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Srivastava D, Gowribidanur-Chinnaswamy P, Gaur P, Spies M, Swaroop A, Artemyev NO. Molecular basis of CRX/DNA recognition and stoichiometry at the Ret4 response element. Structure 2024:S0969-2126(24)00242-9. [PMID: 39084215 DOI: 10.1016/j.str.2024.07.004] [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: 04/19/2024] [Revised: 06/03/2024] [Accepted: 07/04/2024] [Indexed: 08/02/2024]
Abstract
Two retinal transcription factors, cone-rod homeobox (CRX) and neural retina leucine zipper (NRL), cooperate functionally and physically to control photoreceptor development and homeostasis. Mutations in CRX and NRL cause severe retinal diseases. Despite the roles of NRL and CRX, insight into their functions at the molecular level is lacking. Here, we have solved the crystal structure of the CRX homeodomain in complex with its cognate response element (Ret4) from the rhodopsin proximal promoter region. The structure reveals an unexpected 2:1 stoichiometry of CRX/Ret4 and unique orientation of CRX molecules on DNA, and it explains the mechanisms of pathogenic mutations in CRX. Mutations R41Q and E42K disrupt the CRX protein-protein contacts based on the structure and reduce the CRX/Ret4 binding stoichiometry, suggesting a novel disease mechanism. Furthermore, we show that NRL alters the stoichiometry and increases affinity of CRX binding at the rhodopsin promoter, which may enhance transcription of rod-specific genes and suppress transcription of cone-specific genes.
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Affiliation(s)
- Dhiraj Srivastava
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | | | - Paras Gaur
- Department of Biochemistry and Molecular Biology, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nikolai O Artemyev
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA; Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.
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2
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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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3
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Kolesnikov AV, Murphy DP, Corbo JC, Kefalov VJ. Germline knockout of Nr2e3 protects photoreceptors in three distinct mouse models of retinal degeneration. Proc Natl Acad Sci U S A 2024; 121:e2316118121. [PMID: 38442152 PMCID: PMC10945761 DOI: 10.1073/pnas.2316118121] [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: 09/16/2023] [Accepted: 01/17/2024] [Indexed: 03/07/2024] Open
Abstract
Retinitis pigmentosa (RP) is a common form of retinal dystrophy that can be caused by mutations in any one of dozens of rod photoreceptor genes. The genetic heterogeneity of RP represents a significant challenge for the development of effective therapies. Here, we present evidence for a potential gene-independent therapeutic strategy based on targeting Nr2e3, a transcription factor required for the normal differentiation of rod photoreceptors. Nr2e3 knockout results in hybrid rod photoreceptors that express the full complement of rod genes, but also a subset of cone genes. We show that germline deletion of Nr2e3 potently protects rods in three mechanistically diverse mouse models of retinal degeneration caused by bright-light exposure (light damage), structural deficiency (rhodopsin-deficient Rho-/- mice), or abnormal phototransduction (phosphodiesterase-deficient rd10 mice). Nr2e3 knockout confers strong neuroprotective effects on rods without adverse effects on their gene expression, structure, or function. Furthermore, in all three degeneration models, prolongation of rod survival by Nr2e3 knockout leads to lasting preservation of cone morphology and function. These findings raise the possibility that upregulation of one or more cone genes in Nr2e3-deficient rods may be responsible for the neuroprotective effects we observe.
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Affiliation(s)
- Alexander V. Kolesnikov
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA92697
| | - Daniel P. Murphy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO63110
| | - Joseph C. Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO63110
| | - Vladimir J. Kefalov
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA92697
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Loell KJ, Friedman RZ, Myers CA, Corbo JC, Cohen BA, White MA. Transcription factor interactions explain the context-dependent activity of CRX binding sites. PLoS Comput Biol 2024; 20:e1011802. [PMID: 38227575 PMCID: PMC10817189 DOI: 10.1371/journal.pcbi.1011802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 01/26/2024] [Accepted: 01/06/2024] [Indexed: 01/18/2024] Open
Abstract
The effects of transcription factor binding sites (TFBSs) on the activity of a cis-regulatory element (CRE) depend on the local sequence context. In rod photoreceptors, binding sites for the transcription factor (TF) Cone-rod homeobox (CRX) occur in both enhancers and silencers, but the sequence context that determines whether CRX binding sites contribute to activation or repression of transcription is not understood. To investigate the context-dependent activity of CRX sites, we fit neural network-based models to the activities of synthetic CREs composed of photoreceptor TFBSs. The models revealed that CRX binding sites consistently make positive, independent contributions to CRE activity, while negative homotypic interactions between sites cause CREs composed of multiple CRX sites to function as silencers. The effects of negative homotypic interactions can be overcome by the presence of other TFBSs that either interact cooperatively with CRX sites or make independent positive contributions to activity. The context-dependent activity of CRX sites is thus determined by the balance between positive heterotypic interactions, independent contributions of TFBSs, and negative homotypic interactions. Our findings explain observed patterns of activity among genomic CRX-bound enhancers and silencers, and suggest that enhancers may require diverse TFBSs to overcome negative homotypic interactions between TFBSs.
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Affiliation(s)
- Kaiser J. Loell
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
| | - Ryan Z. Friedman
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
| | - Connie A. Myers
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
| | - Joseph C. Corbo
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
| | - Barak A. Cohen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
| | - Michael A. White
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America
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Herrera I, Fernandes JAL, Shir-Mohammadi K, Levesque J, Mattar P. Lamin A upregulation reorganizes the genome during rod photoreceptor degeneration. Cell Death Dis 2023; 14:701. [PMID: 37880237 PMCID: PMC10600220 DOI: 10.1038/s41419-023-06224-x] [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: 01/26/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023]
Abstract
Neurodegenerative diseases are accompanied by dynamic changes in gene expression, including the upregulation of hallmark stress-responsive genes. While the transcriptional pathways that impart adaptive and maladaptive gene expression signatures have been the focus of intense study, the role of higher order nuclear organization in this process is less clear. Here, we examine the role of the nuclear lamina in genome organization during the degeneration of rod photoreceptors. Two proteins had previously been shown to be necessary and sufficient to tether heterochromatin at the nuclear envelope. The lamin B receptor (Lbr) is expressed during development, but downregulates upon rod differentiation. A second tether is the intermediate filament lamin A (LA), which is not normally expressed in murine rods. Here, we show that in the rd1 model of retinitis pigmentosa, LA ectopically upregulates in rod photoreceptors at the onset of degeneration. LA upregulation correlated with increased heterochromatin tethering at the nuclear periphery in rd1 rods, suggesting that LA reorganizes the nucleus. To determine how heterochromatin tethering affects the genome, we used in vivo electroporation to misexpress LA or Lbr in mature rods in the absence of degeneration, resulting in the restoration of conventional nuclear architecture. Using scRNA-seq, we show that reorganizing the nucleus via LA/Lbr misexpression has relatively minor effects on rod gene expression. Next, using ATAC-seq, we show that LA and Lbr both lead to marked increases in genome accessibility. Novel ATAC-seq peaks tended to be associated with stress-responsive genes. Together, our data reveal that heterochromatin tethers have a global effect on genome accessibility, and suggest that heterochromatin tethering primes the photoreceptor genome to respond to stress.
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Affiliation(s)
- Ivana Herrera
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - José Alex Lourenço Fernandes
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Khatereh Shir-Mohammadi
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Jasmine Levesque
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Pierre Mattar
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada.
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
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Friedman RZ, Ramu A, Lichtarge S, Myers CA, Granas DM, Gause M, Corbo JC, Cohen BA, White MA. Active learning of enhancer and silencer regulatory grammar in photoreceptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554146. [PMID: 37662358 PMCID: PMC10473580 DOI: 10.1101/2023.08.21.554146] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Cis-regulatory elements (CREs) direct gene expression in health and disease, and models that can accurately predict their activities from DNA sequences are crucial for biomedicine. Deep learning represents one emerging strategy to model the regulatory grammar that relates CRE sequence to function. However, these models require training data on a scale that exceeds the number of CREs in the genome. We address this problem using active machine learning to iteratively train models on multiple rounds of synthetic DNA sequences assayed in live mammalian retinas. During each round of training the model actively selects sequence perturbations to assay, thereby efficiently generating informative training data. We iteratively trained a model that predicts the activities of sequences containing binding motifs for the photoreceptor transcription factor Cone-rod homeobox (CRX) using an order of magnitude less training data than current approaches. The model's internal confidence estimates of its predictions are reliable guides for designing sequences with high activity. The model correctly identified critical sequence differences between active and inactive sequences with nearly identical transcription factor binding sites, and revealed order and spacing preferences for combinations of motifs. Our results establish active learning as an effective method to train accurate deep learning models of cis-regulatory function after exhausting naturally occurring training examples in the genome.
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Affiliation(s)
- Ryan Z. Friedman
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, MO, 63110
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, 63110
| | - Avinash Ramu
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, MO, 63110
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, 63110
| | - Sara Lichtarge
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, MO, 63110
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, 63110
| | - Connie A. Myers
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110
| | - David M. Granas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, MO, 63110
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, 63110
| | - Maria Gause
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110
| | - Joseph C. Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110
| | - Barak A. Cohen
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, MO, 63110
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, 63110
| | - Michael A. White
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, MO, 63110
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, 63110
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7
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A single-cell massively parallel reporter assay detects cell-type-specific gene regulation. Nat Genet 2023; 55:346-354. [PMID: 36635387 PMCID: PMC9931678 DOI: 10.1038/s41588-022-01278-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/05/2022] [Indexed: 01/14/2023]
Abstract
Massively parallel reporter gene assays are key tools in regulatory genomics but cannot be used to identify cell-type-specific regulatory elements without performing assays serially across different cell types. To address this problem, we developed a single-cell massively parallel reporter assay (scMPRA) to measure the activity of libraries of cis-regulatory sequences (CRSs) across multiple cell types simultaneously. We assayed a library of core promoters in a mixture of HEK293 and K562 cells and showed that scMPRA is a reproducible, highly parallel, single-cell reporter gene assay that detects cell-type-specific cis-regulatory activity. We then measured a library of promoter variants across multiple cell types in live mouse retinas and showed that subtle genetic variants can produce cell-type-specific effects on cis-regulatory activity. We anticipate that scMPRA will be widely applicable for studying the role of CRSs across diverse cell types.
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8
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Sun C, Chen S. Disease-causing mutations in genes encoding transcription factors critical for photoreceptor development. Front Mol Neurosci 2023; 16:1134839. [PMID: 37181651 PMCID: PMC10172487 DOI: 10.3389/fnmol.2023.1134839] [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: 12/30/2022] [Accepted: 04/04/2023] [Indexed: 05/16/2023] Open
Abstract
Photoreceptor development of the vertebrate visual system is controlled by a complex transcription regulatory network. OTX2 is expressed in the mitotic retinal progenitor cells (RPCs) and controls photoreceptor genesis. CRX that is activated by OTX2 is expressed in photoreceptor precursors after cell cycle exit. NEUROD1 is also present in photoreceptor precursors that are ready to specify into rod and cone photoreceptor subtypes. NRL is required for the rod fate and regulates downstream rod-specific genes including the orphan nuclear receptor NR2E3 which further activates rod-specific genes and simultaneously represses cone-specific genes. Cone subtype specification is also regulated by the interplay of several transcription factors such as THRB and RXRG. Mutations in these key transcription factors are responsible for ocular defects at birth such as microphthalmia and inherited photoreceptor diseases such as Leber congenital amaurosis (LCA), retinitis pigmentosa (RP) and allied dystrophies. In particular, many mutations are inherited in an autosomal dominant fashion, including the majority of missense mutations in CRX and NRL. In this review, we describe the spectrum of photoreceptor defects that are associated with mutations in the above-mentioned transcription factors, and summarize the current knowledge of molecular mechanisms underlying the pathogenic mutations. At last, we deliberate the outstanding gaps in our understanding of the genotype-phenotype correlations and outline avenues for future research of the treatment strategies.
