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Bhardwaj A, Sohni A, Lou CH, De Gendt K, Zhang F, Kim E, Subbarayalu P, Chan W, Kerkhofs S, Claessens F, Kimmins S, Rao MK, Meistrich M, Wilkinson MF. Concordant Androgen-Regulated Expression of Divergent Rhox5 Promoters in Sertoli Cells. Endocrinology 2022; 163:6432187. [PMID: 34902009 PMCID: PMC8667857 DOI: 10.1210/endocr/bqab237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Indexed: 11/19/2022]
Abstract
Concordant transcriptional regulation can generate multiple gene products that collaborate to achieve a common goal. Here we report a case of concordant transcriptional regulation that instead drives a single protein to be produced in the same cell type from divergent promoters. This gene product-the RHOX5 homeobox transcription factor-is translated from 2 different mRNAs with different 5' untranslated regions (UTRs) transcribed from alternative promoters. Despite the fact that these 2 promoters-the proximal promoter (Pp) and the distal promoter (Pd)-exhibit different patterns of tissue-specific activity, share no obvious sequence identity, and depend on distinct transcription factors for expression, they exhibit a remarkably similar expression pattern in the testes. In particular, both depend on androgen signaling for expression in the testes, where they are specifically expressed in Sertoli cells and have a similar stage-specific expression pattern during the seminiferous epithelial cycle. We report evidence for 3 mechanisms that collaborate to drive concordant Pp/Pd expression. First, both promoters have an intrinsic ability to respond to androgen receptor and androgen. Second, the Pp acts as an enhancer to promote androgen-dependent transcription from the Pd. Third, Pd transcription is positively autoregulated by the RHOX5 protein, which is first produced developmentally from the Pp. Together, our data support a model in which the Rhox5 homeobox gene evolved multiple mechanisms to activate both of its promoters in Sertoli cells to produce Rhox5 in an androgen-dependent manner during different phases of spermatogenesis.
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Affiliation(s)
- Anjana Bhardwaj
- Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
- Department of Breast Surgical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Abhishek Sohni
- School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Chih-Hong Lou
- School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Karel De Gendt
- School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093-0695, USA
- KU Leuven, Campus Gasthuisberg, O/N1, BE-3000 Leuven, Belgium
| | - Fanmao Zhang
- Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Eunah Kim
- Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
- Department of Environmental Health and Safety, University of Texas Health Sciences Center, Houston, TX, USA
| | - Panneerdoss Subbarayalu
- Department of Cell Systems and Anatomy, University of Texas HealthSan Antonio, San Antonio, TX 78229, USA
| | - Waikin Chan
- Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Frank Claessens
- KU Leuven, Campus Gasthuisberg, O/N1, BE-3000 Leuven, Belgium
| | - Sarah Kimmins
- Department of Animal Sciences, McGill UniversityMontreal, Quebec H3A 0G4, Canada
| | - Manjeet K Rao
- Department of Cell Systems and Anatomy, University of Texas HealthSan Antonio, San Antonio, TX 78229, USA
| | - Marvin Meistrich
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Miles F Wilkinson
- School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093-0695, USA
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Correspondence: M. F. Wilkinson, PhD, University of California San Diego, San Diego, 9500 Gilman Drive # 0695, La Jolla, CA 92093-0695, USA. . Previous Affiliation: Miles F. Wilkinson’s previous affiliation is Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
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Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus. Commun Biol 2021; 4:829. [PMID: 34211114 PMCID: PMC8249380 DOI: 10.1038/s42003-021-02340-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 06/09/2021] [Indexed: 01/22/2023] Open
Abstract
To further the understanding of the evolution of transcriptional regulation, we profiled genome-wide transcriptional start sites (TSSs) in two sub-species, Bos taurus taurus and Bos taurus indicus, that diverged approximately 500,000 years ago. Evolutionary and developmental-stage differences in TSSs were detected across the sub-species, including translocation of dominant TSS and changes in TSS distribution. The 16% of all SNPs located in significant differentially used TSS clusters across sub-species had significant shifts in allele frequency (472 SNPs), indicating they may have been subject to selection. In spleen and muscle, a higher relative TSS expression was observed in Bos indicus than Bos taurus for all heat shock protein genes, which may be responsible for the tropical adaptation of Bos indicus. Forutan et al. measure RNA expression and map transcription start sites (TSSs) between two sub-species of cattle in adult and fetal tissues and demonstrate translocation and changes in TSS distribution between the sub-species. This study provides insight into cattle adaptation and provides support of rapidly evolving TSS between two recently diverged subspecies.
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Campla CK, Mast H, Dong L, Lei J, Halford S, Sekaran S, Swaroop A. Targeted deletion of an NRL- and CRX-regulated alternative promoter specifically silences FERM and PDZ domain containing 1 (Frmpd1) in rod photoreceptors. Hum Mol Genet 2020; 28:804-817. [PMID: 30445545 DOI: 10.1093/hmg/ddy388] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/15/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023] Open
Abstract
Regulation of cell type-specific gene expression is critical for generating neuronal diversity. Transcriptome analyses have unraveled extensive heterogeneity of transcribed sequences in retinal photoreceptors because of alternate splicing and/or promoter usage. Here we show that Frmpd1 (FERM and PDZ domain containing 1) is transcribed from an alternative promoter specifically in the retina. Electroporation of Frmpd1 promoter region, -505 to +382 bp, activated reporter gene expression in mouse retina in vivo. A proximal promoter sequence (-8 to +33 bp) of Frmpd1 binds to neural retina leucine zipper (NRL) and cone-rod homeobox protein (CRX), two rod-specific differentiation factors, and is necessary for activating reporter gene expression in vitro and in vivo. Clustered regularly interspaced short palindromic repeats/Cas9-mediated deletion of the genomic region, including NRL and CRX binding sites, in vivo completely eliminated Frmpd1 expression in rods and dramatically reduced expression in rod bipolar cells, thereby overcoming embryonic lethality caused by germline Frmpd1 deletion. Our studies demonstrate that a cell type-specific regulatory control region is a credible target for creating loss-of-function alleles of widely expressed genes.
