1
|
Armas P, Coux G, Weiner AMJ, Calcaterra NB. What's new about CNBP? Divergent functions and activities for a conserved nucleic acid binding protein. Biochim Biophys Acta Gen Subj 2021; 1865:129996. [PMID: 34474118 DOI: 10.1016/j.bbagen.2021.129996] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Cellular nucleic acid binding protein (CNBP) is a conserved single-stranded nucleic acid binding protein present in most eukaryotes, but not in plants. Expansions in the CNBP gene cause myotonic dystrophy type 2. Initially reported as a transcriptional regulator, CNBP was then also identified acting as a translational regulator. SCOPE OF REVIEW The focus of this review was to link the CNBP structural features and newly reported biochemical activities with the recently described biological functions, in the context of its pathological significance. MAJOR CONCLUSIONS Several post-translational modifications affect CNBP subcellular localization and activity. CNBP participates in the transcriptional and translational regulation of a wide range of genes by remodeling single-stranded nucleic acid secondary structures and/or by modulating the activity of trans-acting factors. CNBP is required for proper neural crest and heart development, and plays a role in cell proliferation control. Besides, CNBP has been linked with neurodegenerative, inflammatory, and congenital diseases, as well as with tumor processes. GENERAL SIGNIFICANCE This review provides an insight into the growing functions of CNBP in cell biology. A unique and robust mechanistic or biochemical connection among these roles has yet not been elucidated. However, the ability of CNBP to dynamically integrate signaling pathways and to act as nucleic acid chaperone may explain most of the roles and functions identified so far.
Collapse
Affiliation(s)
- Pablo Armas
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONIeCET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Esmeralda y Ocampo 531, S2002LRK Rosario, Argentina
| | - Gabriela Coux
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONIeCET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Esmeralda y Ocampo 531, S2002LRK Rosario, Argentina
| | - Andrea M J Weiner
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONIeCET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Esmeralda y Ocampo 531, S2002LRK Rosario, Argentina
| | - Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONIeCET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Esmeralda y Ocampo 531, S2002LRK Rosario, Argentina.
| |
Collapse
|
2
|
Forman TE, Dennison BJC, Fantauzzo KA. The Role of RNA-Binding Proteins in Vertebrate Neural Crest and Craniofacial Development. J Dev Biol 2021; 9:34. [PMID: 34564083 PMCID: PMC8482138 DOI: 10.3390/jdb9030034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/11/2022] Open
Abstract
Cranial neural crest (NC) cells delaminate from the neural folds in the forebrain to the hindbrain during mammalian embryogenesis and migrate into the frontonasal prominence and pharyngeal arches. These cells generate the bone and cartilage of the frontonasal skeleton, among other diverse derivatives. RNA-binding proteins (RBPs) have emerged as critical regulators of NC and craniofacial development in mammals. Conventional RBPs bind to specific sequence and/or structural motifs in a target RNA via one or more RNA-binding domains to regulate multiple aspects of RNA metabolism and ultimately affect gene expression. In this review, we discuss the roles of RBPs other than core spliceosome components during human and mouse NC and craniofacial development. Where applicable, we review data on these same RBPs from additional vertebrate species, including chicken, Xenopus and zebrafish models. Knockdown or ablation of several RBPs discussed here results in altered expression of transcripts encoding components of developmental signaling pathways, as well as reduced cell proliferation and/or increased cell death, indicating that these are common mechanisms contributing to the observed phenotypes. The study of these proteins offers a relatively untapped opportunity to provide significant insight into the mechanisms underlying gene expression regulation during craniofacial morphogenesis.