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Affiliation(s)
- Chi Sun
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, United States
- *Correspondence: Chi Sun,
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, United States
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9
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Niewiadomska-Cimicka A, Hache A, Le Gras S, Keime C, Ye T, Eisenmann A, Harichane I, Roux MJ, Messaddeq N, Clérin E, Léveillard T, Trottier Y. Polyglutamine-expanded ATXN7 alters a specific epigenetic signature underlying photoreceptor identity gene expression in SCA7 mouse retinopathy. J Biomed Sci 2022; 29:107. [PMID: 36539812 PMCID: PMC9768914 DOI: 10.1186/s12929-022-00892-1] [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: 08/02/2022] [Accepted: 12/11/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disorder that primarily affects the cerebellum and retina. SCA7 is caused by a polyglutamine expansion in the ATXN7 protein, a subunit of the transcriptional coactivator SAGA that acetylates histone H3 to deposit narrow H3K9ac mark at DNA regulatory elements of active genes. Defective histone acetylation has been presented as a possible cause for gene deregulation in SCA7 mouse models. However, the topography of acetylation defects at the whole genome level and its relationship to changes in gene expression remain to be determined. METHODS We performed deep RNA-sequencing and chromatin immunoprecipitation coupled to high-throughput sequencing to examine the genome-wide correlation between gene deregulation and alteration of the active transcription marks, e.g. SAGA-related H3K9ac, CBP-related H3K27ac and RNA polymerase II (RNAPII), in a SCA7 mouse retinopathy model. RESULTS Our analyses revealed that active transcription marks are reduced at most gene promoters in SCA7 retina, while a limited number of genes show changes in expression. We found that SCA7 retinopathy is caused by preferential downregulation of hundreds of highly expressed genes that define morphological and physiological identities of mature photoreceptors. We further uncovered that these photoreceptor genes harbor unusually broad H3K9ac profiles spanning the entire gene bodies and have a low RNAPII pausing. This broad H3K9ac signature co-occurs with other features that delineate superenhancers, including broad H3K27ac, binding sites for photoreceptor specific transcription factors and expression of enhancer-related non-coding RNAs (eRNAs). In SCA7 retina, downregulated photoreceptor genes show decreased H3K9 and H3K27 acetylation and eRNA expression as well as increased RNAPII pausing, suggesting that superenhancer-related features are altered. CONCLUSIONS Our study thus provides evidence that distinctive epigenetic configurations underlying high expression of cell-type specific genes are preferentially impaired in SCA7, resulting in a defect in the maintenance of identity features of mature photoreceptors. Our results also suggest that continuous SAGA-driven acetylation plays a role in preserving post-mitotic neuronal identity.
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Affiliation(s)
- Anna Niewiadomska-Cimicka
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Antoine Hache
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Stéphanie Le Gras
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Céline Keime
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Tao Ye
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Aurelie Eisenmann
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Imen Harichane
- grid.462844.80000 0001 2308 1657Department of Genetics, INSERM, CNRS, Institut de la Vision, Sorbonne University, 75012 Paris, France
| | - Michel J. Roux
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Nadia Messaddeq
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Emmanuelle Clérin
- grid.462844.80000 0001 2308 1657Department of Genetics, INSERM, CNRS, Institut de la Vision, Sorbonne University, 75012 Paris, France
| | - Thierry Léveillard
- grid.462844.80000 0001 2308 1657Department of Genetics, INSERM, CNRS, Institut de la Vision, Sorbonne University, 75012 Paris, France
| | - Yvon Trottier
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
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10
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Langouët M, Jolicoeur C, Javed A, Mattar P, Gearhart MD, Daiger SP, Bertelsen M, Tranebjærg L, Rendtorff ND, Grønskov K, Jespersgaard C, Chen R, Sun Z, Li H, Alirezaie N, Majewski J, Bardwell VJ, Sui R, Koenekoop RK, Cayouette M. Mutations in BCOR, a co-repressor of CRX/OTX2, are associated with early-onset retinal degeneration. SCIENCE ADVANCES 2022; 8:eabh2868. [PMID: 36070393 PMCID: PMC9451151 DOI: 10.1126/sciadv.abh2868] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/21/2022] [Indexed: 06/10/2023]
Abstract
Many transcription factors regulating the production, survival, and function of photoreceptor cells have been identified, but little is known about transcriptional co-regulators in retinal health and disease. Here, we show that BCL6 co-repressor (BCOR), a Polycomb repressive complex 1 factor mutated in various cancers, is involved in photoreceptor degenerative diseases. Using proteomics and transcription assays, we report that BCOR interacts with the transcription factors CRX and OTX2 and reduces their ability to activate the promoters of photoreceptor-specific genes. CUT&RUN sequencing further shows that BCOR shares genome-wide binding profiles with CRX/OTX2, consistent with a general co-repression activity. We also identify missense mutations in human BCOR in five families that have no evidence of cancer but present severe early-onset X-linked retinal degeneration. Last, we show that the human BCOR mutants cause degeneration when expressed in the mouse retina and have enhanced repressive activity on OTX2. These results uncover a role for BCOR in photoreceptors in both health and disease.
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Affiliation(s)
- Maéva Langouët
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Christine Jolicoeur
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Awais Javed
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Pierre Mattar
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Micah D. Gearhart
- Department of Genetics, Cell Biology and Development, Development Biology Center, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stephen P. Daiger
- EHGED Department, Human Genetics Center, School of Public Health, University of Texas HSC, Houston, TX 77030, USA
| | - Mette Bertelsen
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
- Department of Ophthalmology, Rigshospitalet, The Kennedy Centre, Glostrup, Denmark
| | - Lisbeth Tranebjærg
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Denmark
| | - Nanna D. Rendtorff
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
| | - Karen Grønskov
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
| | - Catherine Jespersgaard
- Department of Clinical Genetics, Rigshospitalet, The Kennedy Centre, Copenhagen, Denmark
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Zixi Sun
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Hui Li
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Najmeh Alirezaie
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Vivian J. Bardwell
- Department of Genetics, Cell Biology and Development, Development Biology Center, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ruifang Sui
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Robert K. Koenekoop
- Departments of Pediatric Surgery, Human Genetics, Adult Ophthalmology and the McGill Ocular Genetics Laboratory, McGill University Health Center Research Institute, Montreal, QC, Canada
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Anatomy and Cell Biology, Division of Experimental Medicine, McGill University, Montreal, QC, Canada
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11
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Zhang X, Zhang BW, Xiang L, Wu H, Sahiri Alexander SUPITA, Zhou P, Zi-Yu Dai M, Wang X, Xiong W, Zhang Y, Jin ZB, Deng LW. MLL5 is involved in retinal photoreceptor maturation through facilitating CRX-mediated photoreceptor gene transactivation. iScience 2022; 25:104058. [PMID: 35359806 PMCID: PMC8961232 DOI: 10.1016/j.isci.2022.104058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/11/2021] [Accepted: 03/07/2022] [Indexed: 11/06/2022] Open
Abstract
Histone methylation, particularly at the H3K4 position, is thought to contribute to the specification of photoreceptor cell fate; however, the mechanisms linking histone methylation with transcription factor transactivation and photoreceptor gene expression have not yet been determined. Here, we demonstrate that MLL5 is abundantly expressed in the mouse retina. Mll5 deficiency impaired electroretinogram responses, alongside attenuated expression of a number of retina genes. Mechanistic studies revealed that MLL5 interacts with the retina-specific transcription factor, CRX, contributing to its binding to photoreceptor-specific gene promoters. Moreover, depletion of MLL5 impairs H3K4 methylation and H3K79 methylation, which subsequently compromises CRX-CBP assembly and H3 acetylation on photoreceptor promoters. Our data support a scenario in which recognition of H3K4 methylation by MLL5 is required for photoreceptor-specific gene transcription through maintaining a permissive chromatin state and proper CRX-CBP recruitment at promoter sites. MLL5 is essential for the expression of critical photoreceptor genes MLL5 depletion reduces H3K4/K79 methylation at photoreceptor gene promoters MLL5 interacts with CRX via its CD4 domain Recognition of H3K4me2/3 by MLL5 is a prerequisite for CRX recruitment to chromatin
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12
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Sirés A, Turch-Anguera M, Bogdanov P, Sampedro J, Ramos H, Ruíz Lasa A, Huo J, Xu S, Lam KP, López-Soriano J, Pérez-García MJ, Hernández C, Simó R, Solé M, Comella JX. Faim knockout leads to gliosis and late-onset neurodegeneration of photoreceptors in the mouse retina. J Neurosci Res 2021; 99:3103-3120. [PMID: 34713467 DOI: 10.1002/jnr.24978] [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: 04/27/2021] [Revised: 08/13/2021] [Accepted: 09/21/2021] [Indexed: 01/08/2023]
Abstract
Fas Apoptotic Inhibitory Molecule protein (FAIM) is a death receptor antagonist and an apoptosis regulator. It encodes two isoforms, namely FAIM-S (short) and FAIM-L (long), both with significant neuronal functions. FAIM-S, which is ubiquitously expressed, is involved in neurite outgrowth. In contrast, FAIM-L is expressed only in neurons and it protects them from cell death. Interestingly, FAIM-L is downregulated in patients and mouse models of Alzheimer's disease before the onset of neurodegeneration, and Faim transcript levels are decreased in mouse models of retinal degeneration. However, few studies have addressed the role of FAIM in the central nervous system, yet alone the retina. The retina is a highly specialized tissue, and its degeneration has proved to precede pathological mechanisms of neurodegenerative diseases. Here we describe that Faim depletion in mice damages the retina persistently and leads to late-onset photoreceptor death in older mice. Immunohistochemical analyses showed that Faim knockout (Faim-/- ) mice present ubiquitinated aggregates throughout the retina from early ages. Moreover, retinal cells released stress signals that can signal to Müller cells, as shown by immunofluorescence and qRT-PCR. Müller cells monitor retinal homeostasis and trigger a gliotic response in Faim-/- mice that becomes pathogenic when sustained. In this regard, we observed pronounced vascular leakage at later ages, which may be caused by persistent inflammation. These results suggest that FAIM is an important player in the maintenance of retinal homeostasis, and they support the premise that FAIM is a plausible early marker for late photoreceptor and neuronal degeneration.
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Affiliation(s)
- Anna Sirés
- Cell Signaling and Apoptosis Group, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain.,Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Mireia Turch-Anguera
- Cell Signaling and Apoptosis Group, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.,Diabetes and Metabolism Research Unit, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Patricia Bogdanov
- Diabetes and Metabolism Research Unit, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Joel Sampedro
- Diabetes and Metabolism Research Unit, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Hugo Ramos
- Diabetes and Metabolism Research Unit, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Agustín Ruíz Lasa
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain.,Research Center and Memory Clinic. Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Jianxin Huo
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Shengli Xu
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Kong-Peng Lam
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Joaquín López-Soriano
- Cell Signaling and Apoptosis Group, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain.,Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - M Jose Pérez-García
- Cell Signaling and Apoptosis Group, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
| | - Cristina Hernández
- Diabetes and Metabolism Research Unit, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Rafael Simó
- Diabetes and Metabolism Research Unit, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Montse Solé
- Cell Signaling and Apoptosis Group, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain.,Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Joan X Comella
- Cell Signaling and Apoptosis Group, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain.,Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
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13
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Venturini G, Kokona D, Steiner BL, Bulla EG, Jovanovic J, Zinkernagel MS, Escher P. In vivo analysis of onset and progression of retinal degeneration in the Nr2e3 rd7/rd7 mouse model of enhanced S-cone sensitivity syndrome. Sci Rep 2021; 11:19032. [PMID: 34561487 PMCID: PMC8463594 DOI: 10.1038/s41598-021-98271-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 09/06/2021] [Indexed: 12/02/2022] Open
Abstract
The photoreceptor-specific nuclear receptor Nr2e3 is not expressed in Nr2e3rd7/rd7 mice, a mouse model of the recessively inherited retinal degeneration enhanced S-cone sensitivity syndrome (ESCS). We characterized in detail C57BL/6J Nr2e3rd7/rd7 mice in vivo by fundus photography, optical coherence tomography and fluorescein angiography and, post mortem, by histology and immunohistochemistry. White retinal spots and so-called 'rosettes' first appear at postnatal day (P) 12 in the dorsal retina and reach maximal expansion at P21. The highest density in 'rosettes' is observed within a region located between 100 and 350 µM from the optic nerve head. 'Rosettes' disappear between 9 to 12 months. Non-apoptotic cell death markers are detected during the slow photoreceptor degeneration, at a rate of an approximately 3% reduction of outer nuclear layer thickness per month, as observed from 7 to 31 months of age. In vivo analysis of Nr2e3rd7/rd7 Cx3cr1gfp/+ retinas identified microglial cells within 'rosettes' from P21 on. Subretinal macrophages were observed in vivo and by confocal microscopy earliest in 12-months-old Nr2e3rd7/rd7 retinas. At P21, S-opsin expression and the number of S-opsin expressing dorsal cones was increased. The dorso-ventral M-cone gradient was present in Nr2e3rd7/rd7 retinas, but M-opsin expression and M-opsin expressing cones were decreased. Retinal vasculature was normal.