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Affiliation(s)
- Christie K Campla
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.,Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Hannah Mast
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lijin Dong
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jingqi Lei
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Sumathi Sekaran
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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Developmental Requirement of Homeoprotein Otx2 for Specific Habenulo-Interpeduncular Subcircuits. J Neurosci 2018; 39:1005-1019. [PMID: 30593496 DOI: 10.1523/jneurosci.1818-18.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/06/2018] [Accepted: 12/16/2018] [Indexed: 01/11/2023] Open
Abstract
The habenulo-interpeduncular system (HIPS) is now recognized as a critical circuit modulating aversion, reward, and social behavior. There is evidence that dysfunction of this circuit leads to psychiatric disorders. Because psychiatric diseases may originate in developmental abnormalities, it is crucial to investigate the developmental mechanisms controlling the formation of the HIPS. Thus far, this issue has been the focus of limited studies. Here, we explored the developmental processes underlying the formation of the medial habenula (MHb) and its unique output, the interpeduncular nucleus (IPN), in mice independently of their gender. We report that the Otx2 homeobox gene is essential for the proper development of both structures. We show that MHb and IPN neurons require Otx2 at different developmental stages and, in both cases, Otx2 deletion leads to disruption of HIPS subcircuits. Finally, we show that Otx2+ neurons tend to be preferentially interconnected. This study reveals that synaptically connected components of the HIPS, despite radically different developmental strategies, share high sensitivity to Otx2 expression.SIGNIFICANCE STATEMENT Brain reward circuits are highly complex and still poorly understood. In particular, it is important to understand how these circuits form as many psychiatric diseases may arise from their abnormal development. This work shows that Otx2, a critical evolutionary conserved gene implicated in brain development and a predisposing factor for psychiatric diseases, is required for the formation of the habenulo-interpeduncular system (HIPS), an important component of the reward circuit. Otx2 deletion affects multiple processes such as proliferation and migration of HIPS neurons. Furthermore, neurons expressing Otx2 are preferentially interconnected. Therefore, Otx2 expression may represent a code that specifies the connectivity of functional subunits of the HIPS. Importantly, the Otx2 conditional knock-out animals used in this study might represent a new genetic model of psychiatric diseases.
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Hayani H, Song I, Dityatev A. Increased Excitability and Reduced Excitatory Synaptic Input Into Fast-Spiking CA2 Interneurons After Enzymatic Attenuation of Extracellular Matrix. Front Cell Neurosci 2018; 12:149. [PMID: 29899690 PMCID: PMC5988902 DOI: 10.3389/fncel.2018.00149] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/14/2018] [Indexed: 12/21/2022] Open
Abstract
The neural extracellular matrix (ECM) is enriched with hyaluronic acid, chondroitin sulfate proteoglycans (CSPGs) and the glycoprotein tenascin-R, which play important roles in synaptic plasticity, as shown by studies of the CA1 region of the hippocampus. However, ECM molecules are strongly expressed in the CA2 region, which harbors a high number of fast-spiking interneurons (FSIs) surrounded by a particularly condensed form of ECM, perineuronal nets. Despite this intriguing peculiarity, the functional role of ECM in the CA2 region is mostly unknown. Here, we investigate the acute and delayed effects of chondroitinase ABC (ChABC), an enzyme that digests chondroitin sulfate side chains of CSPGs and greatly attenuates neural ECM, on neuronal excitability and excitatory transmission in the CA2 region. Whole-cell patch clamp recordings of CA2 pyramidal cells (PCs) and FSIs in hippocampal slices revealed that 7 days after injection of ChABC into the CA2 region in vivo, there are alterations in excitability of FSIs and PCs. FSIs generated action potentials with larger amplitudes and longer durations in response to less depolarizing currents compared to controls. PCs were excited at less depolarized membrane potentials, resulted in lower latency of spike generation. The frequency of excitatory postsynaptic currents in FSIs was selectively reduced, while the frequency of inhibitory postsynaptic currents was selectively increased. Acute treatment of hippocampal slices with ChABC did not result in any of these effects. This increase in excitability and changes in synaptic inputs to FSIs after attenuation of ECM suggests a crucial role for perineuronal nets associated with FSIs in regulation of synaptic and electrical properties of these cells.
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Affiliation(s)
- Hussam Hayani
- Molecular Neuroplasticity, German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Inseon Song
- Molecular Neuroplasticity, German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Alexander Dityatev
- Molecular Neuroplasticity, German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.,Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
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6
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Heritable, Allele-Specific Chromosomal Looping between Tandem Promoters Specifies Promoter Usage of SHC1. Mol Cell Biol 2018; 38:MCB.00658-17. [PMID: 29440311 DOI: 10.1128/mcb.00658-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/08/2018] [Indexed: 11/20/2022] Open
Abstract
One-half of the genes in the human genome contain alternative promoters, some of which generate products with opposing functions. Aberrant silencing or activation of such alternative promoters is associated with multiple diseases, including cancer, but little is known regarding the molecular mechanisms that control alternative promoter choice. The SHC1 gene encodes p46Shc/p52Shc and p66Shc, proteins oppositely regulating anchorage-independent growth that are produced by transcription initiated from the upstream and downstream tandem promoters of SHC1, respectively. Here we demonstrate that activation of these promoters is mutually exclusive on separate alleles in single primary endothelial cells in a heritable fashion, ensuring expression of both transcripts by the cell. Peripheral blood lymphocytes that do not transcribe p66Shc transcribed p52Shc biallelically. This distinct monoallelic transcription pattern is established by allele-specific chromosomal looping between tandem promoters, which silences the upstream promoter. Our results reveal a new mechanism to control alternative promoter usage through higher-order chromatin structure.