Collapse
Affiliation(s)
| | | | - Katherine A. Fantauzzo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (T.E.F.); (B.J.C.D.)
| |
Collapse
|
3
|
Conservation of Zebrafish MicroRNA-145 and Its Role during Neural Crest Cell Development. Genes (Basel) 2021; 12:genes12071023. [PMID: 34209401 PMCID: PMC8306979 DOI: 10.3390/genes12071023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
The neural crest is a multipotent cell population that develops from the dorsal neural fold of vertebrate embryos in order to migrate extensively and differentiate into a variety of tissues. A number of gene regulatory networks coordinating neural crest cell specification and differentiation have been extensively studied to date. Although several publications suggest a common role for microRNA-145 (miR-145) in molecular reprogramming for cell cycle regulation and/or cellular differentiation, little is known about its role during in vivo cranial neural crest development. By modifying miR-145 levels in zebrafish embryos, abnormal craniofacial development and aberrant pigmentation phenotypes were detected. By whole-mount in situ hybridization, changes in expression patterns of col2a1a and Sry-related HMG box (Sox) transcription factors sox9a and sox9b were observed in overexpressed miR-145 embryos. In agreement, zebrafish sox9b expression was downregulated by miR-145 overexpression. In silico and in vivo analysis of the sox9b 3′UTR revealed a conserved potential miR-145 binding site likely involved in its post-transcriptional regulation. Based on these findings, we speculate that miR-145 participates in the gene regulatory network governing zebrafish chondrocyte differentiation by controlling sox9b expression.
Collapse
|
4
|
Dubucs C, Chassaing N, Sergi C, Aubert-Mucca M, Attié-Bitach T, Lacombe D, Thauvin-Robinet C, Arpin S, Perez MJ, Cabrol C, Chen CP, Aziza J, Colin E, Martinovic J, Calvas P, Plaisancié J. Re-focusing on Agnathia-Otocephaly complex. Clin Oral Investig 2020; 25:1353-1362. [PMID: 32643087 DOI: 10.1007/s00784-020-03443-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 07/03/2020] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Agnathia-otocephaly complex is a rare condition characterized by mandibular hypoplasia or agnathia, ear anomalies (melotia/synotia) and microstomia with aglossia. This severe anomaly of the first branchial arch is most often lethal. The estimated incidence is less than 1 in 70.000 births, with etiologies linked to both genetic and teratogenic factors. Most of the cases are sporadic. To date, two genes have been described in humans to be involved in this condition: OTX2 and PRRX1. Nevertheless, the overall proportion of mutated cases is unknown and a significant number of patients remain without molecular diagnosis. Thus, the involvement of other genes than OTX2 and PRRX1 in the agnathia-otocephaly complex is not unlikely. Heterozygous mutations in Cnbp in mice are responsible for mandibular and eye defects mimicking the agnathia-otocephaly complex in humans and appear as a good candidate. Therefore, in this study, we aimed (i) to collect patients presenting with agnathia-otocephaly complex for screening CNBP, in parallel with OTX2 and PRRX1, to check its possible implication in the human phenotype and (ii) to compare our results with the literature data to estimate the proportion of mutated cases after genetic testing. MATERIALS AND METHODS In this work, we describe 10 patients suffering from the agnathia-otocephaly complex. All of them benefited from array-CGH and Sanger sequencing of OTX2, PRRX1 and CNBP. A complete review of the literature was made using the Pubmed database to collect all the patients described with a phenotype of agnathia-otocephaly complex during the 20 last years (1998-2019) in order (i) to study etiology (genetic causes, iatrogenic causes…) and (ii), when genetic testing was performed, to study which genes were tested and by which type of technologies. RESULTS In our 10 patients' cohort, no point mutation in the three tested genes was detected by Sanger sequencing, while array-CGH has allowed identifying a 107-kb deletion encompassing OTX2 responsible for the agnathia-otocephaly complex phenotype in 1 of them. In 4 of the 70 cases described in the literature, a toxic cause was identified and 22 out the 66 remaining cases benefited from genetic testing. Among those 22 patients, 6 were carrying mutation or deletion in the OTX2 gene and 4 in the PRRX1 gene. Thus, when compiling results from our cohort and the literature, a total of 32 patients benefited from genetic testing, with only 34% (11/32) of patients having a mutation in one of the two known genes, OTX2 or PRRX1. CONCLUSIONS From our work and the literature review, only mutations in OTX2 and PRRX1 have been found to date in patients, explaining around one third of the etiologies after genetic testing. Thus, agnathia-otocephaly complex remains unexplained in the majority of the patients, which indicates that other factors might be involved. Although involved in first branchial arch defects, no mutation in the CNBP gene was found in this study. This suggests that mutations in CNBP might not be involved in such phenotype in humans or that, unlike in mice, a compensatory effect might exist in humans. Nevertheless, given that agnathia-otocephaly complex is a rare phenotype, more patients have to be screened for CNBP mutations before we definitively conclude about its potential implication. Therefore, this work presents the current state of knowledge on agnathia-otocephaly complex and underlines the need to expand further the understanding of the genetic bases of this disorder, which remains largely unknown. CLINICAL RELEVANCE We made here an update and focus on the clinical and genetic aspects of agnathia-otocephaly complex as well as a more general review of craniofacial development.