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Affiliation(s)
- Giulia Venturini
- Department of Ophthalmology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Despina Kokona
- Department of Ophthalmology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Beatrice L Steiner
- Department of Ophthalmology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Emanuele G Bulla
- Department of Ophthalmology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Joel Jovanovic
- Department of Ophthalmology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Martin S Zinkernagel
- Department of Ophthalmology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Pascal Escher
- Department of Ophthalmology, Inselspital, Bern University Hospital, Bern, Switzerland.
- Department of BioMedical Research, University of Bern, Bern, Switzerland.
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14
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Friedman RZ, Granas DM, Myers CA, Corbo JC, Cohen BA, White MA. Information content differentiates enhancers from silencers in mouse photoreceptors. eLife 2021; 10:67403. [PMID: 34486522 PMCID: PMC8492058 DOI: 10.7554/elife.67403] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/03/2021] [Indexed: 12/12/2022] Open
Abstract
Enhancers and silencers often depend on the same transcription factors (TFs) and are conflated in genomic assays of TF binding or chromatin state. To identify sequence features that distinguish enhancers and silencers, we assayed massively parallel reporter libraries of genomic sequences targeted by the photoreceptor TF cone-rod homeobox (CRX) in mouse retinas. Both enhancers and silencers contain more TF motifs than inactive sequences, but relative to silencers, enhancers contain motifs from a more diverse collection of TFs. We developed a measure of information content that describes the number and diversity of motifs in a sequence and found that, while both enhancers and silencers depend on CRX motifs, enhancers have higher information content. The ability of information content to distinguish enhancers and silencers targeted by the same TF illustrates how motif context determines the activity of cis-regulatory sequences. Different cell types are established by activating and repressing the activity of specific sets of genes, a process controlled by proteins called transcription factors. Transcription factors work by recognizing and binding short stretches of DNA in parts of the genome called cis-regulatory sequences. A cis-regulatory sequence that increases the activity of a gene when bound by transcription factors is called an enhancer, while a sequence that causes a decrease in gene activity is called a silencer. To establish a cell type, a particular transcription factor will act on both enhancers and silencers that control the activity of different genes. For example, the transcription factor cone-rod homeobox (CRX) is critical for specifying different types of cells in the retina, and it acts on both enhancers and silencers. In rod photoreceptors, CRX activates rod genes by binding their enhancers, while repressing cone photoreceptor genes by binding their silencers. However, CRX always recognizes and binds to the same DNA sequence, known as its binding site, making it unclear why some cis-regulatory sequences bound to CRX act as silencers, while others act as enhancers. Friedman et al. sought to understand how enhancers and silencers, both bound by CRX, can have different effects on the genes they control. Since both enhancers and silencers contain CRX binding sites, the difference between the two must lie in the sequence of the DNA surrounding these binding sites. Using retinas that have been explanted from mice and kept alive in the laboratory, Friedman et al. tested the activity of thousands of CRX-binding sequences from the mouse genome. This showed that both enhancers and silencers have more copies of CRX-binding sites than sequences of the genome that are inactive. Additionally, the results revealed that enhancers have a diverse collection of binding sites for other transcription factors, while silencers do not. Friedman et al. developed a new metric they called information content, which captures the diverse combinations of different transcription binding sites that cis-regulatory sequences can have. Using this metric, Friedman et al. showed that it is possible to distinguish enhancers from silencers based on their information content. It is critical to understand how the DNA sequences of cis-regulatory regions determine their activity, because mutations in these regions of the genome can cause disease. However, since every person has thousands of benign mutations in cis-regulatory sequences, it is a challenge to identify specific disease-causing mutations, which are relatively rare. One long-term goal of models of enhancers and silencers, such as Friedman et al.’s information content model, is to understand how mutations can affect cis-regulatory sequences, and, in some cases, lead to disease.
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Affiliation(s)
- Ryan Z Friedman
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, United States.,Department of Genetics, Washington University School of Medicine, St. Louis, United States
| | - David M Granas
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, United States.,Department of Genetics, Washington University School of Medicine, St. Louis, United States
| | - Connie A Myers
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, United States
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, United States
| | - Barak A Cohen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, United States.,Department of Genetics, Washington University School of Medicine, St. Louis, United States
| | - Michael A White
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, United States.,Department of Genetics, Washington University School of Medicine, St. Louis, United States
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15
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Aghaizu ND, Warre-Cornish KM, Robinson MR, Waldron PV, Maswood RN, Smith AJ, Ali RR, Pearson RA. Repeated nuclear translocations underlie photoreceptor positioning and lamination of the outer nuclear layer in the mammalian retina. Cell Rep 2021; 36:109461. [PMID: 34348137 PMCID: PMC8356022 DOI: 10.1016/j.celrep.2021.109461] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 11/19/2019] [Accepted: 07/09/2021] [Indexed: 12/28/2022] Open
Abstract
In development, almost all stratified neurons must migrate from their birthplace to the appropriate neural layer. Photoreceptors reside in the most apical layer of the retina, near their place of birth. Whether photoreceptors require migratory events for fine-positioning and/or retention within this layer is not well understood. Here, we show that photoreceptor nuclei of the developing mouse retina cyclically exhibit rapid, dynein-1-dependent translocation toward the apical surface, before moving more slowly in the basal direction, likely due to passive displacement by neighboring retinal nuclei. Attenuating dynein 1 function in rod photoreceptors results in their ectopic basal displacement into the outer plexiform layer and inner nuclear layer. Synapse formation is also compromised in these displaced cells. We propose that repeated, apically directed nuclear translocation events are necessary to ensure retention of post-mitotic photoreceptors within the emerging outer nuclear layer during retinogenesis, which is critical for correct neuronal lamination.
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Affiliation(s)
- Nozie D Aghaizu
- University College London Institute of Ophthalmology, London EC1V 9EL, UK.
| | | | - Martha R Robinson
- University College London Institute of Ophthalmology, London EC1V 9EL, UK
| | - Paul V Waldron
- University College London Institute of Ophthalmology, London EC1V 9EL, UK
| | - Ryea N Maswood
- University College London Institute of Ophthalmology, London EC1V 9EL, UK
| | - Alexander J Smith
- University College London Institute of Ophthalmology, London EC1V 9EL, UK; Centre for Cell and Gene Therapy, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Robin R Ali
- University College London Institute of Ophthalmology, London EC1V 9EL, UK; Centre for Cell and Gene Therapy, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Rachael A Pearson
- University College London Institute of Ophthalmology, London EC1V 9EL, UK; Centre for Cell and Gene Therapy, King's College London, Guy's Hospital, London SE1 9RT, UK.
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16
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Mattar P, Jolicoeur C, Dang T, Shah S, Clark BS, Cayouette M. A Casz1-NuRD complex regulates temporal identity transitions in neural progenitors. Sci Rep 2021; 11:3858. [PMID: 33594190 PMCID: PMC7886867 DOI: 10.1038/s41598-021-83395-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/02/2021] [Indexed: 12/14/2022] Open
Abstract
Neural progenitor cells undergo identity transitions during development to ensure the generation different types of neurons and glia in the correct sequence and proportions. A number of temporal identity factors that control these transitions in progenitor competence have been identified, but the molecular mechanisms underlying their function remain unclear. Here, we asked how Casz1, the mammalian orthologue of Drosophila castor, regulates competence during retinal development. We show that Casz1 is required to control the transition between neurogenesis and gliogenesis. Using BioID proteomics, we reveal that Casz1 interacts with the nucleosome remodeling and deacetylase (NuRD) complex in retinal cells. Finally, we show that both the NuRD and the polycomb repressor complexes are required for Casz1 to promote the rod fate and suppress gliogenesis. As additional temporal identity factors have been found to interact with the NuRD complex in other contexts, we propose that these factors might act through this common biochemical process to regulate neurogenesis.
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Affiliation(s)
- Pierre Mattar
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, H2W 1R7, Canada. .,Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada. .,Ottawa Health Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada.
| | - Christine Jolicoeur
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, H2W 1R7, Canada
| | - Thanh Dang
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.,Ottawa Health Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
| | - Sujay Shah
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.,Ottawa Health Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
| | - Brian S Clark
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, H2W 1R7, Canada. .,Department of Anatomy and Cell Biology, and Division of Experimental Medicine, McGill University, Montreal, QC, H3A 0G4, Canada. .,Department of Medicine, Université de Montréal, Montreal, QC, H3T 1J4, Canada.
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17
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Schmid V, Plössl K, Schmid C, Bernklau S, Weber BHF, Friedrich U. Retinoschisin and Cardiac Glycoside Crosstalk at the Retinal Na/K-ATPase. Invest Ophthalmol Vis Sci 2020; 61:1. [PMID: 32392309 PMCID: PMC7405613 DOI: 10.1167/iovs.61.5.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Purpose Mutations in the RS1 gene, which encodes retinoschisin, cause X-linked juvenile retinoschisis, a retinal dystrophy in males. Retinoschisin specifically interacts with the retinal sodium–potassium adenosine triphosphatase (Na/K-ATPase), a transmembrane ion pump. Na/K-ATPases also bind cardiac glycosides, which control the activity of the pump and have been linked to disturbances in retinal homeostasis. In this study, we investigated the crosstalk between retinoschisin and cardiac glycosides at the retinal Na/K-ATPase and the consequences of this interplay on retinal integrity. Methods The effect of cardiac glycosides (ouabain and digoxin) on the binding of retinoschisin to the retinal Na/K-ATPase was investigated via western blot and immunocytochemistry. Also, the influence of retinoschisin on the binding of cardiac glycosides was analyzed via enzymatic assays, which quantified cardiac glycoside-sensitive Na/K-ATPase pump activity. Moreover, retinoschisin-dependent binding of tritium-labeled ouabain to the Na/K-ATPase was determined. Finally, a reciprocal effect of retinoschisin and cardiac glycosides on Na/K-ATPase localization and photoreceptor degeneration was addressed using immunohistochemistry in retinoschisin-deficient murine retinal explants. Results Cardiac glycosides displaced retinoschisin from the retinal Na/K-ATPase; however, retinoschisin did not affect cardiac glycoside binding. Notably, cardiac glycosides reduced the capacity of retinoschisin to regulate Na/K-ATPase localization and to protect against photoreceptor degeneration. Conclusions Our findings reveal opposing effects of retinoschisin and cardiac glycosides on retinal Na/K-ATPase binding and on retinal integrity, suggesting that a fine-tuned interplay between both components is required to maintain retinal homeostasis. This observation provides new insight into the mechanisms underlying the pathological effects of cardiac glycoside treatment on retinal integrity.
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18
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Vaclavik V, Naderi F, Schaller A, Escher P. Longitudinal case study and phenotypic multimodal characterization of McArdle disease-linked retinopathy: insight into pathomechanisms. Ophthalmic Genet 2020; 41:73-78. [PMID: 32124677 DOI: 10.1080/13816810.2020.1727536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Background: We present a longitudinal clinical characterization of PYGM-linked pattern dystrophy in an adult male patient.Materials and Methods: A patient affected by McArdle disease (glycogen storage disease type V) and homozygous for the nonsense variant PYGM c.148C>T p.(Arg50*) underwent ophthalmic examinations over a 9-year-interval, including fundus photography, fundus autofluorescence, optical coherence tomography (OCT), OCT-angiography and electroretinography (ERG).Results: At age 52, the patient was asymptomatic but yellow flecks were first observed in the macula of both eyes. This yellow flecks at the posterior pole progressed towards a pattern-like dystrophy over a 5-year-period. By fundus autofluorescence imaging the appearance of new hyperautofluorescent flecks and the extension of existing ones was observed over time. Concomitantly, a slow progression of the size of atrophic areas was seen at the posterior pole. Scotopic ERGs were within normal limits, but photopic Flicker responses were decreased, indicating reduced cone function.Conclusions: This additional case of PYGM-linked pattern dystrophy further confirms retinopathy as a clinical phenotype associated with McArdle disease. PYGM expression pattern suggests a disease mechanism involving impaired glycogen metabolism both in the retinal pigment epithelium and in cone photoreceptors.