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Kole C, Klipfel L, Yang Y, Ferracane V, Blond F, Reichman S, Millet-Puel G, Clérin E, Aït-Ali N, Pagan D, Camara H, Delyfer MN, Nandrot EF, Sahel JA, Goureau O, Léveillard T. Otx2-Genetically Modified Retinal Pigment Epithelial Cells Rescue Photoreceptors after Transplantation. Mol Ther 2017; 26:219-237. [PMID: 28988713 PMCID: PMC5762984 DOI: 10.1016/j.ymthe.2017.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 08/17/2017] [Accepted: 09/03/2017] [Indexed: 12/13/2022] Open
Abstract
Inherited retinal degenerations are blinding diseases characterized by the loss of photoreceptors. Their extreme genetic heterogeneity complicates treatment by gene therapy. This has motivated broader strategies for transplantation of healthy retinal pigmented epithelium to protect photoreceptors independently of the gene causing the disease. The limited clinical benefit for visual function reported up to now is mainly due to dedifferentiation of the transplanted cells that undergo an epithelial-mesenchymal transition. We have studied this mechanism in vitro and revealed the role of the homeogene OTX2 in preventing dedifferentiation through the regulation of target genes. We have overexpressed OTX2 in retinal pigmented epithelial cells before their transplantation in the eye of a model of retinitis pigmentosa carrying a mutation in Mertk, a gene specifically expressed by retinal pigmented epithelial cells. OTX2 increases significantly the protection of photoreceptors as seen by histological and functional analyses. We observed that the beneficial effect of OTX2 is non-cell autonomous, and it is at least partly mediated by unidentified trophic factors. Transplantation of OTX2-genetically modified cells may be medically effective for other retinal diseases involving the retinal pigmented epithelium as age-related macular degeneration.
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Affiliation(s)
- Christo Kole
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France
| | - Laurence Klipfel
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France
| | - Ying Yang
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France
| | - Vanessa Ferracane
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France
| | - Frederic Blond
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France
| | - Sacha Reichman
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France
| | - Géraldine Millet-Puel
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France
| | - Emmanuelle Clérin
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France
| | - Najate Aït-Ali
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France
| | - Delphine Pagan
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France
| | - Hawa Camara
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France
| | - Marie-Noëlle Delyfer
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France; Unité Rétine, Uvéite et Neuro-Ophtalmologie, Département d'Ophtalmologie, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Emeline F Nandrot
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France
| | - Jose-Alain Sahel
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France
| | - Olivier Goureau
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France
| | - Thierry Léveillard
- INSERM, U968, Paris 75012, France; Sorbonne Universités, UPMC Univ Paris 06 UMR_S 968, Institut de la Vision, Paris 75012, France; CNRS, UMR_7210, Paris 75012, France.
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Maheu ME, Ressler KJ. Developmental pathway genes and neural plasticity underlying emotional learning and stress-related disorders. Learn Mem 2017; 24:492-501. [PMID: 28814475 PMCID: PMC5580529 DOI: 10.1101/lm.044271.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/18/2017] [Indexed: 11/24/2022]
Abstract
The manipulation of neural plasticity as a means of intervening in the onset and progression of stress-related disorders retains its appeal for many researchers, despite our limited success in translating such interventions from the laboratory to the clinic. Given the challenges of identifying individual genetic variants that confer increased risk for illnesses like depression and post-traumatic stress disorder, some have turned their attention instead to focusing on so-called "master regulators" of plasticity that may provide a means of controlling these potentially impaired processes in psychiatric illnesses. The mammalian homolog of Tailless (TLX), Wnt, and the homeoprotein Otx2 have all been proposed to constitute master regulators of different forms of plasticity which have, in turn, each been implicated in learning and stress-related disorders. In the present review, we provide an overview of the changing distribution of these genes and their roles both during development and in the adult brain. We further discuss how their distinct expression profiles provide clues as to their function, and may inform their suitability as candidate drug targets in the treatment of psychiatric disorders.
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Affiliation(s)
- Marissa E Maheu
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts 02478, USA
| | - Kerry J Ressler
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts 02478, USA
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Wang X, Hou J, Quedenau C, Chen W. Pervasive isoform-specific translational regulation via alternative transcription start sites in mammals. Mol Syst Biol 2016; 12:875. [PMID: 27430939 PMCID: PMC4965872 DOI: 10.15252/msb.20166941] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/17/2016] [Accepted: 06/21/2016] [Indexed: 12/02/2022] Open
Abstract
Transcription initiated at alternative sites can produce mRNA isoforms with different 5'UTRs, which are potentially subjected to differential translational regulation. However, the prevalence of such isoform-specific translational control across mammalian genomes is currently unknown. By combining polysome profiling with high-throughput mRNA 5' end sequencing, we directly measured the translational status of mRNA isoforms with distinct start sites. Among 9,951 genes expressed in mouse fibroblasts, we identified 4,153 showed significant initiation at multiple sites, of which 745 genes exhibited significant isoform-divergent translation. Systematic analyses of the isoform-specific translation revealed that isoforms with longer 5'UTRs tended to translate less efficiently. Further investigation of cis-elements within 5'UTRs not only provided novel insights into the regulation by known sequence features, but also led to the discovery of novel regulatory sequence motifs. Quantitative models integrating all these features explained over half of the variance in the observed isoform-divergent translation. Overall, our study demonstrated the extensive translational regulation by usage of alternative transcription start sites and offered comprehensive understanding of translational regulation by diverse sequence features embedded in 5'UTRs.
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Affiliation(s)
- Xi Wang
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Jingyi Hou
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Claudia Quedenau
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Wei Chen
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, China
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Alfano G, Shah AZ, Jeffery G, Bhattacharya SS. First insights into the expression of VAX2 in humans and its localization in the adult primate retina. Exp Eye Res 2016; 148:24-29. [DOI: 10.1016/j.exer.2016.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/29/2016] [Accepted: 05/09/2016] [Indexed: 01/21/2023]
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Identification of an Alternative Splicing Product of the Otx2 Gene Expressed in the Neural Retina and Retinal Pigmented Epithelial Cells. PLoS One 2016; 11:e0150758. [PMID: 26985665 PMCID: PMC4795653 DOI: 10.1371/journal.pone.0150758] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 01/20/2016] [Indexed: 12/16/2022] Open
Abstract
To investigate the complexity of alternative splicing in the retina, we sequenced and analyzed a total of 115,706 clones from normalized cDNA libraries from mouse neural retina (66,217) and rat retinal pigmented epithelium (49,489). Based upon clustering the cDNAs and mapping them with their respective genomes, the estimated numbers of genes were 9,134 for the mouse neural retina and 12,050 for the rat retinal pigmented epithelium libraries. This unique collection of retinal of messenger RNAs is maintained and accessible through a web-base server to the whole community of retinal biologists for further functional characterization. The analysis revealed 3,248 and 3,202 alternative splice events for mouse neural retina and rat retinal pigmented epithelium, respectively. We focused on transcription factors involved in vision. Among the six candidates suitable for functional analysis, we selected Otx2S, a novel variant of the Otx2 gene with a deletion within the homeodomain sequence. Otx2S is expressed in both the neural retina and retinal pigmented epithelium, and encodes a protein that is targeted to the nucleus. OTX2S exerts transdominant activity on the tyrosinase promoter when tested in the physiological environment of primary RPE cells. By overexpressing OTX2S in primary RPE cells using an adeno associated viral vector, we identified 10 genes whose expression is positively regulated by OTX2S. We find that OTX2S is able to bind to the chromatin at the promoter of the retinal dehydrogenase 10 (RDH10) gene.
