated by a localized function of Notch in multipotent retinal progenitor cells to repress the formation of restricted progenitor cells.
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Affiliation(s)
- Xueqing Chen
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, 10016, USA
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Mark M Emerson
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, 10016, USA.
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA.
- Biochemistry PhD Program, The Graduate Center, The City University of New York, New York, NY, 10016, USA.
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9
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Lonfat N, Wang S, Lee C, Garcia M, Choi J, Park PJ, Cepko C. Cis-regulatory dissection of cone development reveals a broad role for Otx2 and Oc transcription factors. Development 2021; 148:dev198549. [PMID: 33929509 PMCID: PMC8126413 DOI: 10.1242/dev.198549] [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: 11/13/2020] [Accepted: 03/31/2021] [Indexed: 11/20/2022]
Abstract
The vertebrate retina is generated by retinal progenitor cells (RPCs), which produce >100 cell types. Although some RPCs produce many cell types, other RPCs produce restricted types of daughter cells, such as a cone photoreceptor and a horizontal cell (HC). We used genome-wide assays of chromatin structure to compare the profiles of a restricted cone/HC RPC and those of other RPCs in chicks. These data nominated regions of regulatory activity, which were tested in tissue, leading to the identification of many cis-regulatory modules (CRMs) active in cone/HC RPCs and developing cones. Two transcription factors, Otx2 and Oc1, were found to bind to many of these CRMs, including those near genes important for cone development and function, and their binding sites were required for activity. We also found that Otx2 has a predicted autoregulatory CRM. These results suggest that Otx2, Oc1 and possibly other Onecut proteins have a broad role in coordinating cone development and function. The many newly discovered CRMs for cones are potentially useful reagents for gene therapy of cone diseases.
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Affiliation(s)
- Nicolas Lonfat
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
- Department of Ophthalmology, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Su Wang
- Department of Biomedical Informatics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - ChangHee Lee
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Mauricio Garcia
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
- Department of Ophthalmology, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Jiho Choi
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
- Department of Ophthalmology, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Peter J. Park
- Department of Biomedical Informatics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Connie Cepko
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
- Department of Ophthalmology, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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10
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Schick E, Gonzalez KC, Dutta P, Hossain K, Ghinia Tegla MG, Emerson MM. Early cis-regulatory events in the formation of retinal horizontal cells. Dev Biol 2021; 476:88-100. [PMID: 33774011 DOI: 10.1016/j.ydbio.2021.03.016] [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: 12/01/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 11/25/2022]
Abstract
During retinal development, multipotent and restricted progenitor cells generate all of the neuronal cells of the retina. Among these are horizontal cells, which are interneurons that modulate the light-induced signal from photoreceptors. This study utilizes the identification of novel cis-regulatory elements as a method to examine the gene regulatory networks that direct the development of horizontal cells. Here we describe a screen for cis-regulatory elements, or enhancers, for the horizontal cell-associated genes PTF1A, ONECUT1 (OC1), TFAP2A (AP2A), and LHX1. The OC1ECR22 and Tfap2aACR5 elements were shown to be potential enhancers for OC1 and TFAP2A, respectively, and to be specifically active in developing horizontal cells. The OC1ECR22 element is activated by PTF1A and RBPJ, which translates to regulation of OC1 expression and suggests that PTF1A is a direct activator of OC1 expression in developing horizontal cells. The region within the Tfap2aACR5 element that is responsible for its activation was determined to be a 100 bp sequence named Motif 4. Both OC1ECR22 and Tfap2aACR5 are negatively regulated by the nuclear receptors THRB and RXRG, as is the expression of OC1 and AP2A, suggesting that nuclear receptors may have a role in the negative regulation of horizontal cell development.
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Affiliation(s)
- Estie Schick
- Biology PhD Program, Graduate Center, City University of New York, New York, NY, 10016, USA
| | - Kevin C Gonzalez
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA
| | - Pooja Dutta
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA
| | - Kazi Hossain
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA
| | - Miruna G Ghinia Tegla
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA
| | - Mark M Emerson
- Biology PhD Program, Graduate Center, City University of New York, New York, NY, 10016, USA; Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA; Biochemistry PhD Program, Graduate Center, City University of New York, New York, NY, 10016, USA.