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Affiliation(s)
- Veronika Vaclavik
- Ophthalmology Departement, HFR, Hôpital Cantonal, Fribourg, Switzerland.,Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Lausanne, Switzerland
| | - Francine Naderi
- Ophthalmology Departement, HFR, Hôpital Cantonal, Fribourg, Switzerland
| | - André Schaller
- Department of BioMedical Research, University of Bern, Bern, Switzerland.,Division of Human Genetics, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Pascal Escher
- Department of BioMedical Research, University of Bern, Bern, Switzerland.,Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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19
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Perez-Cervantes C, Smith LA, Nadadur RD, Hughes AEO, Wang S, Corbo JC, Cepko C, Lonfat N, Moskowitz IP. Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types. Development 2020; 147:dev184432. [PMID: 31915147 PMCID: PMC7033740 DOI: 10.1242/dev.184432] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/13/2019] [Indexed: 12/30/2022]
Abstract
Identification of cell type-specific cis-regulatory elements (CREs) is crucial for understanding development and disease, although identification of functional regulatory elements remains challenging. We hypothesized that context-specific CREs could be identified by context-specific non-coding RNA (ncRNA) profiling, based on the observation that active CREs produce ncRNAs. We applied ncRNA profiling to identify rod and cone photoreceptor CREs from wild-type and mutant mouse retinas, defined by presence or absence, respectively, of the rod-specific transcription factor (TF) NrlNrl-dependent ncRNA expression strongly correlated with epigenetic profiles of rod and cone photoreceptors, identified thousands of candidate rod- and cone-specific CREs, and identified motifs for rod- and cone-specific TFs. Colocalization of NRL and the retinal TF CRX correlated with rod-specific ncRNA expression, whereas CRX alone favored cone-specific ncRNA expression, providing quantitative evidence that heterotypic TF interactions distinguish cell type-specific CRE activity. We validated the activity of novel Nrl-dependent ncRNA-defined CREs in developing cones. This work supports differential ncRNA profiling as a platform for the identification of cell type-specific CREs and the discovery of molecular mechanisms underlying TF-dependent CRE activity.
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Affiliation(s)
- Carlos Perez-Cervantes
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Linsin A Smith
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Rangarajan D Nadadur
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Andrew E O Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sui Wang
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Constance Cepko
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nicolas Lonfat
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
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20
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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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21
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Murphy DP, Hughes AEO, Lawrence KA, Myers CA, Corbo JC. Cis-regulatory basis of sister cell type divergence in the vertebrate retina. eLife 2019; 8:e48216. [PMID: 31633482 PMCID: PMC6802965 DOI: 10.7554/elife.48216] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 09/19/2019] [Indexed: 12/27/2022] Open
Abstract
Multicellular organisms evolved via repeated functional divergence of transcriptionally related sister cell types, but the mechanisms underlying sister cell type divergence are not well understood. Here, we study a canonical pair of sister cell types, retinal photoreceptors and bipolar cells, to identify the key cis-regulatory features that distinguish them. By comparing open chromatin maps and transcriptomic profiles, we found that while photoreceptor and bipolar cells have divergent transcriptomes, they share remarkably similar cis-regulatory grammars, marked by enrichment of K50 homeodomain binding sites. However, cell class-specific enhancers are distinguished by enrichment of E-box motifs in bipolar cells, and Q50 homeodomain motifs in photoreceptors. We show that converting K50 motifs to Q50 motifs represses reporter expression in bipolar cells, while photoreceptor expression is maintained. These findings suggest that partitioning of Q50 motifs within cell type-specific cis-regulatory elements was a critical step in the evolutionary divergence of the bipolar transcriptome from that of photoreceptors.
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Affiliation(s)
- Daniel P Murphy
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
| | - Andrew EO Hughes
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
| | - Karen A Lawrence
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
| | - Connie A Myers
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
| | - Joseph C Corbo
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
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22
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Langer BE, Hiller M. TFforge utilizes large-scale binding site divergence to identify transcriptional regulators involved in phenotypic differences. Nucleic Acids Res 2019; 47:e19. [PMID: 30496469 PMCID: PMC6393245 DOI: 10.1093/nar/gky1200] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/06/2018] [Accepted: 11/15/2018] [Indexed: 12/19/2022] Open
Abstract
Changes in gene regulation are important for phenotypic and in particular morphological evolution. However, it remains challenging to identify the transcription factors (TFs) that contribute to differences in gene regulation and thus to phenotypic differences between species. Here, we present TFforge (Transcription Factor forward genomics), a computational method to identify TFs that are involved in the loss of phenotypic traits. TFforge screens an input set of regulatory genomic regions to detect TFs that exhibit a significant binding site divergence signature in species that lost a particular phenotypic trait. Using simulated data of modular and pleiotropic regulatory elements, we show that TFforge can identify the correct TFs for many different evolutionary scenarios. We applied TFforge to available eye regulatory elements to screen for TFs that exhibit a significant binding site decay signature in subterranean mammals. This screen identified interacting and co-binding eye-related TFs, and thus provides new insights into which TFs likely contribute to eye degeneration in these species. TFforge has broad applicability to identify the TFs that contribute to phenotypic changes between species, and thus can help to unravel the gene-regulatory differences that underlie phenotypic evolution.
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Affiliation(s)
- Björn E Langer
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Germany
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23
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Kaufman ML, Park KU, Goodson NB, Chew S, Bersie S, Jones KL, Lamba DA, Brzezinski JA. Transcriptional profiling of murine retinas undergoing semi-synchronous cone photoreceptor differentiation. Dev Biol 2019; 453:155-167. [PMID: 31163126 DOI: 10.1016/j.ydbio.2019.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/24/2019] [Accepted: 05/29/2019] [Indexed: 12/12/2022]
Abstract
Uncovering the gene regulatory networks that control cone photoreceptor formation has been hindered because cones only make up a few percent of the retina and form asynchronously during development. To overcome these limitations, we used a γ-secretase inhibitor, DAPT, to disrupt Notch signaling and force proliferating retinal progenitor cells to rapidly adopt neuronal identity. We treated mouse retinal explants at the peak of cone genesis with DAPT and examined tissues at several time-points by histology and bulk RNA-sequencing. We found that this treatment caused supernumerary cone formation in an overwhelmingly synchronized fashion. This analysis revealed several categorical patterns of gene expression changes over time relative to DMSO treated control explants. These were placed in the temporal context of the activation of Otx2, a transcription factor that is expressed at the onset of photoreceptor development and that is required for both rod and cone formation. One group of interest had genes, such as Mybl1, Ascl1, Neurog2, and Olig2, that became upregulated by DAPT treatment before Otx2. Two other groups showed upregulated gene expression shortly after Otx2, either transiently or permanently. This included genes such as Mybl1, Meis2, and Podxl. Our data provide a developmental timeline of the gene expression events that underlie the initial steps of cone genesis and maturation. Applying this strategy to human retinal organoid cultures was also sufficient to induce a massive increase in cone genesis. Taken together, our results provide a temporal framework that can be used to elucidate the gene regulatory logic controlling cone photoreceptor development.
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Affiliation(s)
- Michael L Kaufman
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Noah B Goodson
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Shereen Chew
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Stephanie Bersie
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Deepak A Lamba
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Joseph A Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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24
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Abstract
Enhancer activity is determined by both the activity and occupancy of transcription factors as well as the specific sequences they bind. Experimental investigation of this dynamic requires the ability to manipulate components of the system, ideally in as close to an in vivo context as possible. Here we use electroporation of plasmid reporters to define critical parameters of a specific cis-regulatory element, ThrbCRM1, during retinal development. ThrbCRM1 is associated with cone photoreceptor genesis and activated in a subset of developing retinal cells that co-express the Otx2 and Onecut1 (OC1) transcription factors. Variation of reporter plasmid concentration was used to generate dose response curves and revealed an effect of binding site availability on the number and strength of cells with reporter activity. Critical sequence elements of the ThrbCRM1 element were defined using both mutagenesis and misexpression of the Otx2 and OC1 transcription factors in the developing retina. Additionally, these experiments suggest that the ThrbCRM1 element is co-regulated by Otx2 and OC1 even under conditions of sub-optimal binding of OC1.
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Affiliation(s)
- Benjamin Souferi
- Department of Biology, The City College of New York, City University of New York, New York, NY 10031, USA
| | - Mark M Emerson
- Department of Biology, The City College of New York, City University of New York, New York, NY 10031, USA .,Graduate Center, City University of New York, New York, NY 10031, USA
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25
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Jean-Charles N, Buenaventura DF, Emerson MM. Identification and characterization of early photoreceptor cis-regulatory elements and their relation to Onecut1. Neural Dev 2018; 13:26. [PMID: 30466480 PMCID: PMC6251108 DOI: 10.1186/s13064-018-0121-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/31/2018] [Indexed: 12/19/2022] Open
Abstract
Background Cone and rod photoreceptors are two of the primary cell types affected in human retinal disease. Potential strategies to combat these diseases are the use of gene therapy to rescue compromised photoreceptors or to generate new functional photoreceptors to replace those lost in the diseased retina. Cis-regulatory elements specific to cones, rods, or both types of photoreceptors are critical components of successful implementation of these two strategies. The purpose of this study was to identify and characterize the cell type specificity and activity of cis-regulatory elements active in developing photoreceptors. Methods Cis-regulatory elements were introduced into the developing chicken and mouse retina by electroporation. Characterization of reporter activity in relation with cell type markers was determined using confocal microscopy. In addition, two high-throughput flow cytometry assay were developed to assess whether these elements were downstream of Onecut1 in the photoreceptor specification network. Results The majority of cis-regulatory elements were active in both cone and rod photoreceptors and were largely uninfluenced by a Onecut1 dominant-negative construct. Elements associated with the Thrb, Nr2e3, and Rhodopsin genes showed highly enriched activity in cones or rods, and were affected by interference in Onecut1 signaling. Rhodopsin promoter activity was the most highly influenced by Onecut1 activity and its induction could be modulated by the Maf family transcription factor L-Maf. Nr2e3 elements were observed to have activity in cone photoreceptors and Nr2e3 protein was expressed in developing cone photoreceptors, suggesting a role for this predominant rod gene in cone photoreceptor development. Conclusions The analysis presented here provides an experimental framework to determine the specificity and strength of photoreceptor elements within specific genetic networks during development. The Onecut1 transcription factor is one such factor that influences the gene regulatory networks specific to cones and rods, but not those that are common to both. Electronic supplementary material The online version of this article (10.1186/s13064-018-0121-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nathalie Jean-Charles
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA.,Current Address: The Public Health Laboratory, NYC Department of Health and Mental Hygeine, New York, NY, 10016, USA
| | - Diego F Buenaventura
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA.,Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, 10031, USA
| | - Mark M Emerson
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA. .,Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, 10031, USA.
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26
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Zheng C, Jin FQ, Trippe BL, Wu J, Chalfie M. Inhibition of cell fate repressors secures the differentiation of the touch receptor neurons of Caenorhabditis elegans. Development 2018; 145:dev.168096. [PMID: 30291162 DOI: 10.1242/dev.168096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/24/2018] [Indexed: 12/14/2022]
Abstract
Terminal differentiation generates the specialized features and functions that allow postmitotic cells to acquire their distinguishing characteristics. This process is thought to be controlled by transcription factors called 'terminal selectors' that directly activate a set of downstream effector genes. In Caenorhabditis elegans, the differentiation of both the mechanosensory touch receptor neurons (TRNs) and the multidendritic nociceptor FLP neurons uses the terminal selectors UNC-86 and MEC-3. The FLP neurons fail to activate TRN genes, however, because a complex of two transcriptional repressors (EGL-44/EGL-46) prevents their expression. Here, we show that the ZEB family transcriptional factor ZAG-1 promotes TRN differentiation not by activating TRN genes but by preventing the expression of EGL-44/EGL-46. As EGL-44/EGL-46 also inhibits the production of ZAG-1, these proteins form a bistable, negative-feedback loop that regulates the choice between the two neuronal fates.