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Changes in Otx2 and parvalbumin immunoreactivity in the superior colliculus in the platelet-derived growth factor receptor-β knockout mice. BIOMED RESEARCH INTERNATIONAL 2013; 2013:848265. [PMID: 24319691 PMCID: PMC3844215 DOI: 10.1155/2013/848265] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/30/2013] [Indexed: 12/11/2022]
Abstract
The superior colliculus (SC), a relay nucleus in the subcortical visual pathways, is implicated in socioemotional behaviors. Homeoprotein Otx2 and β subunit of receptors of platelet-derived growth factor (PDGFR-β) have been suggested to play an important role in development of the visual system and development and maturation of GABAergic neurons. Although PDGFR-β-knockout (KO) mice displayed socio-emotional deficits associated with parvalbumin (PV-)immunoreactive (IR) neurons, their anatomical bases in the SC were unknown. In the present study, Otx2 and PV-immunolabeling in the adult mouse SC were investigated in the PDGFR-β KO mice. Although there were no differences in distribution patterns of Otx2 and PV-IR cells between the wild type and PDGFR-β KO mice, the mean numbers of both of the Otx2- and PV-IR cells were significantly reduced in the PDGFR-β KO mice. Furthermore, average diameters of Otx2- and PV-IR cells were significantly reduced in the PDGFR-β KO mice. These findings suggest that PDGFR-β plays a critical role in the functional development of the SC through its effects on Otx2- and PV-IR cells, provided specific roles of Otx2 protein and PV-IR cells in the development of SC neurons and visual information processing, respectively.
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Beby F, Lamonerie T. The homeobox gene Otx2 in development and disease. Exp Eye Res 2013; 111:9-16. [DOI: 10.1016/j.exer.2013.03.007] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/07/2013] [Accepted: 03/11/2013] [Indexed: 01/04/2023]
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Park WJ, Kothapalli KSD, Reardon HT, Lawrence P, Qian SB, Brenna JT. A novel FADS1 isoform potentiates FADS2-mediated production of eicosanoid precursor fatty acids. J Lipid Res 2012; 53:1502-12. [PMID: 22619218 DOI: 10.1194/jlr.m025312] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The fatty acid desaturase (FADS) genes code for the rate-limiting enzymes required for the biosynthesis of long-chain polyunsaturated fatty acids (LCPUFA). Here we report discovery and function of a novel FADS1 splice variant. FADS1 alternative transcript 1 (FADS1AT1) enhances desaturation of FADS2, leading to increased production of eicosanoid precursors, the first case of an isoform modulating the enzymatic activity encoded by another gene. Multiple protein isoforms were detected in primate liver, thymus, and brain. In human neuronal cells, their expression patterns are modulated by differentiation and result in alteration of cellular fatty acids. FADS1, but not FADS1AT1, localizes to endoplasmic reticulum and mitochondria. Ribosomal footprinting demonstrates that all three FADS genes are translated at similar levels. The noncatalytic regulation of FADS2 desaturation by FADS1AT1 is a novel, plausible mechanism by which several phylogenetically conserved FADS isoforms may regulate LCPUFA biosynthesis in a manner specific to tissue, organelle, and developmental stage.
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Affiliation(s)
- Woo Jung Park
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
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15
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Westenskow PD, McKean JB, Kubo F, Nakagawa S, Fuhrmann S. Ectopic Mitf in the embryonic chick retina by co-transfection of β-catenin and Otx2. Invest Ophthalmol Vis Sci 2010; 51:5328-35. [PMID: 20463321 PMCID: PMC3066625 DOI: 10.1167/iovs.09-5015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 03/26/2010] [Accepted: 04/15/2010] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Development of the retinal pigment epithelium (RPE) is controlled by intrinsic and extrinsic regulators including orthodenticle homeobox 2 (Otx2) and the Wnt/β-catenin pathway, respectively. Otx2 and β-catenin are necessary for the expression of the RPE key regulator microphthalmia-associated transcription factor (Mitf); however, neither factor is sufficient to promote Mitf expression in vivo. The study was conducted to determine whether Otx2 and β-catenin act in a combinatorial manner and tested whether co-expression in the presumptive chick retina induces ectopic Mitf expression. METHODS The sufficiency of Wnt/β-catenin activation and/or Otx2 expression to induce RPE-specific gene expression was examined in chick optic vesicle explant cultures or in the presumptive neural retina using in ovo-electroporation. Luciferase assays were used to examine the transactivation potentials of Otx2 and β-catenin on the Mitf-D enhancer and autoregulation of the Mitf-D and Otx2T0 enhancers. RESULTS In optic vesicles explant cultures, RPE-specific gene expression was activated by lithium chloride, a Wnt/β-catenin agonist. However, in vivo, Mitf was induced only in the presumptive retina if both β-catenin and Otx2 are co-expressed. Furthermore, both Mitf and Otx2 can autoregulate their own enhancers in vitro. CONCLUSIONS The present study provides evidence that β-catenin and Otx2 are sufficient, at least in part, to convert retinal progenitor cells into presumptive RPE cells expressing Mitf. Otx2 may act as a competence factor that allows RPE specification in concert with additional RPE-promoting factors such as β-catenin.