Collapse
Affiliation(s)
- C Dubucs
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France.,Département d'Anatomie et de Cytologie Pathologiques, Institut Universitaire du cancer de Toulouse, Toulouse, France
| | - N Chassaing
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France.,INSERM U1056, Université Toulouse III, Toulouse, France
| | - C Sergi
- Department of Lab. Med. & Pathology (5B4.09), University of Alberta, Edmonton, AB, Canada
| | - M Aubert-Mucca
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - T Attié-Bitach
- Unité d'Embryofœtopathologie, Service d'Histologie Embryologie Cytogénétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris (APHP), Paris, France.,Institut Imagine, INSERM U1163, Université Paris Descartes, Sorbonne Paris Cite, Paris, France
| | - D Lacombe
- Service de Génétique Médicale, CRMR, CHU de Bordeaux, Bordeaux, France.,INSERM U1211, Université de Bordeaux, 33076, Bordeaux, France
| | - C Thauvin-Robinet
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon, Dijon, Bourgogne, France.,Centre de Référence maladies rares "Anomalies du Développement et syndromes malformatifs," Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - S Arpin
- Service de Génétique Clinique, Centre Hospitalier Régional Universitaire de Tours, Tours, France
| | - M J Perez
- Department of Medical Genetics, Reference Center for Developmental Abnormalities and Constitutional Bone Diseases, CHRU, Montpellier, France
| | - C Cabrol
- Centre de Génétique Humaine, Centre Hospitalier Universitaire, Université de Franche-Comté, Besançon, France
| | - C P Chen
- Department of Materials Engineering, Ming Chi University of Technology, New Taipei City, Taiwan
| | - J Aziza
- Département d'Anatomie et de Cytologie Pathologiques, Institut Universitaire du cancer de Toulouse, Toulouse, France
| | - E Colin
- Department de Biochimie et Génétique, Centre Hospitalier Universitaire, Angers, France.,UMR CNRS 6214-INSERM 1083 and PREMMI, Université d'Angers, Angers, France
| | - J Martinovic
- Unit of Fetal Pathology, AP-HP Antoine Béclère Hospital, Clamart, France
| | - P Calvas
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France.,INSERM U1056, Université Toulouse III, Toulouse, France
| | - Julie Plaisancié
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France. .,INSERM U1056, Université Toulouse III, Toulouse, France.