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Affiliation(s)
- Chaogu Zheng
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Felix Qiaochu Jin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Brian Loeber Trippe
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Ji Wu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Martin Chalfie
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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27
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Hughes AEO, Myers CA, Corbo JC. A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo. Genome Res 2018; 28:1520-1531. [PMID: 30158147 PMCID: PMC6169884 DOI: 10.1101/gr.231886.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 08/27/2018] [Indexed: 12/20/2022]
Abstract
Cone-rod homeobox (CRX) is a paired-like homeodomain transcription factor (TF) and a master regulator of photoreceptor development in vertebrates. The in vitro DNA binding preferences of CRX have been described in detail, but the degree to which in vitro binding affinity is correlated with in vivo enhancer activity is not known. In addition, paired-class homeodomain TFs can bind DNA cooperatively as both homodimers and heterodimers at inverted TAAT half-sites separated by 2 or 3 nucleotides. This dimeric configuration is thought to mediate target specificity, but whether monomeric and dimeric sites encode distinct levels of activity is not known. Here, we used a massively parallel reporter assay to determine how local sequence context shapes the regulatory activity of CRX binding sites in mouse photoreceptors. We assayed inactivating mutations in more than 1700 TF binding sites and found that dimeric CRX binding sites act as stronger enhancers than monomeric CRX binding sites. Furthermore, the activity of dimeric half-sites is cooperative, dependent on a strict 3-bp spacing, and tuned by the identity of the spacer nucleotides. Saturating single-nucleotide mutagenesis of 195 CRX binding sites showed that, on average, changes in TF binding site affinity are correlated with changes in regulatory activity, but this relationship is obscured when considering mutations across multiple cis-regulatory elements (CREs). Taken together, these results demonstrate that the activity of CRX binding sites is highly dependent on sequence context, providing insight into photoreceptor gene regulation and illustrating functional principles of homeodomain binding sites that may be conserved in other cell types.
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Affiliation(s)
- Andrew E O Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Connie A Myers
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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28
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Abstract
Eukaryotic cells depend on precise genome organization within the nucleus to maintain an appropriate gene-expression profile. Critical to this process is the packaging of functional domains of open and closed chromatin to specific regions of the nucleus, but how this is regulated remains unclear. In this study, we show that the zinc finger protein Casz1 regulates higher-order nuclear organization of rod photoreceptors in the mouse retina by repressing nuclear lamina function, which leads to central localization of heterochromatin. Loss of Casz1 in rods leads to an abnormal transcriptional profile followed by degeneration. These results identify Casz1 as a regulator of higher-order genome organization. Genome organization plays a fundamental role in the gene-expression programs of numerous cell types, but determinants of higher-order genome organization are poorly understood. In the developing mouse retina, rod photoreceptors represent a good model to study this question. They undergo a process called “chromatin inversion” during differentiation, in which, as opposed to classic nuclear organization, heterochromatin becomes localized to the center of the nucleus and euchromatin is restricted to the periphery. While previous studies showed that the lamin B receptor participates in this process, the molecular mechanisms regulating lamina function during differentiation remain elusive. Here, using conditional genetics, we show that the zinc finger transcription factor Casz1 is required to establish and maintain the inverted chromatin organization of rod photoreceptors and to safeguard their gene-expression profile and long-term survival. At the mechanistic level, we show that Casz1 interacts with the polycomb repressor complex in a splice variant-specific manner and that both are required to suppress the expression of the nuclear envelope intermediate filament lamin A/C in rods. Lamin A is in turn sufficient to regulate heterochromatin organization and nuclear position. Furthermore, we show that Casz1 is sufficient to expand and centralize the heterochromatin of fibroblasts, suggesting a general role for Casz1 in nuclear organization. Together, these data support a model in which Casz1 cooperates with polycomb to control rod genome organization, in part by silencing lamin A/C.
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29
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Ruzycki PA, Zhang X, Chen S. CRX directs photoreceptor differentiation by accelerating chromatin remodeling at specific target sites. Epigenetics Chromatin 2018; 11:42. [PMID: 30068366 PMCID: PMC6069558 DOI: 10.1186/s13072-018-0212-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/22/2018] [Indexed: 12/24/2022] Open
Abstract
Background Recent technological advances have delivered the genome-wide targets of many important transcription factors (TFs). However, increasing evidence suggests that not all target sites mediate regulatory function, raising the questions of how to determine which sites are active, what are the epigenetic consequences of TF binding at these sites, and how the specificity is coded. To address these questions, we focused on CRX, a disease-associated homeodomain TF required for photoreceptor gene expression and development. Since CRX binds more than 6000 sites across the genome in the retina, we profiled chromatin landscape changes at each binding site during normal development and in the absence of CRX and interpreted the results by thorough investigation of other epigenomic datasets and sequence features. Results CRX is required for chromatin remodeling at only a subset of its binding sites, which undergo retina or neuronal specific activation during photoreceptor differentiation. Genes near these “CRX Dependent” sites code for proteins important for photoreceptor physiology and function, and their transcription is significantly reduced in Crx deficient retinas. In addition, the nucleotide and motif content distinguish these CRX Dependent sites from other CRX-bound sites. Conclusions Together, our results suggest that CRX acts only at select, uniquely-coded binding sites to accelerate chromatin remodeling during photoreceptor differentiation. This study emphasizes the importance of connecting TF binding with its functional consequences and provides a framework for making such a connection using comparative analyses of available genomic datasets. Finally, this study prioritizes sets of non-coding DNA sites for future functional interrogation and identification of mutations associated with retinal disease. Electronic supplementary material The online version of this article (10.1186/s13072-018-0212-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Philip A Ruzycki
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA.,Molecular Genetics and Genomics Graduate Program, Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaodong Zhang
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA. .,Molecular Genetics and Genomics Graduate Program, Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA.
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30
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Plössl K, Schmid V, Straub K, Schmid C, Ammon M, Merkl R, Weber BHF, Friedrich U. Pathomechanism of mutated and secreted retinoschisin in X-linked juvenile retinoschisis. Exp Eye Res 2018; 177:23-34. [PMID: 30040949 DOI: 10.1016/j.exer.2018.07.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/20/2018] [Accepted: 07/20/2018] [Indexed: 01/08/2023]
Abstract
Mutations in the RS1 gene encoding retinoschisin cause X-linked juvenile retinoschisis (XLRS), a hereditary retinal dystrophy in males. While most of the XLRS associated mutations strongly interfere with cellular secretion, this is not true for mutants RS1-F108C, -R141G, -R141H, -R182C, -H207Q and -R209H. Native retinoschisin builds double-octamers and binds to retinal membranes, interacting with the retinal Na/K-ATPase. Functionally, it regulates MAP kinase signaling and Na/K-ATPase localization, and hampers photoreceptor degeneration. In this study, we investigated the capacity of the retinoschisin mutants still secreted extracellularly to fulfil these tasks. We addressed secretion and oligomerization of the heterologously expressed mutants as well as their binding to recombinant retinal Na/K-ATPases and murine retinoschisin-deficient (Rs1h-/Y) retinal and non-retinal explants. This has refined the categorization of secreted retinoschisin mutants: (i) no octamerization, unspecific membrane binding (RS1-F108C and -R182C), (ii) double-octamerization but no membrane binding (RS1-R141H), and (iii) double-octamerization and unspecific membrane binding (RS1-R141G, -H207Q, and -R209H). Notably, selected mutants of all categories (RS1-F108C, -R141H, and -R209H) failed to regulate retinal MAP kinase signaling and Na/K-ATPase localization in Rs1h-/Y retinal explants, and could not attenuate photoreceptor degeneration. Bioinformatic modeling of the secreted mutants depicted prominent alterations in the spatial and temporal conformation of a substructure called "spike 3" and its vicinity, implying a crucial role of this substructure for binding capacity and specificity. Taken together, our data point to a pathomechanism for secreted retinoschisin mutants, specifically to disturbances of the retinoschisin interface accompanied by unphysiological membrane interactions and impaired regulatory functions.
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Affiliation(s)
- Karolina Plössl
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Verena Schmid
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93040 Regensburg, Germany
| | - Carina Schmid
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Mirjam Ammon
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93040 Regensburg, Germany
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Ulrike Friedrich
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany.
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31
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Garancher A, Lin CY, Morabito M, Richer W, Rocques N, Larcher M, Bihannic L, Smith K, Miquel C, Leboucher S, Herath NI, Dupuy F, Varlet P, Haberler C, Walczak C, El Tayara N, Volk A, Puget S, Doz F, Delattre O, Druillennec S, Ayrault O, Wechsler-Reya RJ, Eychène A, Bourdeaut F, Northcott PA, Pouponnot C. NRL and CRX Define Photoreceptor Identity and Reveal Subgroup-Specific Dependencies in Medulloblastoma. Cancer Cell 2018; 33. [PMID: 29533784 PMCID: PMC6368680 DOI: 10.1016/j.ccell.2018.02.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer cells often express differentiation programs unrelated to their tissue of origin, although the contribution of these aberrant phenotypes to malignancy is poorly understood. An aggressive subgroup of medulloblastoma, a malignant pediatric brain tumor of the cerebellum, expresses a photoreceptor differentiation program normally expressed in the retina. We establish that two photoreceptor-specific transcription factors, NRL and CRX, are master regulators of this program and are required for tumor maintenance in this subgroup. Beyond photoreceptor lineage genes, we identify BCL-XL as a key transcriptional target of NRL and provide evidence substantiating anti-BCL therapy as a rational treatment opportunity for select MB patients. Our results highlight the utility of studying aberrant differentiation programs in cancer and their potential as selective therapeutic vulnerabilities.