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Affiliation(s)
- Peter D. Westenskow
- From the Department of Ophthalmology and Visual Sciences, Moran Eye Center, and
- the Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, Utah; and
| | - Jon B. McKean
- From the Department of Ophthalmology and Visual Sciences, Moran Eye Center, and
| | - Fumi Kubo
- the RIKEN Advanced Science Institute, Wako, Saitama, Japan
| | | | - Sabine Fuhrmann
- From the Department of Ophthalmology and Visual Sciences, Moran Eye Center, and
- the Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, Utah; and
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Béby F, Housset M, Fossat N, Le Greneur C, Flamant F, Godement P, Lamonerie T. Otx2 gene deletion in adult mouse retina induces rapid RPE dystrophy and slow photoreceptor degeneration. PLoS One 2010; 5:e11673. [PMID: 20657788 PMCID: PMC2908139 DOI: 10.1371/journal.pone.0011673] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 06/16/2010] [Indexed: 11/23/2022] Open
Abstract
Background Many developmental genes are still active in specific tissues after development is completed. This is the case for the homeobox gene Otx2, an essential actor of forebrain and head development. In adult mouse, Otx2 is strongly expressed in the retina. Mutations of this gene in humans have been linked to severe ocular malformation and retinal diseases. It is, therefore, important to explore its post-developmental functions. In the mature retina, Otx2 is expressed in three cell types: bipolar and photoreceptor cells that belong to the neural retina and retinal pigment epithelium (RPE), a neighbour structure that forms a tightly interdependent functional unit together with photoreceptor cells. Methodology/Principal Findings Conditional self-knockout was used to address the late functions of Otx2 gene in adult mice. This strategy is based on the combination of a knock-in CreERT2 allele and a floxed allele at the Otx2 locus. Time-controlled injection of tamoxifen activates the recombinase only in Otx2 expressing cells, resulting in selective ablation of the gene in its entire domain of expression. In the adult retina, loss of Otx2 protein causes slow degeneration of photoreceptor cells. By contrast, dramatic changes of RPE activity rapidly occur, which may represent a primary cause of photoreceptor disease. Conclusions Our novel mouse model uncovers new Otx2 functions in adult retina. We show that this transcription factor is necessary for long-term maintenance of photoreceptors, likely through the control of specific activities of the RPE.
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Affiliation(s)
- Francis Béby
- Institut de Génomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, Institut National de la Recherche Agronomique, Université de Lyon, Lyon, France
| | - Michael Housset
- Institut de Biologie du Développement et Cancer, Centre National de la Recherche Scientifique, Université de Nice Sophia-Antipolis, Nice, France
| | - Nicolas Fossat
- Embryology Unit, Children's Medical Research Institute, Sydney Medical School, University of Sydney, Wentworthville, Australia
| | - Coralie Le Greneur
- Institut de Génomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, Institut National de la Recherche Agronomique, Université de Lyon, Lyon, France
- Institut de Biologie du Développement et Cancer, Centre National de la Recherche Scientifique, Université de Nice Sophia-Antipolis, Nice, France
| | - Frédéric Flamant
- Institut de Génomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, Institut National de la Recherche Agronomique, Université de Lyon, Lyon, France
| | - Pierre Godement
- Institut de Génomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, Institut National de la Recherche Agronomique, Université de Lyon, Lyon, France
| | - Thomas Lamonerie
- Institut de Génomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, Institut National de la Recherche Agronomique, Université de Lyon, Lyon, France
- Institut de Biologie du Développement et Cancer, Centre National de la Recherche Scientifique, Université de Nice Sophia-Antipolis, Nice, France
- * E-mail:
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17
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Dateki S, Kosaka K, Hasegawa K, Tanaka H, Azuma N, Yokoya S, Muroya K, Adachi M, Tajima T, Motomura K, Kinoshita E, Moriuchi H, Sato N, Fukami M, Ogata T. Heterozygous orthodenticle homeobox 2 mutations are associated with variable pituitary phenotype. J Clin Endocrinol Metab 2010; 95:756-64. [PMID: 19965921 DOI: 10.1210/jc.2009-1334] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CONTEXT Although recent studies have suggested a positive role of OTX2 in pituitary as well as ocular development and function, detailed pituitary phenotypes in OTX2 mutations and OTX2 target genes for pituitary function other than HESX1 and POU1F1 remain to be determined. OBJECTIVE We aimed to examine such unresolved issues. SUBJECTS We studied 94 Japanese patients with various ocular or pituitary abnormalities. RESULTS We identified heterozygous p.K74fsX103 in case 1, p.A72fsX86 in case 2, p.G188X in two unrelated cases (3 and 4), and a 2,860,561-bp microdeletion involving OTX2 in case 5. Clinical studies revealed isolated GH deficiency in cases 1 and 5; combined pituitary hormone deficiency in case 3; abnormal pituitary structures in cases 1, 3, and 5; and apparently normal pituitary function in cases 2 and 4, together with ocular anomalies in cases 1-5. The wild-type Orthodenticle homeobox 2 (OTX2) protein transactivated the GNRH1 promoter as well as the HESX1, POU1F1, and IRBP (interstitial retinoid-binding protein) promoters, whereas the p.K74fsX103-OTX2 and p.A72fsX86-OTX2 proteins had no transactivation functions and the p.G188X-OTX2 protein had reduced ( approximately 50%) transactivation functions for the four promoters, with no dominant-negative effect. cDNA screening identified positive OTX2 expression in the hypothalamus. CONCLUSIONS The results imply that OTX2 mutations are associated with variable pituitary phenotype, with no genotype-phenotype correlations, and that OTX2 can transactivate GNRH1 as well as HESX1 and POU1F1.
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Affiliation(s)
- Sumito Dateki
- Department of Endocrinology and Metabolism, National Research Institute for Child Health and Development, 2-10-1 Ohkura, Setagaya, Tokyo 157-8535, Japan
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18
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Acampora D, Di Giovannantonio LG, Di Salvio M, Mancuso P, Simeone A. Selective inactivation of Otx2 mRNA isoforms reveals isoform-specific requirement for visceral endoderm anteriorization and head morphogenesis and highlights cell diversity in the visceral endoderm. Mech Dev 2009; 126:882-97. [PMID: 19615442 DOI: 10.1016/j.mod.2009.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 07/07/2009] [Indexed: 10/20/2022]
Abstract
Genetic and embryological experiments demonstrated that the visceral endoderm (VE) is essential for positioning the primitive streak at one pole of the embryo and head morphogenesis through antagonism of the Wnt and Nodal signaling pathways. The transcription factor Otx2 is required for VE anteriorization and specification of rostral neuroectoderm at least in part by controlling the expression of Dkk1 and Lefty1. Here, we investigated the relevance of the Otx2 transcriptional control in these processes. Otx2 protein is encoded by different mRNAs variants, which, on the basis of their transcription start site, may be distinguished in distal and proximal. Distal isoforms are prevalently expressed in the epiblast and neuroectoderm, while proximal isoforms prevalently in the VE. Selective inactivation of Otx2 variants reveals that distal isoforms are not required for gastrulation, but essential for maintenance of forebrain and midbrain identities; conversely, proximal isoforms control VE anteriorization and, indirectly, primitive streak positioning through the activation of Dkk1 and Lefty1. Moreover, in these mutants the expression of proximal isoforms is not affected by the lack of distal mRNAs and vice versa. Taken together these findings indicate that proximal and distal isoforms, whose expression is independently regulated in the VE and epiblast-derived neuroectoderm, functionally cooperate to provide these tissues with the sufficient level of Otx2 necessary to promote a normal development. Furthermore, we discovered that in the VE the expression of Otx2 isoforms is tightly controlled at single cell level, and we hypothesize that this molecular diversity may potentially confer specific functional properties to different subsets of VE cells.