| |
Collapse
|
5
|
David AP, Pipier A, Pascutti F, Binolfi A, Weiner AMJ, Challier E, Heckel S, Calsou P, Gomez D, Calcaterra NB, Armas P. CNBP controls transcription by unfolding DNA G-quadruplex structures. Nucleic Acids Res 2019; 47:7901-7913. [PMID: 31219592 PMCID: PMC6735679 DOI: 10.1093/nar/gkz527] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/19/2019] [Accepted: 06/17/2019] [Indexed: 01/17/2023] Open
Abstract
Guanine-rich DNA strands can fold into non-canonical four-stranded secondary structures named G-quadruplexes (G4). Experimental evidences suggest that G4-DNA surrounding transcription start sites act as cis-regulatory elements by either stimulating or inhibiting gene transcription. Therefore, proteins able to target and regulate specific G4 formation/unfolding are crucial for G4-mediated transcriptional control. Here we present data revealing that CNBP acts in vitro as a G4-unfolding protein over a tetramolecular G4 formed by the TG4T oligonucleotide, as well as over the G4 folded in the promoters of several oncogenes. CNBP depletion in cellulo led to a reduction in the transcription of endogenous KRAS, suggesting a regulatory role of CNBP in relieving the transcriptional abrogation due to G4 formation. CNBP activity was also assayed over the evolutionary conserved G4 enhancing the transcription of NOGGIN (NOG) developmental gene. CNBP unfolded in vitro NOG G4 and experiments performed in cellulo and in vivo in developing zebrafish showed a repressive role of CNBP on the transcription of this gene by G4 unwinding. Our results shed light on the mechanisms underlying CNBP way of action, as well as reinforce the notion about the existence and function of G4s in whole living organisms.
Collapse
Affiliation(s)
- Aldana P David
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP, Rosario, Argentina
| | - Angélique Pipier
- Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS-Université de Toulouse, Equipe Labellisée Ligue Nationale contre le Cancer 2018, 31077, Toulouse, France
| | - Federico Pascutti
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP, Rosario, Argentina
| | - Andrés Binolfi
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP, Rosario, Argentina
| | - Andrea M J Weiner
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP, Rosario, Argentina
| | - Emilse Challier
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP, Rosario, Argentina
| | - Sofía Heckel
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP, Rosario, Argentina
| | - Patrick Calsou
- Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS-Université de Toulouse, Equipe Labellisée Ligue Nationale contre le Cancer 2018, 31077, Toulouse, France
| | - Dennis Gomez
- Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS-Université de Toulouse, Equipe Labellisée Ligue Nationale contre le Cancer 2018, 31077, Toulouse, France
| | - Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP, Rosario, Argentina
| | - Pablo Armas
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP, Rosario, Argentina
| |
Collapse
|
6
|
Proteasomal inhibition attenuates craniofacial malformations in a zebrafish model of Treacher Collins Syndrome. Biochem Pharmacol 2019; 163:362-370. [PMID: 30849304 DOI: 10.1016/j.bcp.2019.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/04/2019] [Indexed: 01/07/2023]
Abstract
Treacher Collins Syndrome (TCS) is a congenital disease characterized by defects in the craniofacial skeleton and absence of mental alterations. Recently we modelled TCS in zebrafish (Danio rerio) embryos through the microinjection of Morpholino® oligonucleotides blocking the translation of the ortholog of the main causative gene (TCOF1). We showed that Cnbp, a key cytoprotective protein involved in normal rostral head development, was detected in lower levels (without changes in its mRNA expression) in TCS-like embryos. As previous reports suggested that Cnbp is degraded through the proteasomal pathway, we tested whether proteasome inhibitors (MG132 and Bortezomib (Velcade®, Millennium laboratories)) were able to ameliorate cranial skeleton malformations in TCS. Here we show that treatment with both proteasome inhibitors produced a robust craniofacial cartilage phenotype recovery. This recovery seems to be consequence of a decreased degradation of Cnbp in TCS-like embryos. Critical TCS manifestations, such as neuroepithelial cell death and cell redox imbalance were attenuated. Thus, proteasome inhibitors may offer an opportunity for TCS molecular and phenotypic manifestation's prevention. Although further development of new safe inhibitors compatible with administration during pregnancy is required, our results encourage this therapeutic approach.