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Affiliation(s)
- Alexandra Garancher
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France; INSERM U1021, Centre Universitaire, Orsay 91405, France; CNRS UMR 3347, Centre Universitaire, Orsay 91405, France; Université Paris Sud-11, 91405 Orsay, France; PSL Research University, Paris, France
| | - Charles Y Lin
- Baylor College of Medicine, Department of Molecular and Human Genetics, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Morgane Morabito
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France; INSERM U1021, Centre Universitaire, Orsay 91405, France; CNRS UMR 3347, Centre Universitaire, Orsay 91405, France; Université Paris Sud-11, 91405 Orsay, France; PSL Research University, Paris, France
| | - Wilfrid Richer
- PSL Research University, Paris, France; Institut Curie, Paris 75248, France; INSERM U830, Paris 75248, France; Translational Research in Pediatric Oncology, Institut Curie SiRIC, Paris, France
| | - Nathalie Rocques
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France; INSERM U1021, Centre Universitaire, Orsay 91405, France; CNRS UMR 3347, Centre Universitaire, Orsay 91405, France; Université Paris Sud-11, 91405 Orsay, France; PSL Research University, Paris, France
| | - Magalie Larcher
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France; INSERM U1021, Centre Universitaire, Orsay 91405, France; CNRS UMR 3347, Centre Universitaire, Orsay 91405, France; Université Paris Sud-11, 91405 Orsay, France; PSL Research University, Paris, France
| | - Laure Bihannic
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France; INSERM U1021, Centre Universitaire, Orsay 91405, France; CNRS UMR 3347, Centre Universitaire, Orsay 91405, France; Université Paris Sud-11, 91405 Orsay, France; PSL Research University, Paris, France; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS325, Memphis, TN 38017, USA
| | - Kyle Smith
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS325, Memphis, TN 38017, USA
| | - Catherine Miquel
- Departement de Neuropathologie, Hôpital Sainte-Anne, INSERM UMR_S1165, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Sophie Leboucher
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France
| | - Nirmitha I Herath
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France; INSERM U1021, Centre Universitaire, Orsay 91405, France; CNRS UMR 3347, Centre Universitaire, Orsay 91405, France; Université Paris Sud-11, 91405 Orsay, France; PSL Research University, Paris, France
| | - Fanny Dupuy
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France; INSERM U1021, Centre Universitaire, Orsay 91405, France; CNRS UMR 3347, Centre Universitaire, Orsay 91405, France; Université Paris Sud-11, 91405 Orsay, France; PSL Research University, Paris, France
| | - Pascale Varlet
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France; Departement de Neuropathologie, Hôpital Sainte-Anne, INSERM U894, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Christine Walczak
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France; Université Paris Sud-11, 91405 Orsay, France; PSL Research University, Paris, France; INSERM U1196, CNRS UMR9187, Centre Universitaire, Orsay 91405, France
| | - Nadine El Tayara
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France; Université Paris Sud-11, 91405 Orsay, France; PSL Research University, Paris, France; INSERM U1196, CNRS UMR9187, Centre Universitaire, Orsay 91405, France
| | - Andreas Volk
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France; Université Paris Sud-11, 91405 Orsay, France; PSL Research University, Paris, France; INSERM U1196, CNRS UMR9187, Centre Universitaire, Orsay 91405, France
| | - Stéphanie Puget
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France; AP-HP, Hôpital Necker-Enfants Malades, Département Neurochirurgie pédiatrique, Paris, France
| | - François Doz
- Institut Curie, Paris 75248, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; SIREDO Center (Care, innovation, Research in pediatric, adolescent and young adult oncology), Institut Curie, Paris, France
| | - Olivier Delattre
- PSL Research University, Paris, France; Institut Curie, Paris 75248, France; INSERM U830, Paris 75248, France; SIREDO Center (Care, innovation, Research in pediatric, adolescent and young adult oncology), Institut Curie, Paris, France
| | - Sabine Druillennec
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France; INSERM U1021, Centre Universitaire, Orsay 91405, France; CNRS UMR 3347, Centre Universitaire, Orsay 91405, France; Université Paris Sud-11, 91405 Orsay, France; PSL Research University, Paris, France
| | - Olivier Ayrault
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France; INSERM U1021, Centre Universitaire, Orsay 91405, France; CNRS UMR 3347, Centre Universitaire, Orsay 91405, France; Université Paris Sud-11, 91405 Orsay, France; PSL Research University, Paris, France
| | - Robert J Wechsler-Reya
- Tumor Initiation & Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Alain Eychène
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France; INSERM U1021, Centre Universitaire, Orsay 91405, France; CNRS UMR 3347, Centre Universitaire, Orsay 91405, France; Université Paris Sud-11, 91405 Orsay, France; PSL Research University, Paris, France
| | - Franck Bourdeaut
- PSL Research University, Paris, France; Institut Curie, Paris 75248, France; INSERM U830, Paris 75248, France; Translational Research in Pediatric Oncology, Institut Curie SiRIC, Paris, France; SIREDO Center (Care, innovation, Research in pediatric, adolescent and young adult oncology), Institut Curie, Paris, France
| | - Paul A Northcott
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS325, Memphis, TN 38017, USA.
| | - Celio Pouponnot
- Institut Curie - Recherche, Laboratoire 110, Centre Universitaire, Orsay Cedex 91405, France; INSERM U1021, Centre Universitaire, Orsay 91405, France; CNRS UMR 3347, Centre Universitaire, Orsay 91405, France; Université Paris Sud-11, 91405 Orsay, France; PSL Research University, Paris, France.
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A Simple Grammar Defines Activating and Repressing cis-Regulatory Elements in Photoreceptors. Cell Rep 2017; 17:1247-1254. [PMID: 27783940 DOI: 10.1016/j.celrep.2016.09.066] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/06/2016] [Accepted: 09/20/2016] [Indexed: 12/22/2022] Open
Abstract
Transcription factors often activate and repress different target genes in the same cell. How activation and repression are encoded by different arrangements of transcription factor binding sites in cis-regulatory elements is poorly understood. We investigated how sites for the transcription factor CRX encode both activation and repression in photoreceptors by assaying thousands of genomic and synthetic cis-regulatory elements in wild-type and Crx-/- retinas. We found that sequences with high affinity for CRX repress transcription, whereas sequences with lower affinity activate. This rule is modified by a cooperative interaction between CRX sites and sites for the transcription factor NRL, which overrides the repressive effect of high affinity for CRX. Our results show how simple rearrangements of transcription factor binding sites encode qualitatively different responses to a single transcription factor and explain how CRX plays multiple cis-regulatory roles in the same cell.
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Samd7 is a cell type-specific PRC1 component essential for establishing retinal rod photoreceptor identity. Proc Natl Acad Sci U S A 2017; 114:E8264-E8273. [PMID: 28900001 DOI: 10.1073/pnas.1707021114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Precise transcriptional regulation controlled by a transcription factor network is known to be crucial for establishing correct neuronal cell identities and functions in the CNS. In the retina, the expression of various cone and rod photoreceptor cell genes is regulated by multiple transcription factors; however, the role of epigenetic regulation in photoreceptor cell gene expression has been poorly understood. Here, we found that Samd7, a rod-enriched sterile alpha domain (SAM) domain protein, is essential for silencing nonrod gene expression through H3K27me3 regulation in rod photoreceptor cells. Samd7-null mutant mice showed ectopic expression of nonrod genes including S-opsin in rod photoreceptor cells and rod photoreceptor cell dysfunction. Samd7 physically interacts with Polyhomeotic homologs (Phc proteins), components of the Polycomb repressive complex 1 (PRC1), and colocalizes with Phc2 and Ring1B in Polycomb bodies. ChIP assays showed a significant decrease of H3K27me3 in the genes up-regulated in the Samd7-deficient retina, showing that Samd7 deficiency causes the derepression of nonrod gene expression in rod photoreceptor cells. The current study suggests that Samd7 is a cell type-specific PRC1 component epigenetically defining rod photoreceptor cell identity.
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Plössl K, Royer M, Bernklau S, Tavraz NN, Friedrich T, Wild J, Weber BHF, Friedrich U. Retinoschisin is linked to retinal Na/K-ATPase signaling and localization. Mol Biol Cell 2017; 28:2178-2189. [PMID: 28615319 PMCID: PMC5531734 DOI: 10.1091/mbc.e17-01-0064] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 01/30/2023] Open
Abstract
Retinoschisin binds to the extracellular domain of Na/K-ATPase subunit β2. Retinoschisin inhibits Na/K-ATPase–associated signaling cascades and affects Na/K-ATPase localization. The retinoschisin-Na/K-ATPase complex overlaps with signaling mediators. Defective Na/K-ATPase signaling by retinoschisin deficiency may promote retinal dystrophy. Mutations in the RS1 gene cause X-linked juvenile retinoschisis (XLRS), a hereditary retinal dystrophy. We recently showed that retinoschisin, the protein encoded by RS1, regulates ERK signaling and apoptosis in retinal cells. In this study, we explored an influence of retinoschisin on the functionality of the Na/K-ATPase, its interaction partner at retinal plasma membranes. We show that retinoschisin binding requires the β2-subunit of the Na/K-ATPase, whereas the α-subunit is exchangeable. Our investigations revealed no effect of retinoschisin on Na/K-ATPase–mediated ATP hydrolysis and ion transport. However, we identified an influence of retinoschisin on Na/K-ATPase–regulated signaling cascades and Na/K-ATPase localization. In addition to the known ERK deactivation, retinoschisin treatment of retinoschisin-deficient (Rs1h-/Y) murine retinal explants decreased activation of Src, an initial transmitter in Na/K-ATPase signal transduction, and of Ca2+ signaling marker Camk2. Immunohistochemistry on murine retinae revealed an overlap of the retinoschisin–Na/K-ATPase complex with proteins involved in Na/K-ATPase signaling, such as caveolin, phospholipase C, Src, and the IP3 receptor. Finally, retinoschisin treatment altered Na/K-ATPase localization in photoreceptors of Rs1h-/Y retinae. Taken together, our results suggest a regulatory effect of retinoschisin on Na/K-ATPase signaling and localization, whereas Na/K-ATPase-dysregulation caused by retinoschisin deficiency could represent an initial step in XLRS pathogenesis.
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Affiliation(s)
- Karolina Plössl
- Institute of Human Genetics, University of Regensburg, 93053 Regensburg, Germany
| | - Melanie Royer
- Institute of Human Genetics, University of Regensburg, 93053 Regensburg, Germany
| | - Sarah Bernklau
- Institute of Human Genetics, University of Regensburg, 93053 Regensburg, Germany
| | - Neslihan N Tavraz
- Institute of Chemistry, Technical University of Berlin, 10623 Berlin, Germany
| | - Thomas Friedrich
- Institute of Chemistry, Technical University of Berlin, 10623 Berlin, Germany
| | - Jens Wild
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, 93053 Regensburg, Germany
| | - Ulrike Friedrich
- Institute of Human Genetics, University of Regensburg, 93053 Regensburg, Germany
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Occelli LM, Tran NM, Narfström K, Chen S, Petersen-Jones SM. CrxRdy Cat: A Large Animal Model for CRX-Associated Leber Congenital Amaurosis. Invest Ophthalmol Vis Sci 2017; 57:3780-92. [PMID: 27427859 PMCID: PMC4960999 DOI: 10.1167/iovs.16-19444] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Purpose Mutations in the retinal transcription factor cone-rod homeobox (CRX) gene result in severe dominant retinopathies. A large animal model, the Rdy cat, carrying a spontaneous frameshift mutation in Crx, was reported previously. The present study aimed to further understand pathogenesis in this model by thoroughly characterizing the Rdy retina. Methods Structural and functional changes were found in a comparison between the retinas of CrxRdy/+ kittens and those of wild-type littermates and were determined at various ages by fundus examination, electroretinography (ERG), optical coherence tomography, and histologic analyses. RNA and protein expression changes of Crx and key target genes were analyzed using quantitative reverse-transcribed PCR, Western blot analysis, and immunohistochemistry. Transcription activity of the mutant Crx was measured by a dual-luciferase transactivation assay. Results CrxRdy/+ kittens had no recordable cone ERGs. Rod responses were delayed in development and markedly reduced at young ages and lost by 20 weeks. Photoreceptor outer segment development was incomplete and was followed by progressive outer retinal thinning starting in the cone-rich area centralis. Expression of cone and rod Crx target genes was significantly down-regulated. The mutant Crx allele was overexpressed, leading to high levels of the mutant protein lacking transactivation activity. Conclusions The CrxRdy mutation exerts a dominant negative effect on wild-type Crx by overexpressing mutant protein. These findings, consistent with those of studies in a mouse model, support a conserved pathogenic mechanism for CRX frameshift mutations. The similarities between the feline eye and the human eye with the presence of a central region of high cone density makes the CrxRdy/+ cat a valuable model for preclinical testing of therapies for dominant CRX diseases.
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Affiliation(s)
- Laurence M Occelli
- Small Animal Clinical Sciences Michigan State University, East Lansing, Michigan, United States
| | - Nicholas M Tran
- Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Kristina Narfström
- Department of Veterinary Medicine and Surgery, University of Missouri-Columbia, Columbia, Missouri, United States
| | - Shiming Chen
- Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Simon M Petersen-Jones
- Small Animal Clinical Sciences Michigan State University, East Lansing, Michigan, United States
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Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors. Sci Rep 2017; 7:43184. [PMID: 28256534 PMCID: PMC5335693 DOI: 10.1038/srep43184] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/19/2017] [Indexed: 12/24/2022] Open
Abstract
Rod photoreceptors are specialized neurons that mediate vision in dim light and are the predominant photoreceptor type in nocturnal mammals. The rods of nocturnal mammals are unique among vertebrate cell types in having an ‘inverted’ nuclear architecture, with a dense mass of heterochromatin in the center of the nucleus rather than dispersed clumps at the periphery. To test if this unique nuclear architecture is correlated with a unique epigenomic landscape, we performed ATAC-seq on mouse rods and their most closely related cell type, cone photoreceptors. We find that thousands of loci are selectively closed in rods relative to cones as well as >60 additional cell types. Furthermore, we find that the open chromatin profile of photoreceptors lacking the rod master regulator Nrl is nearly indistinguishable from that of native cones, indicating that Nrl is required for selective chromatin closure in rods. Finally, we identified distinct enrichments of transcription factor binding sites in rods and cones, revealing key differences in the cis-regulatory grammar of these cell types. Taken together, these data provide insight into the development and maintenance of photoreceptor identity, and highlight rods as an attractive system for studying the relationship between nuclear organization and local changes in gene regulation.