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Davuluri RV, Suzuki Y, Sugano S, Plass C, Huang THM. The functional consequences of alternative promoter use in mammalian genomes. Trends Genet 2008; 24:167-77. [PMID: 18329129 DOI: 10.1016/j.tig.2008.01.008] [Citation(s) in RCA: 238] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 01/17/2008] [Accepted: 01/18/2008] [Indexed: 12/19/2022]
Abstract
We are beginning to appreciate the increasing complexity of mammalian gene structure. A phenomenon that adds an important dimension to this complexity is the use of alternative gene promoters that drive widespread cell type, tissue type or developmental gene regulation. Recent annotations of the human genome suggest that almost one half of the protein-coding genes contain alternative promoters, including those of many disease-associated genes. Aberrant use of one promoter over another has been found to be associated with various diseases, including cancer. Here we discuss the functional consequences of use and misuse of alternative promoters in normal and disease genomes and review the molecular mechanisms regulating alternative promoter use in mammalian genomes.
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Affiliation(s)
- Ramana V Davuluri
- Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA.
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20
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A new GFP-tagged line reveals unexpected Otx2 protein localization in retinal photoreceptors. BMC DEVELOPMENTAL BIOLOGY 2007; 7:122. [PMID: 17980036 PMCID: PMC2204009 DOI: 10.1186/1471-213x-7-122] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Accepted: 11/02/2007] [Indexed: 12/03/2022]
Abstract
Background Dynamic monitoring of protein expression and localization is fundamental to the understanding of biological processes. The paired-class homeodomain-containing transcription factor Otx2 is essential for normal head and brain development in vertebrates. Recent conditional knockout studies have pointed to multiple roles of this protein during late development and post-natal life. Yet, later expression and functions remain poorly characterized as specific reagents to detect the protein at any stage of development are still missing. Results We generated a new mouse line harbouring an insertion of the GFP gene within the Otx2 coding sequence to monitor the gene activity while preserving most of its functions. Our results demonstrate that this line represents a convenient tool to capture the dynamics of Otx2 gene expression from early embryonic stages to adulthood. In addition, we could visualize the intracellular location of Otx2 protein. In the retina, we reinterpret the former view of protein distribution and show a further level of regulation of intranuclear protein localization, which depends on the cell type. Conclusion The GFP-tagged Otx2 mouse line fully recapitulates previously known expression patterns and brings additional accuracy and easiness of detection of Otx2 gene activity. This opens up the way to live imaging of a highly dynamic actor of brain development and can be adapted to any mutant background to probe for genetic interaction between Otx2 and the mutated gene.
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21
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Kimura-Yoshida C, Tian E, Nakano H, Amazaki S, Shimokawa K, Rossant J, Aizawa S, Matsuo I. Crucial roles of Foxa2 in mouse anterior-posterior axis polarization via regulation of anterior visceral endoderm-specific genes. Proc Natl Acad Sci U S A 2007; 104:5919-24. [PMID: 17389379 PMCID: PMC1851592 DOI: 10.1073/pnas.0607779104] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Anterior visceral endoderm (AVE) plays essential roles with respect to anterior-posterior axis development in the early mouse embryo. To assess the genetic cascade involved in AVE formation, the cis-regulatory elements directing expression of vertebrate Otx2 genes in the AVE were analyzed via generation of transgenic mice. Otx2 expression in AVE is regulated directly by the forkhead transcription factor, Foxa2. Moreover, Foxa2 is essential for expression of the Wnt antagonists, Dkk1 and Cerl, in visceral endoderm during the pre- to early streak stages; however, Foxa2 appears to be dispensable for subsequent Dkk1 expression associated with forebrain induction. Thus, we propose that Foxa2 is crucial in early anterior-posterior axis polarization in terms of regulation of expression of AVE-specific genes. These findings provide profound insights into conserved roles of Foxa2 transcription factors in anterior specification throughout the evolution of the chordate body plan.
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Affiliation(s)
- Chiharu Kimura-Yoshida
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
- Head Organizer Project, Vertebrate Body Plan Group, RIKEN Center for Developmental Biology (CDB), Kobe, Hyogo 650-0047, Japan
| | - E. Tian
- Department of Morphogenesis, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Hiroshi Nakano
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
- Head Organizer Project, Vertebrate Body Plan Group, RIKEN Center for Developmental Biology (CDB), Kobe, Hyogo 650-0047, Japan
| | - Saori Amazaki
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
| | - Kayo Shimokawa
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
| | - Janet Rossant
- Program in Developmental Biology, Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada M5G 1X8; and
| | - Shinichi Aizawa
- Vertebrate Body Plan Group, RIKEN CDB, Kobe, Hyogo 650-0047, Japan
| | - Isao Matsuo
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
- Head Organizer Project, Vertebrate Body Plan Group, RIKEN Center for Developmental Biology (CDB), Kobe, Hyogo 650-0047, Japan
- To whom correspondence should be addressed. E-mail:
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22
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Worch S, Fiedler E, Hansmann I, Schlote D. Genomic organization and expression pattern of scapinin (PHACTR3) in mouse and human. Cytogenet Genome Res 2006; 115:23-9. [PMID: 16974080 DOI: 10.1159/000094797] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Accepted: 02/28/2006] [Indexed: 11/19/2022] Open
Abstract
Scapinin has been found to bind to cytoplasmic actin and is also a putative regulatory subunit of protein phosphatase-1 (PP1). It is found attached to the nuclear matrix-intermediate filament (NM-IF) and is down-regulated by differentiation of tumor cells. We have analyzed the genomic structure and tissue-specific expression pattern of both the human scapinin gene (PHACTR3) and the orthologous mouse gene. Both genes showed a highly conserved complex genomic organization with four different leader exons. Alternative splicing of exon 5 was found to be limited to human and variable polyadenylation in mouse transcripts only. In both species expression seems to occur predominantly in the brain. By Northern blot analysis two major transcripts in human and three transcripts in mouse were detected. Expression analysis in the mouse revealed a tissue-specific complex transcription pattern in the brain and a specific pattern was observed during prenatal development. Based on the transcriptional data we therefore assume scapinin to have a distinct biological function in the mammalian brain.