Collapse
|
7
|
Weiner AMJ, Scampoli NL, Steeman TJ, Dooley CM, Busch-Nentwich EM, Kelsh RN, Calcaterra NB. Dicer1 is required for pigment cell and craniofacial development in zebrafish. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:472-485. [PMID: 30840854 DOI: 10.1016/j.bbagrm.2019.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 02/22/2019] [Accepted: 02/23/2019] [Indexed: 12/22/2022]
Abstract
The multidomain RNase III endoribonuclease DICER is required for the generation of most functional microRNAs (miRNAs). Loss of Dicer affects developmental processes at different levels. Here, we characterized the zebrafish Dicer1 mutant, dicer1sa9205, which has a single point mutation induced by N-ethyl-N-nitrosourea mutagenesis. Heterozygous dicer1sa9205 developed normally, being phenotypically indistinguishable from wild-type siblings. Homozygous dicer1sa9205 mutants display smaller eyes, abnormal craniofacial development and aberrant pigmentation. Reduced numbers of both iridophores and melanocytes were observed in the head and ventral trunk of dicer1sa9205 homozygotes; the effect on melanocytes was stronger and detectable earlier in development. The expression of microphthalmia-associated transcription factor a (mitfa), the master gene for melanocytes differentiation, was enhanced in dicer1-depleted fish. Similarly, the expression of SRY-box containing gene 10 (sox10), required for mitfa activation, was higher in mutants than in wild types. In silico and in vivo analyses of either sox10 or mitfa 3'UTRs revealed conserved potential miRNA binding sites likely involved in the post-transcriptional regulation of both genes. Based on these findings, we propose that dicer1 participates in the gene regulatory network governing zebrafish melanocyte differentiation by controlling the expression of mitfa and sox10.
Collapse
Affiliation(s)
- Andrea M J Weiner
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP Rosario, Argentina.
| | - Nadia L Scampoli
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP Rosario, Argentina
| | - Tomás J Steeman
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP Rosario, Argentina
| | - Christopher M Dooley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Elisabeth M Busch-Nentwich
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Robert N Kelsh
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP Rosario, Argentina.
| |
Collapse
|
8
|
Armas P, Calcaterra NB. G-quadruplex in animal development: Contribution to gene expression and genomic heterogeneity. Mech Dev 2018; 154:64-72. [DOI: 10.1016/j.mod.2018.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/18/2018] [Accepted: 05/09/2018] [Indexed: 12/21/2022]
|
9
|
Latin American contributions to the neural crest field. Mech Dev 2018; 153:17-29. [PMID: 30081090 DOI: 10.1016/j.mod.2018.07.009] [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: 03/31/2018] [Revised: 07/15/2018] [Accepted: 07/26/2018] [Indexed: 11/21/2022]
Abstract
The neural crest (NC) is one of the most fascinating structures during embryonic development. Unique to vertebrate embryos, these cells give rise to important components of the craniofacial skeleton, such as the jaws and skull, as well as melanocytes and ganglia of the peripheral nervous system. Worldwide, several groups have been studying NC development and specifically in the Latin America (LA) they have been growing in numbers since the 1990s. It is important for the world to recognize the contributions of LA researchers on the knowledge of NC development, as it can stimulate networking and improvement in the field. We developed a database of LA publications on NC development using ORCID and PUBMED as search engines. We thoroughly describe all of the contributions from LA, collected in five major topics on NC development mechanisms: i) induction and specification; ii) migration; iii) differentiation; iv) adult NC; and, v) neurocristopathies. Further analysis was done to correlate each LA country with topics and animal models, and to access collaboration between LA countries. We observed that some LA countries have made important contributions to the comprehension of NC development. Interestingly, some LA countries have a topic and an animal model as their strength; in addition, collaboration between LA countries is almost inexistent. This review will help LA NC research to be acknowledged, and to facilitate networking between students and researchers worldwide.