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11
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Vassalli QA, Colantuono C, Nittoli V, Ferraioli A, Fasano G, Berruto F, Chiusano ML, Kelsh RN, Sordino P, Locascio A. Onecut Regulates Core Components of the Molecular Machinery for Neurotransmission in Photoreceptor Differentiation. Front Cell Dev Biol 2021; 9:602450. [PMID: 33816460 PMCID: PMC8012850 DOI: 10.3389/fcell.2021.602450] [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] [Received: 09/03/2020] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Photoreceptor cells (PRC) are neurons highly specialized for sensing light stimuli and have considerably diversified during evolution. The genetic mechanisms that underlie photoreceptor differentiation and accompanied the progressive increase in complexity and diversification of this sensory cell type are a matter of great interest in the field. A role of the homeodomain transcription factor Onecut (Oc) in photoreceptor cell formation is proposed throughout multicellular organisms. However, knowledge of the identity of the Oc downstream-acting factors that mediate specific tasks in the differentiation of the PRC remains limited. Here, we used transgenic perturbation of the Ciona robusta Oc protein to show its requirement for ciliary PRC differentiation. Then, transcriptome profiling between the trans-activation and trans-repression Oc phenotypes identified differentially expressed genes that are enriched in exocytosis, calcium homeostasis, and neurotransmission. Finally, comparison of RNA-Seq datasets in Ciona and mouse identifies a set of Oc downstream genes conserved between tunicates and vertebrates. The transcription factor Oc emerges as a key regulator of neurotransmission in retinal cell types.
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Affiliation(s)
- Quirino Attilio Vassalli
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Chiara Colantuono
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Valeria Nittoli
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Anna Ferraioli
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Giulia Fasano
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Federica Berruto
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Maria Luisa Chiusano
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Agriculture, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Robert Neil Kelsh
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, London, United Kingdom
| | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Annamaria Locascio
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
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12
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Ghinia Tegla MG, Buenaventura DF, Kim DY, Thakurdin C, Gonzalez KC, Emerson MM. OTX2 represses sister cell fate choices in the developing retina to promote photoreceptor specification. eLife 2020; 9:e54279. [PMID: 32347797 PMCID: PMC7237216 DOI: 10.7554/elife.54279] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/28/2020] [Indexed: 12/20/2022] Open
Abstract
During vertebrate retinal development, subsets of progenitor cells generate progeny in a non-stochastic manner, suggesting that these decisions are tightly regulated. However, the gene-regulatory network components that are functionally important in these progenitor cells are largely unknown. Here we identify a functional role for the OTX2 transcription factor in this process. CRISPR/Cas9 gene editing was used to produce somatic mutations of OTX2 in the chick retina and identified similar phenotypes to those observed in human patients. Single cell RNA sequencing was used to determine the functional consequences OTX2 gene editing on the population of cells derived from OTX2-expressing retinal progenitor cells. This confirmed that OTX2 is required for the generation of photoreceptors, but also for repression of specific retinal fates and alternative gene regulatory networks. These include specific subtypes of retinal ganglion and horizontal cells, suggesting that in this context, OTX2 functions to repress sister cell fate choices.
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Affiliation(s)
| | - Diego F Buenaventura
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
- PhD Program in Biology, The Graduate Center of the City University of New York (CUNY)New YorkUnited States
| | - Diana Y Kim
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
| | - Cassandra Thakurdin
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
| | - Kevin C Gonzalez
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
| | - Mark M Emerson
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
- PhD Program in Biology, The Graduate Center of the City University of New York (CUNY)New YorkUnited States
- PhD Program in Biochemistry, The Graduate Center of the City University of New York (CUNY)New YorkUnited States
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Patoori S, Jean-Charles N, Gopal A, Sulaiman S, Gopal S, Wang B, Souferi B, Emerson MM. Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells. Neural Dev 2020; 15:5. [PMID: 32192535 PMCID: PMC7082998 DOI: 10.1186/s13064-020-00142-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/27/2020] [Indexed: 01/03/2023] Open
Abstract
Background The vertebrate retina consists of six major classes of neuronal cells. During development, these cells are generated from a pool of multipotent retinal progenitor cells (RPCs) that express the gene Vsx2. Fate-restricted RPCs have recently been identified, with limited mitotic potential and cell fate possibilities compared to multipotent RPCs. One population of fate-restricted RPCs, marked by activity of the regulatory element ThrbCRM1, gives rise to both cone photoreceptors and horizontal cells. These cells do not express Vsx2, but co-express the transcription factors (TFs) Onecut1 and Otx2, which bind to ThrbCRM1. The components of the gene regulatory networks that control the transition from multipotent to fate-restricted gene expression are not known. This work aims to identify and evaluate cis-regulatory elements proximal to Onecut1 to identify the gene regulatory networks involved in RPC fate-restriction. Method We identified regulatory elements through ATAC-seq and conservation, followed by reporter assays to screen for activity based on temporal and spatial criteria. The regulatory elements of interest were subject to deletion and mutation analysis to identify functional sequences and evaluated by quantitative flow cytometry assays. Finally, we combined the enhancer::reporter assays with candidate TF overexpression to evaluate the relationship between the TFs, the enhancers, and early vertebrate retinal development. Statistical tests included ANOVA, Kruskal-Wallis, or unpaired t-tests. Results Two regulatory elements, ECR9 and ECR65, were identified to be active in ThrbCRM1(+) restricted RPCs. Candidate bHLH binding sites were identified as critical sequences in both elements. Overexpression of candidate bHLH TFs revealed specific enhancer-bHLH interactions. Nhlh1 overexpression expanded ECR65 activity into the Vsx2(+) RPC population, and overexpression of NeuroD1/NeuroG2/NeuroD4 had a similar effect on ECR9. Furthermore, bHLHs that were able to activate ectopic ECR9 reporter were able to induce endogenous Otx2 expression. Conclusions This work reports a large-scale screen to identify spatiotemporally specific regulatory elements near the Onecut1 locus. These elements were used to identify distinct populations in the developing retina. In addition, fate-restricted regulatory elements responded differentially to bHLH factors, and suggest a role for retinal bHLHs upstream of the Otx2 and Onecut1 genes during the formation of restricted RPCs from multipotent RPCs.