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Affiliation(s)
- S Worch
- Institut fur Humangenetik und Medizinische Biologie, Martin-Luther-Universitat Halle-Wittenberg, Halle/Saale, Germany
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23
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Chatelain G, Fossat N, Brun G, Lamonerie T. Molecular dissection reveals decreased activity and not dominant negative effect in human OTX2 mutants. J Mol Med (Berl) 2006; 84:604-15. [PMID: 16607563 DOI: 10.1007/s00109-006-0048-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Accepted: 01/18/2006] [Indexed: 10/24/2022]
Abstract
The paired-type homeodomain transcription factor Otx2 is essential for forebrain and eye development. Severe ocular malformations in humans have recently been associated with heterozygous OTX2 mutations. To document the molecular defects in human mutants, Otx2 structural characterization was carried out. A collection of deletion and point mutants was created to perform transactivation, DNA binding, and subcellular localization analyses. Transactivation was ascribed to both N- and C-termini of the protein, and DNA binding to the minimal homeodomain, where critical amino acid residues were identified. Acute nuclear localization appeared controlled by a nuclear localization sequence located within the homeodomain which acts in conjunction with a novel nuclear retention domain that we unraveled located in the central part of the protein. This region, which is poorly conserved among Otx proteins, was also endowed with dominant negative activity suggesting that it might confer unique properties to Otx2. Molecular diagnostic of human mutant OTX2 proteins discriminates hypomorphic and loss of function mutations from other mutations that may not be relevant to ocular pathology.
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Affiliation(s)
- Gilles Chatelain
- LBMC, ENS-Lyon, IFR128 Lyon-Gerland, 46 allée d'Italie, 69364, Lyon, Cedex 07, France
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24
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Rath MF, Muñoz E, Ganguly S, Morin F, Shi Q, Klein DC, Møller M. Expression of the Otx2 homeobox gene in the developing mammalian brain: embryonic and adult expression in the pineal gland. J Neurochem 2006; 97:556-66. [PMID: 16539656 DOI: 10.1111/j.1471-4159.2006.03773.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Otx2 is a vertebrate homeobox gene, which has been found to be essential for the development of rostral brain regions and appears to play a role in the development of retinal photoreceptor cells and pinealocytes. In this study, the temporal expression pattern of Otx2 was revealed in the rat brain, with special emphasis on the pineal gland throughout late embryonic and postnatal stages. Widespread high expression of Otx2 in the embryonic brain becomes progressively restricted in the adult to the pineal gland. Crx (cone-rod homeobox), a downstream target gene of Otx2, showed a pineal expression pattern similar to that of Otx2, although there was a distinct lag in time of onset. Otx2 protein was identified in pineal extracts and found to be localized in pinealocytes. Total pineal Otx2 mRNA did not show day-night variation, nor was it influenced by removal of the sympathetic input, indicating that the level of Otx2 mRNA appears to be independent of the photoneural input to the gland. Our results are consistent with the view that pineal expression of Otx2 is required for development and we hypothesize that it plays a role in the adult in controlling the expression of the cluster of genes associated with phototransduction and melatonin synthesis.
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Affiliation(s)
- Martin F Rath
- Institute of Medical Anatomy, Panum Institute, University of Copenhagen, Denmark
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25
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Acampora D, Annino A, Tuorto F, Puelles E, Lucchesi W, Papalia A, Simeone A. Otx genes in the evolution of the vertebrate brain. Brain Res Bull 2005; 66:410-20. [PMID: 16144623 DOI: 10.1016/j.brainresbull.2005.02.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Indexed: 12/01/2022]
Abstract
Only until a decade ago, animal phylogeny was traditionally based on the assumption that evolution of bilaterians went from simple to complex through gradual steps in which the extant species would represent grades of intermediate complexity that reflect the organizational levels of their ancestors. The advent of more sophisticated molecular biology techniques combined to an increasing variety of functional experiments has provided new tools, which lead us to consider evolutionary studies under a brand new light. An ancestral versus derived low-complexity of a given organism has now to be carefully re-assessed and also the molecular data so far accumulated needs to be re-evaluated. Conserved gene families expressed in the nervous system of all the species have been extensively used to reconstruct evolutionary steps, which may lead to identify the morphological as well as molecular features of the last common ancestor of bilaterians (Urbilateria). The Otx gene family is among these and will be here reviewed.
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Affiliation(s)
- Dario Acampora
- MRC Centre for Developmental Neurobiology, New Hunt's House, 4th Floor, King's College London, UK
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26
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Fossat N, Courtois V, Chatelain G, Brun G, Lamonerie T. Alternative usage ofOtx2 promoters during mouse development. Dev Dyn 2005; 233:154-60. [PMID: 15759271 DOI: 10.1002/dvdy.20287] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Our previous structural analysis of mouse Otx2 transcripts has revealed the existence of three different promoters and suggested that the corresponding mRNAs could exhibit specific expression patterns. Here, we analyze the precise dynamics of their expression throughout mouse development. Their spatial distribution was determined by isoform-specific in situ hybridization and their relative abundance by real-time reverse transcriptase-polymerase chain reaction. Although the three promoters may be used in the same areas, we show that transcription preferentially occurs from the proximal promoter at onset of gene activity in early embryogenesis, and switches to the more distal one in most of the sites of expression in the adult brain. During gestation, their relative utilization becomes inverted. The third promoter, which shows no activity in embryonic stem cells and is moderately expressed during embryogenesis, is mostly used in specific areas derived from the rostral part of the neural tube.