Collapse
|
10
|
Webb AE, Youngworth IA, Kaya M, Gitter CL, O'Hare EA, May B, Cheng HH, Delany ME. Narrowing the wingless-2 mutation to a 227 kb candidate region on chicken chromosome 12. Poult Sci 2018; 97:1872-1880. [PMID: 29562287 PMCID: PMC5951118 DOI: 10.3382/ps/pey073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/27/2018] [Indexed: 01/01/2023] Open
Abstract
Wingless-2 (wg-2) is an autosomal recessive mutation in chicken that results in an embryonic lethal condition. Affected individuals exhibit a multisystem syndrome characterized by absent wings, truncated legs, and craniofacial, kidney, and feather malformations. Previously, work focused on phenotype description, establishing the autosomal recessive pattern of Mendelian inheritance and placing the mutation on an inbred genetic background to create the congenic line UCD Wingless-2.331. The research described in this paper employed the complementary tools of breeding, genetics, and genomics to map the chromosomal location of the mutation and successively narrow the size of the region for analysis of the causative element. Specifically, the wg-2 mutation was initially mapped to a 7 Mb region of chromosome 12 using an Illumina 3 K SNP array. Subsequent SNP genotyping and exon sequencing combined with analysis from improved genome assemblies narrowed the region of interest to a maximum size of 227 kb. Within this region, 3 validated and 3 predicted candidate genes are found, and these are described. The wg-2 mutation is a valuable resource to contribute to an improved understanding of the developmental pathways involved in chicken and avian limb development as well as serving as a model for human development, as the resulting syndrome shares features with human congenital disorders.
Collapse
Affiliation(s)
- A E Webb
- Department of Animal Science, University of California, Davis 95616
| | - I A Youngworth
- Department of Animal Science, University of California, Davis 95616
| | - M Kaya
- USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI 48823
| | - C L Gitter
- Department of Animal Science, University of California, Davis 95616
| | - E A O'Hare
- Department of Animal Science, University of California, Davis 95616
| | - B May
- Department of Animal Science, University of California, Davis 95616
| | - H H Cheng
- USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI 48823
| | - M E Delany
- Department of Animal Science, University of California, Davis 95616
| |
Collapse
|
11
|
Liao Y, Zhuang X, Huang X, Peng Y, Ma X, Huang ZX, Liu F, Xu J, Wang Y, Chen WM, Ye WC, Shi L. A Bivalent Securinine Compound SN3-L6 Induces Neuronal Differentiation via Translational Upregulation of Neurogenic Transcription Factors. Front Pharmacol 2018; 9:290. [PMID: 29674963 PMCID: PMC5895701 DOI: 10.3389/fphar.2018.00290] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/13/2018] [Indexed: 11/30/2022] Open
Abstract
Developing therapeutic approaches that target neuronal differentiation will be greatly beneficial for the regeneration of neurons and synaptic networks in neurological diseases. Protein synthesis (mRNA translation) has recently been shown to regulate neurogenesis of neural stem/progenitor cells (NSPCs). However, it has remained unknown whether engineering translational machinery is a valid approach for manipulating neuronal differentiation. The present study identifies that a bivalent securinine compound SN3-L6, previously designed and synthesized by our group, induces potent neuronal differentiation through a novel translation-dependent mechanism. An isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis in Neuro-2a progenitor cells revealed that SN3-L6 upregulated a group of neurogenic transcription regulators, and also upregulated proteins involved in RNA processing, translation, and protein metabolism. Notably, puromycylation and metabolic labeling of newly synthesized proteins demonstrated that SN3-L6 induced rapid and robust activation of general mRNA translation. Importantly, mRNAs of the proneural transcription factors Foxp1, Foxp4, Hsf1, and Erf were among the targets that were translationally upregulated by SN3-L6. Either inhibition of translation or knockdown of these transcription factors blocked SN3-L6 activity. We finally confirmed that protein synthesis of a same set of transcription factors was upregulated in primary cortical NPCs. These findings together identify a new compound for translational activation and neuronal differentiation, and provide compelling evidence that reprogramming transcriptional regulation network at translational levels is a promising strategy for engineering NSPCs.