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Homma K, Usui S, Kaneda M. Knock-in strategy at 3′-end ofCrxgene by CRISPR/Cas9 system shows the gene expression profiles during human photoreceptor differentiation. Genes Cells 2017; 22:250-264. [DOI: 10.1111/gtc.12472] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/22/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Kohei Homma
- Department of Physiology; Nippon Medical School; 1-25-16 Nezu Bunkyo-ku Tokyo 113-0031 Japan
| | - Sumiko Usui
- Department of Physiology; Nippon Medical School; 1-25-16 Nezu Bunkyo-ku Tokyo 113-0031 Japan
| | - Makoto Kaneda
- Department of Physiology; Nippon Medical School; 1-25-16 Nezu Bunkyo-ku Tokyo 113-0031 Japan
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Wolf A, Aslanidis A, Langmann T. Retinal expression and localization of Mef2c support its important role in photoreceptor gene expression. Biochem Biophys Res Commun 2016; 483:346-351. [PMID: 28017720 DOI: 10.1016/j.bbrc.2016.12.141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 11/17/2022]
Abstract
Photoreceptor-specific gene expression is controlled by a hierarchical network of transcription factors, including the master regulators cone-rod homeobox (Crx) and neural retina leucine zipper (Nrl). Myocyte-enhancer factor 2c (Mef2c) is an ubiquitously expressed transcription factor with important functions in the cardiovascular system. Here, we performed a detailed analysis of Mef2c expression, localization and function in the retina to further elucidate its potential role for photoreceptor gene regulation. We showed that murine retinal Mef2c mRNA expression was high at birth and peaked at late postnatal developmental stages. Using immunohistochemistry and Western blot, Mef2c protein was detected in the outer nuclear layer of adult mouse and human retinas and localized to the nucleus of 661W photoreceptor-like cells. Mef2c knock-down in 661W cells reduced the expression of arrestin 3 (Arr3) and medium-wave-sensitive cone opsin (Opn1mw) but increased transcript levels of mitogen-activated protein kinase 15 (Mapk15) and phosphodiesterase 6h (Pde6h). In conclusion, Mef2c is highly expressed in the retina where it modulates photoreceptor-specific gene expression.
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Affiliation(s)
- Anne Wolf
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Cologne, Germany
| | - Alexander Aslanidis
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Cologne, Germany
| | - Thomas Langmann
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Cologne, Germany.
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Plössl K, Weber BHF, Friedrich U. The X-linked juvenile retinoschisis protein retinoschisin is a novel regulator of mitogen-activated protein kinase signalling and apoptosis in the retina. J Cell Mol Med 2016; 21:768-780. [PMID: 27995734 PMCID: PMC5345684 DOI: 10.1111/jcmm.13019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/26/2016] [Indexed: 02/01/2023] Open
Abstract
X-linked juvenile retinoschisis (XLRS) is a hereditary retinal dystrophy in young males, caused by mutations in the RS1 gene. The function of the encoded protein, termed retinoschisin, and the molecular mechanisms underlying XLRS pathogenesis are still unresolved, although a direct interaction partner of the secreted retinoschisin, the retinal Na/K-ATPase, was recently identified. Earlier gene expression studies in retinoschisin-deficient (Rs1h-/Y ) mice provided a first indication of pathological up-regulation of mitogen-activated protein (MAP) kinase signalling in disease pathogenesis. To further investigate the role for retinoschisin in MAP kinase regulation, we exposed Y-79 cells and murine Rs1h-/Y retinae to recombinant retinoschisin and the XLRS-associated mutant RS1-C59S. Although normal retinoschisin stably bound to retinal cells, RS1-C59S exhibited a strongly reduced binding affinity. Simultaneously, exposure to normal retinoschisin significantly reduced phosphorylation of C-RAF and MAP kinases ERK1/2 in Y-79 cells and murine Rs1h-/Y retinae. Expression of MAP kinase target genes C-FOS and EGR1 was also down-regulated in both model systems. Finally, retinoschisin treatment decreased pro-apoptotic BAX-2 transcript levels in Y-79 cells and Rs1h-/Y retinae. Upon retinoschisin treatment, these cells showed increased resistance against apoptosis, reflected by decreased caspase-3 activity (in Y-79 cells) and increased photoreceptor survival (in Rs1h-/Y retinal explants). RS1-C59S did not influence C-RAF or ERK1/2 activation, C-FOS or EGR1 expression, or apoptosis. Our data imply that retinoschisin is a novel regulator of MAP kinase signalling and exerts an anti-apoptotic effect on retinal cells. We therefore discuss that disturbances of MAP kinase signalling by retinoschisin deficiency could be an initial step in XLRS pathogenesis.
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Affiliation(s)
- Karolina Plössl
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Ulrike Friedrich
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
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Sebag J, Sadun AA, Pierce EA. Paradigm Shifts in Ophthalmic Diagnostics. TRANSACTIONS OF THE AMERICAN OPHTHALMOLOGICAL SOCIETY 2016; 114:WP1. [PMID: 28008209 PMCID: PMC5141845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
PURPOSE Future advances in ophthalmology will see a paradigm shift in diagnostics from a focus on dysfunction and disease to better measures of psychophysical function and health. Practical methods to define genotypes will be increasingly important and non-invasive nanotechnologies are needed to detect molecular changes that predate histopathology. METHODS This is not a review nor meant to be comprehensive. Specific topics have been selected to illustrate the principles of important paradigm shifts that will influence the future of ophthalmic diagnostics. It is our impression that future evaluation of vision will go beyond visual acuity to assess ocular health in terms of psychophysical function. The definition of disease will incorporate genotype into what has historically been a phenotype-centric discipline. Non-invasive nanotechnologies will enable a paradigm shift from disease detection on a cellular level to a sub-cellular molecular level. RESULTS Vision can be evaluated beyond visual acuity by measuring contrast sensitivity, color vision, and macular function, as these provide better insights into the impact of aging and disease. Distortions can be quantified and the psychophysical basis of vision can be better evaluated than in the past by designing tests that assess particular macular cell function(s). Advances in our understanding of the genetic basis of eye diseases will enable better characterization of ocular health and disease. Non-invasive nanotechnologies can assess molecular changes in the lens, vitreous, and macula that predate visible pathology. Oxygen metabolism and circulatory physiology are measurable indices of ocular health that can detect variations of physiology and early disease. CONCLUSIONS This overview of paradigm shifts in ophthalmology suggests that the future will see significant improvements in ophthalmic diagnostics. The selected topics illustrate the principles of these paradigm shifts and should serve as a guide to further research and development. Indeed, successful implementation of these paradigm shifts in ophthalmology may provide useful guidance for similar developments in all of healthcare.
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Affiliation(s)
- J Sebag
- Dr. Sebag: VMR Institute for Vitreous Macula Retina, Huntington Beach, CA; Dr. Sadun: Doheny Eye Institute/UCLA, Los Angeles, CA; Dr. Pierce: Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School
| | - Alfredo A Sadun
- Dr. Sebag: VMR Institute for Vitreous Macula Retina, Huntington Beach, CA; Dr. Sadun: Doheny Eye Institute/UCLA, Los Angeles, CA; Dr. Pierce: Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School
| | - Eric A Pierce
- Dr. Sebag: VMR Institute for Vitreous Macula Retina, Huntington Beach, CA; Dr. Sadun: Doheny Eye Institute/UCLA, Los Angeles, CA; Dr. Pierce: Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School
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Boulling A, Escher P. Coupling ex vivo electroporation of mouse retinas and luciferase reporter assays to assess rod-specific promoter activity. Exp Eye Res 2016; 148:79-82. [PMID: 27268947 DOI: 10.1016/j.exer.2016.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/30/2016] [Accepted: 06/01/2016] [Indexed: 11/26/2022]
Abstract
Ex vivo electroporation of mouse retinas is an established tool to modulate gene expression and to study cell type-specific gene expression. Here we coupled ex vivo electroporation to luciferase reporter assays to facilitate the study of rod-photoreceptor-specific gene promoters. The activity of the rod-specific proximal bovine rhodopsin promoter was significantly increased in C57BL/6J wild-type retinas at postnatal days 1 and 7 by 3.4-fold and 8.7-fold respectively. In C57BL/6J Nr2e3(rd7/rd7) retinas, where the rod photoreceptor-specific nuclear receptor Nr2e3 is not expressed, a significant increase by 2.5-fold was only observed at postnatal day 7. Cone-specific S-opsin promoter activity was not modulated in C57BL/6J wild-type and Nr2e3(rd7/rd7) retinas. Taken together, we describe an easily implementable protocol to assess rod-specific promoter activity in a physiological context resembling that of the developing postnatal mouse retina.
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Affiliation(s)
- Arnaud Boulling
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, 1004 Lausanne, Switzerland; Institute for Research in Ophthalmology, 1950 Sion, Switzerland
| | - Pascal Escher
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, 1004 Lausanne, Switzerland.
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Mo A, Luo C, Davis FP, Mukamel EA, Henry GL, Nery JR, Urich MA, Picard S, Lister R, Eddy SR, Beer MA, Ecker JR, Nathans J. Epigenomic landscapes of retinal rods and cones. eLife 2016; 5:e11613. [PMID: 26949250 PMCID: PMC4798964 DOI: 10.7554/elife.11613] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 02/18/2016] [Indexed: 12/28/2022] Open
Abstract
Rod and cone photoreceptors are highly similar in many respects but they have important functional and molecular differences. Here, we investigate genome-wide patterns of DNA methylation and chromatin accessibility in mouse rods and cones and correlate differences in these features with gene expression, histone marks, transcription factor binding, and DNA sequence motifs. Loss of NR2E3 in rods shifts their epigenomes to a more cone-like state. The data further reveal wide differences in DNA methylation between retinal photoreceptors and brain neurons. Surprisingly, we also find a substantial fraction of DNA hypo-methylated regions in adult rods that are not in active chromatin. Many of these regions exhibit hallmarks of regulatory regions that were active earlier in neuronal development, suggesting that these regions could remain undermethylated due to the highly compact chromatin in mature rods. This work defines the epigenomic landscapes of rods and cones, revealing features relevant to photoreceptor development and function. DOI:http://dx.doi.org/10.7554/eLife.11613.001 Vision in humans is made possible by a light-sensing sheet of cells at the back of the eye called the retina. The surface of the retina is populated by specialized sensory cells, known as rods and cones. The rod cells detect very dim light, while the cones are less sensitive to light but are used to detect color. Together, the rods and cones gather the information needed to create a picture that is then transmitted to the brain. Rods and cones have been studied for decades, and genetic analyses have revealed the patterns of gene expression that lead a cell to develop into either a rod or a cone. Researchers have also identified several key regulatory genes that control these patterns, but less is known about the role of other factors that control the expression of genes. Chemical modifications to DNA or modifications to the proteins associated with DNA – which are collectively called epigenetic modifications – can either promote or inhibit the activation of nearby genes. Now, Mo et al. have shown that rods and cones from mice have very different patterns of epigenetic modifications. The experiments also revealed that many sections of DNA that are marked to promote gene activation contain known rod-specific or cone-specific genes; and that rod cells need a known regulatory gene to develop their specific pattern of epigenetic modifications. Finally, Mo et al. showed that epigenetic regulation differed between brain cells and rods and cones. These insights into epigenetic regulation of rod and cone genes may help explain why some people with eye diseases caused by the same genetic mutation may develop symptoms at different ages or lose vision at different rates. The new information about gene regulation may also help scientists to reprogram stem cells to become healthy rods or cones that could be transplanted into people with eye disease to restore their vision. DOI:http://dx.doi.org/10.7554/eLife.11613.002
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Affiliation(s)
- Alisa Mo
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Chongyuan Luo
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, United States
| | - Fred P Davis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Eran A Mukamel
- Department of Cognitive Science, University of California San Diego, La Jolla, United States
| | - Gilbert L Henry
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
| | - Mark A Urich
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
| | - Serge Picard
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Ryan Lister
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Australia
| | - Sean R Eddy
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Michael A Beer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, United States
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, United States
| | - Jeremy Nathans
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, United States.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
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Autosomal recessive retinitis pigmentosa with homozygous rhodopsin mutation E150K and non-coding cis-regulatory variants in CRX-binding regions of SAMD7. Sci Rep 2016; 6:21307. [PMID: 26887858 PMCID: PMC4758057 DOI: 10.1038/srep21307] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/19/2016] [Indexed: 01/17/2023] Open
Abstract
The aim of this study was to unravel the molecular pathogenesis of an unusual retinitis pigmentosa (RP) phenotype observed in a Turkish consanguineous family. Homozygosity mapping revealed two candidate genes, SAMD7 and RHO. A homozygous RHO mutation c.448G > A, p.E150K was found in two affected siblings, while no coding SAMD7 mutations were identified. Interestingly, four non-coding homozygous variants were found in two SAMD7 genomic regions relevant for binding of the retinal transcription factor CRX (CRX-bound regions, CBRs) in these affected siblings. Three variants are located in a promoter CBR termed CBR1, while the fourth is located more downstream in CBR2. Transcriptional activity of these variants was assessed by luciferase assays and electroporation of mouse retinal explants with reporter constructs of wild-type and variant SAMD7 CBRs. The combined CBR2/CBR1 variant construct showed significantly decreased SAMD7 reporter activity compared to the wild-type sequence, suggesting a cis-regulatory effect on SAMD7 expression. As Samd7 is a recently identified Crx-regulated transcriptional repressor in retina, we hypothesize that these SAMD7 variants might contribute to the retinal phenotype observed here, characterized by unusual, recognizable pigment deposits, differing from the classic spicular intraretinal pigmentation observed in other individuals homozygous for p.E150K, and typically associated with RP in general.