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Affiliation(s)
- Nicolas Fossat
- LBMC, ENS-Lyon, IFR128 Lyon-Gerland, 69364 Lyon Cedex 07, France
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27
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Steinthorsdottir V, Stefansson H, Ghosh S, Birgisdottir B, Bjornsdottir S, Fasquel AC, Olafsson O, Stefansson K, Gulcher JR. Multiple novel transcription initiation sites for NRG1. Gene 2004; 342:97-105. [PMID: 15527969 DOI: 10.1016/j.gene.2004.07.029] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2004] [Revised: 07/19/2004] [Accepted: 07/29/2004] [Indexed: 01/12/2023]
Abstract
The large neuregulin 1 gene (NRG1) has been mapped to a 1.125 Mb region on chromosome 8p11-21. Three major forms of NRG1 (types I-III), all with distinct amino-termini encoded by unique 5'-exons, have been described. We report here the discovery of nine novel NRG1 exons, including six alternative 5'-exons, increasing the number of potential promoters in NRG1 from three to nine. The novel transcripts of NRG1 described here use the novel 5'-exons which are either coding or non-coding. The functional relevance of the predicted proteins they encode has not been evaluated. Three of the novel 5'-exons are well conserved in syntenic rat and mouse sequences; they encode proteins with novel amino-termini, here termed types IV-VI. NRG1 plays a central role in neural development and is most likely involved in regulation of synaptic plasticity, or how the brain responds or adapts to the environment. The unusually complex gene structure may facilitate spatial and temporal regulation of NRG1 expression, fine-tune NRG1 protein function at different stages during development of the nervous system, and adapt responses to the environment in the adult brain.
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28
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Kurokawa D, Takasaki N, Kiyonari H, Nakayama R, Kimura-Yoshida C, Matsuo I, Aizawa S. Regulation ofOtx2expression and its functions in mouse epiblast and anterior neuroectoderm. Development 2004; 131:3307-17. [PMID: 15201223 DOI: 10.1242/dev.01219] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have identified cis-regulatory sequences acting on Otx2expression in epiblast (EP) and anterior neuroectoderm (AN) at about 90 kb 5′ upstream. The activity of the EP enhancer is found in the inner cell mass at E3.5 and the entire epiblast at E5.5. The AN enhancer activity is detected initially at E7.0 and ceases by E8.5; it is found later in the dorsomedial aspect of the telencephalon at E10.5. The EP enhancer includes multiple required domains over 2.3 kb, and the AN enhancer is an essential component of the EP enhancer. Mutants lacking the AN enhancer have demonstrated that these cis-sequences indeed regulate Otx2 expression in EP and AN. At the same time, our analysis indicates that another EP and AN enhancer must exist outside of the –170 kb to +120 kb range. In Otx2ΔAN/– mutants, in which one Otx2allele lacks the AN enhancer and the other allele is null, anteroposterior axis forms normally and anterior neuroectoderm is normally induced. Subsequently, however, forebrain and midbrain are lost, indicating that Otx2 expression under the AN enhancer functions to maintain anterior neuroectoderm once induced. Furthermore, Otx2 under the AN enhancer cooperates with Emx2 in diencephalon development. The AN enhancer region is conserved among mouse, human and Xenopus; moreover, the counterpart region in Xenopus exhibited an enhancer activity in mouse anterior neuroectoderm.
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Affiliation(s)
- Daisuke Kurokawa
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB RIKEN Kobe, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0046, Japan
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Nishida A, Furukawa A, Koike C, Tano Y, Aizawa S, Matsuo I, Furukawa T. Otx2 homeobox gene controls retinal photoreceptor cell fate and pineal gland development. Nat Neurosci 2003; 6:1255-63. [PMID: 14625556 DOI: 10.1038/nn1155] [Citation(s) in RCA: 437] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2003] [Accepted: 10/29/2003] [Indexed: 12/11/2022]
Abstract
Understanding the molecular mechanisms by which distinct cell fate is determined during organogenesis is a central issue in development and disease. Here, using conditional gene ablation in mice, we show that the transcription factor Otx2 is essential for retinal photoreceptor cell fate determination and development of the pineal gland. Otx2-deficiency converted differentiating photoreceptor cells to amacrine-like neurons and led to a total lack of pinealocytes in the pineal gland. We also found that Otx2 transactivates the cone-rod homeobox gene Crx, which is required for terminal differentiation and maintenance of photoreceptor cells. Furthermore, retroviral gene transfer of Otx2 steers retinal progenitor cells toward becoming photoreceptors. Thus, Otx2 is a key regulatory gene for the cell fate determination of retinal photoreceptor cells. Our results reveal the key molecular steps required for photoreceptor cell-fate determination and pinealocyte development.
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Affiliation(s)
- Akihiro Nishida
- Osaka Bioscience Institute, 6-2-4 Furuedai, Suita, Osaka 565-0874, Japan
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Martínez-Morales JR, Dolez V, Rodrigo I, Zaccarini R, Leconte L, Bovolenta P, Saule S. OTX2 activates the molecular network underlying retina pigment epithelium differentiation. J Biol Chem 2003; 278:21721-31. [PMID: 12663655 DOI: 10.1074/jbc.m301708200] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The retina pigment epithelium (RPE) is fundamental for the development and function of the vertebrate eye. Molecularly, the presumptive RPE can be identified by the early expression of two transcription factors, Mitf and Otx. In mice deficient for either gene, RPE development is impaired with loss of melanogenic gene expression, raising the possibility that in the eye OTX proteins operate either in a feedback loop or in cooperation with MITF for the control of RPE-specific gene expression. Here we show that Otx2 induces a pigmented phenotype when overexpressed in avian neural retina cells. In addition, OTX2 binds specifically to a bicoid motif present in the promoter regions of three Mitf target genes, QNR71, TRP-1, and tyrosinase, leading to their transactivation. OTX2 and MITF co-localize in the nuclei of RPE cells and physically interact, and their co-expression results in a cooperative activation of QNR71 and tyrosinase promoters. Collectively, these data suggest that both transcription factors operate at the same hierarchical level to establish the identity of the RPE.
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