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Affiliation(s)
- Sruti Patoori
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, 10016, USA.,Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Nathalie Jean-Charles
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Ariana Gopal
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Sacha Sulaiman
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Sneha Gopal
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA.,Present Address: Doctoral program in Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Brian Wang
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Benjamin Souferi
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA.,Present Address: Touro College of Osteopathic Medicine, New York, NY, 10027, USA
| | - Mark M Emerson
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, 10016, USA. .,Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA. .,Biochemistry PhD Program, Graduate Center, City University of New York, New York, NY, 10016, USA.
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14
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Buenaventura DF, Corseri A, Emerson MM. Identification of Genes With Enriched Expression in Early Developing Mouse Cone Photoreceptors. Invest Ophthalmol Vis Sci 2019; 60:2787-2799. [PMID: 31260032 PMCID: PMC6607928 DOI: 10.1167/iovs.19-26951] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Purpose The early transcriptional events that occur in newly generated cone photoreceptors are not well described. Knowledge of these events is critical to provide benchmarks for in vitro-derived cone photoreceptors and to understand the process of cone and rod photoreceptor diversification. We sought to identify genes with differential gene expression in embryonic mouse cone photoreceptors. Methods The specificity of expression of the LHX4 transcription factor in developing cone photoreceptors was examined using immunofluorescence visualization in both mouse and chicken retinas. A LHX4 transgenic reporter line with high specificity for developing mouse cone photoreceptors was identified and used to purify early-stage cone photoreceptors for profiling by single-cell RNA sequencing. Comparisons were made to previous datasets targeting photoreceptors. Results The LHX4 transcription factor and a transgenic reporter were determined to be highly specific to early developing cone photoreceptors in the mouse. Single-cell transcriptional profiling identified new genes with enriched expression in cone photoreceptors relative to concurrent cell populations. Comparison to previous profiling datasets allowed for further characterization of these genes across developmental time, species, photoreceptor type, and gene regulatory network. Conclusions The LHX4 gene is highly enriched in developing cone photoreceptors as are several new genes identified through transcriptional profiling, some of which are expressed in subclusters of cones. Many of these cone-enriched genes do not show obvious de-repression in profiling of retinas mutant for the rod-specific transcription factor NRL, highlighting differences between endogenous cones and those induced in NRL mutants.
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Affiliation(s)
- Diego F Buenaventura
- Department of Biology, The City College of New York, City University of New York, New York, New York, United States.,Biology PhD Program, Graduate Center, City University of New York, New York, New York, United States
| | - Adrianne Corseri
- Department of Biology, The City College of New York, City University of New York, New York, New York, United States
| | - Mark M Emerson
- Department of Biology, The City College of New York, City University of New York, New York, New York, United States.,Biology PhD Program, Graduate Center, City University of New York, New York, New York, United States.,Biochemistry PhD Program, Graduate Center, City University of New York, New York, New York, United States
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15
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Lineage tracing analysis of cone photoreceptor associated cis-regulatory elements in the developing chicken retina. Sci Rep 2019; 9:9358. [PMID: 31249345 PMCID: PMC6597718 DOI: 10.1038/s41598-019-45750-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/14/2019] [Indexed: 02/02/2023] Open
Abstract
During vertebrate retinal development, transient populations of retinal progenitor cells with restricted cell fate choices are formed. One of these progenitor populations expresses the Thrb gene and can be identified by activity of the ThrbCRM1 cis-regulatory element. Short-term assays have concluded that these cells preferentially generate cone photoreceptors and horizontal cells, however developmental timing has precluded an extensive cell type characterization of their progeny. Here we describe the development and validation of a recombinase-based lineage tracing system for the chicken embryo to further characterize the lineage of these cells. The ThrbCRM1 element was found to preferentially form photoreceptors and horizontal cells, as well as a small number of retinal ganglion cells. The photoreceptor cell progeny are exclusively cone photoreceptors and not rod photoreceptors, confirming that ThrbCRM1 progenitor cells are restricted from the rod fate. In addition, specific subtypes of horizontal cells and retinal ganglion cells were overrepresented, suggesting that ThrbCRM1 progenitor cells are not only restricted for cell type, but for cell subtype as well.
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