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Abstract
Photoreceptors have been the most intensively studied retinal cell type. Early lineage studies showed that photoreceptors are produced by retinal progenitor cells (RPCs) that produce only photoreceptor cells and by RPCs that produce both photoreceptor cells and other retinal cell types. More recent lineage studies have shown that there are intrinsic, molecular differences among these RPCs and that these molecular differences operate in gene regulatory networks (GRNs) that lead to the choice of the rod versus the cone fate. In addition, there are GRNs that lead to the choice of a photoreceptor fate and that of another retinal cell type. An example of such a GRN is one that drives the binary fate choice between a rod photoreceptor and bipolar cell. This GRN has many elements, including both feedforward and feedback regulatory loops, highlighting the complexity of such networks. This and other examples of retinal cell fate determination are reviewed here, focusing on the events that direct the choice of rod and cone photoreceptor fate.
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Affiliation(s)
- Constance L Cepko
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115;
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45
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Shen SQ, Myers CA, Hughes AEO, Byrne LC, Flannery JG, Corbo JC. Massively parallel cis-regulatory analysis in the mammalian central nervous system. Genome Res 2015; 26:238-55. [PMID: 26576614 PMCID: PMC4728376 DOI: 10.1101/gr.193789.115] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 11/12/2015] [Indexed: 01/23/2023]
Abstract
Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies in functionally interpreting these data. To address this issue, massively parallel reporter assays (MPRAs) have emerged, in which barcoded reporter libraries are introduced into cells, and the resulting barcoded transcripts are quantified by next-generation sequencing. Thus far, MPRAs have been largely restricted to assaying short CREs in a limited repertoire of cultured cell types. Here, we present two advances that extend the biological relevance and applicability of MPRAs. First, we adapt exome capture technology to instead capture candidate CREs, thereby tiling across the targeted regions and markedly increasing the length of CREs that can be readily assayed. Second, we package the library into adeno-associated virus (AAV), thereby allowing delivery to target organs in vivo. As a proof of concept, we introduce a capture library of about 46,000 constructs, corresponding to roughly 3500 DNase I hypersensitive (DHS) sites, into the mouse retina by ex vivo plasmid electroporation and into the mouse cerebral cortex by in vivo AAV injection. We demonstrate tissue-specific cis-regulatory activity of DHSs and provide examples of high-resolution truncation mutation analysis for multiplex parsing of CREs. Our approach should enable massively parallel functional analysis of a wide range of CREs in any organ or species that can be infected by AAV, such as nonhuman primates and human stem cell–derived organoids.
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Affiliation(s)
- Susan Q Shen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Connie A Myers
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Andrew E O Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Leah C Byrne
- Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, USA
| | - John G Flannery
- Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, USA
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Zhang C, Myers CA, Qi Z, Mitra RD, Corbo JC, Havranek JJ. Redesign of the monomer-monomer interface of Cre recombinase yields an obligate heterotetrameric complex. Nucleic Acids Res 2015; 43:9076-85. [PMID: 26365240 PMCID: PMC4605323 DOI: 10.1093/nar/gkv901] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/26/2015] [Accepted: 08/28/2015] [Indexed: 11/22/2022] Open
Abstract
Cre recombinase catalyzes the cleavage and religation of DNA at loxP sites. The enzyme is a homotetramer in its functional state, and the symmetry of the protein complex enforces a pseudo-palindromic symmetry upon the loxP sequence. The Cre-lox system is a powerful tool for many researchers. However, broader application of the system is limited by the fixed sequence preferences of Cre, which are determined by both the direct DNA contacts and the homotetrameric arrangement of the Cre monomers. As a first step toward achieving recombination at arbitrary asymmetric target sites, we have broken the symmetry of the Cre tetramer assembly. Using a combination of computational and rational protein design, we have engineered an alternative interface between Cre monomers that is functional yet incompatible with the wild-type interface. Wild-type and engineered interface halves can be mixed to create two distinct Cre mutants, neither of which are functional in isolation, but which can form an active heterotetramer when combined. When these distinct mutants possess different DNA specificities, control over complex assembly directly discourages recombination at unwanted half-site combinations, enhancing the specificity of asymmetric site recombination. The engineered Cre mutants exhibit this assembly pattern in a variety of contexts, including mammalian cells.
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Affiliation(s)
- Chi Zhang
- Program in Computational and Systems Biology, Washington University in St Louis, St Louis, MO 63110, USA
| | - Connie A Myers
- Department of Pathology and Immunology, Washington University in St Louis, St Louis, MO 63110, USA
| | - Zongtai Qi
- Program in Molecular Genetics and Genomics, Washington University in St Louis, St Louis, MO 63110, USA
| | - Robi D Mitra
- Department of Genetics, Washington University in St Louis, St Louis, MO 63110, USA
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University in St Louis, St Louis, MO 63110, USA
| | - James J Havranek
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, St Louis, MO 63110, USA
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Graded gene expression changes determine phenotype severity in mouse models of CRX-associated retinopathies. Genome Biol 2015; 16:171. [PMID: 26324254 PMCID: PMC4556057 DOI: 10.1186/s13059-015-0732-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/28/2015] [Indexed: 01/28/2023] Open
Abstract
Background Mutations in the cone-rod-homeobox protein CRX are typically associated with dominant blinding retinopathies with variable age of onset and severity. Five well-characterized mouse models carrying different Crx mutations show a wide range of disease phenotypes. To determine if the phenotype variability correlates with distinct changes in CRX target gene expression, we perform RNA-seq analyses on three of these models and compare the results with published data. Results Despite dramatic phenotypic differences between the three models tested, graded expression changes in shared sets of genes are detected. Phenotype severity correlates with the down-regulation of genes encoding key rod and cone phototransduction proteins. Interestingly, in increasingly severe mouse models, the transcription of many rod-enriched genes decreases decrementally, whereas that of cone-enriched genes increases incrementally. Unlike down-regulated genes, which show a high degree of CRX binding and dynamic epigenetic profiles in normal retinas, the up-regulated cone-enriched genes do not correlate with direct activity of CRX, but instead likely reflect a change in rod cell-fate integrity. Furthermore, these analyses describe the impact of minor gene expression changes on the phenotype, as two mutants showed marginally distinguishable expression patterns but huge phenotypic differences, including distinct mechanisms of retinal degeneration. Conclusions Our results implicate a threshold effect of gene expression level on photoreceptor function and survival, highlight the importance of CRX in photoreceptor subtype development and maintenance, and provide a molecular basis for phenotype variability in CRX-associated retinopathies. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0732-z) contains supplementary material, which is available to authorized users.
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48
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Rax Homeoprotein Regulates Photoreceptor Cell Maturation and Survival in Association with Crx in the Postnatal Mouse Retina. Mol Cell Biol 2015; 35:2583-96. [PMID: 25986607 DOI: 10.1128/mcb.00048-15] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 05/10/2015] [Indexed: 12/11/2022] Open
Abstract
The Rax homeobox gene plays essential roles in multiple processes of vertebrate retina development. Many vertebrate species possess Rax and Rax2 genes, and different functions have been suggested. In contrast, mice contain a single Rax gene, and its functional roles in late retinal development are still unclear. To clarify mouse Rax function in postnatal photoreceptor development and maintenance, we generated conditional knockout mice in which Rax in maturing or mature photoreceptor cells was inactivated by tamoxifen treatment (Rax iCKO mice). When Rax was inactivated in postnatal Rax iCKO mice, developing photoreceptor cells showed a significant decrease in the level of the expression of rod and cone photoreceptor genes and mature adult photoreceptors exhibited a specific decrease in cone cell numbers. In luciferase assays, we found that Rax and Crx cooperatively transactivate Rhodopsin and cone opsin promoters and that an optimum Rax expression level to transactivate photoreceptor gene expression exists. Furthermore, Rax and Crx colocalized in maturing photoreceptor cells, and their coimmunoprecipitation was observed in cultured cells. Taken together, these results suggest that Rax plays essential roles in the maturation of both cones and rods and in the survival of cones by regulating photoreceptor gene expression with Crx in the postnatal mouse retina.
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49
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MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers. Neuron 2015; 86:247-63. [PMID: 25801704 DOI: 10.1016/j.neuron.2015.02.038] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/30/2015] [Accepted: 02/20/2015] [Indexed: 11/20/2022]
Abstract
Organismal development requires the precise coordination of genetic programs to regulate cell fate and function. MEF2 transcription factors (TFs) play essential roles in this process but how these broadly expressed factors contribute to the generation of specific cell types during development is poorly understood. Here we show that despite being expressed in virtually all mammalian tissues, in the retina MEF2D binds to retina-specific enhancers and controls photoreceptor cell development. MEF2D achieves specificity by cooperating with a retina-specific factor CRX, which recruits MEF2D away from canonical MEF2 binding sites and redirects it to retina-specific enhancers that lack the consensus MEF2-binding sequence. Once bound to retina-specific enhancers, MEF2D and CRX co-activate the expression of photoreceptor-specific genes that are critical for retinal function. These findings demonstrate that broadly expressed TFs acquire specific functions through competitive recruitment to enhancers by tissue-specific TFs and through selective activation of these enhancers to regulate tissue-specific genes.
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50
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Omori Y, Kitamura T, Yoshida S, Kuwahara R, Chaya T, Irie S, Furukawa T. Mef2d is essential for the maturation and integrity of retinal photoreceptor and bipolar cells. Genes Cells 2015; 20:408-26. [PMID: 25757744 DOI: 10.1111/gtc.12233] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 01/30/2015] [Indexed: 11/29/2022]
Abstract
Mef2 transcription factors play a crucial role in cardiac and skeletal muscle differentiation. We found that Mef2d is highly expressed in the mouse retina and its loss causes photoreceptor degeneration similar to that observed in human retinitis pigmentosa patients. Electroretinograms (ERGs) were severely impaired in Mef2d-/- mice. Immunohistochemistry showed that photoreceptor and bipolar cell synapse protein levels severely decreased in the Mef2d-/- retina. Expression profiling by microarray analysis showed that Mef2d is required for the expression of various genes in photoreceptor and bipolar cells, including cone arrestin, Guca1b, Pde6h and Cacna1s, which encode outer segment and synapse proteins. We also observed that Mef2d synergistically activates the cone arrestin (Arr3) promoter with Crx, suggesting that functional cooperation between Mef2d and Crx is important for photoreceptor cell gene regulation. Taken together, our results show that Mef2d is essential for photoreceptor and bipolar cell gene expression, either independently or cooperatively with Crx.
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Affiliation(s)
- Yoshihiro Omori
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan; JST, CREST, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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