Collapse
Affiliation(s)
- Yumei Liao
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, Guangzhou, China.,College of Pharmacy, Jinan University, Guangzhou, China
| | - Xiaoji Zhuang
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, Guangzhou, China.,College of Pharmacy, Jinan University, Guangzhou, China
| | - Xiaojie Huang
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, Guangzhou, China.,College of Pharmacy, Jinan University, Guangzhou, China
| | - Yinghui Peng
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, Guangzhou, China.,College of Pharmacy, Jinan University, Guangzhou, China
| | - Xuanyue Ma
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, Guangzhou, China.,College of Pharmacy, Jinan University, Guangzhou, China
| | | | - Feng Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Junyu Xu
- Department of Neurobiology, Key Laboratory of Medical Neurobiology of Ministry of Health of China, Zhejiang Province Key Laboratory of Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Wang
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, Guangzhou, China.,College of Pharmacy, Jinan University, Guangzhou, China
| | - Wei-Min Chen
- College of Pharmacy, Jinan University, Guangzhou, China
| | - Wen-Cai Ye
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, Guangzhou, China.,College of Pharmacy, Jinan University, Guangzhou, China
| | - Lei Shi
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, Guangzhou, China.,College of Pharmacy, Jinan University, Guangzhou, China
| |
Collapse
|
12
|
Lee E, Lee TA, Kim JH, Park A, Ra EA, Kang S, Choi HJ, Choi JL, Huh HD, Lee JE, Lee S, Park B. CNBP acts as a key transcriptional regulator of sustained expression of interleukin-6. Nucleic Acids Res 2017; 45:3280-3296. [PMID: 28168305 PMCID: PMC5389554 DOI: 10.1093/nar/gkx071] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/26/2017] [Indexed: 12/17/2022] Open
Abstract
The transcription of inflammatory genes is an essential step in host defense activation. Here, we show that cellular nucleic acid-binding protein (CNBP) acts as a transcription regulator that is required for activating the innate immune response. We identified specific CNBP-binding motifs present in the promoter region of sustained inflammatory cytokines, thus, directly inducing the expression of target genes. In particular, lipopolysaccharide (LPS) induced cnbp expression through an NF-κB-dependent manner and a positive autoregulatory mechanism, which enables prolonged il-6 gene expression. This event depends strictly on LPS-induced CNBP nuclear translocation through phosphorylation-mediated dimerization. Consequently, cnbp-depleted zebrafish are highly susceptible to Shigella flexneri infection in vivo. Collectively, these observations identify CNBP as a key transcriptional regulator required for activating and maintaining the immune response.
Collapse
Affiliation(s)
- Eunhye Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
- These authors contributed equally to the paper as first authors
| | - Taeyun A. Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
- These authors contributed equally to the paper as first authors
| | - Ji Hyun Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, South Korea
- These authors contributed equally to the paper as first authors
| | - Areum Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Eun A. Ra
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Sujin Kang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Hyun jin Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Junhee L. Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Hyunbin D. Huh
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Ji Eun Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, South Korea
- Samsung Genome Institute (SGI), Samsung Medical Center, Seoul 06351, South Korea
- To whom correspondence should be addressed. Tel: +82 2 2123 5655; Fax: +82 2 312 5657; . Correspondence may also be addressed to Ji Eun Lee. Tel: +82 2 3410 6129; Fax: +82 2 3410 0534; . Correspondence may also be addressed to Sungwook Lee. Tel: +82 31 920 2537; Fax: +82 31 920 2542;
| | - Sungwook Lee
- Cancer Immunology Branch, Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 10408, South Korea
- To whom correspondence should be addressed. Tel: +82 2 2123 5655; Fax: +82 2 312 5657; . Correspondence may also be addressed to Ji Eun Lee. Tel: +82 2 3410 6129; Fax: +82 2 3410 0534; . Correspondence may also be addressed to Sungwook Lee. Tel: +82 31 920 2537; Fax: +82 31 920 2542;
| | - Boyoun Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, South Korea
- To whom correspondence should be addressed. Tel: +82 2 2123 5655; Fax: +82 2 312 5657; . Correspondence may also be addressed to Ji Eun Lee. Tel: +82 2 3410 6129; Fax: +82 2 3410 0534; . Correspondence may also be addressed to Sungwook Lee. Tel: +82 31 920 2537; Fax: +82 31 920 2542;
| |
Collapse
|
13
|
Eb-Levadoux Y, Frelon S, Simon O, Arnaudguilhem C, Lobinski R, Mounicou S. In vivo identification of potential uranium protein targets in zebrafish ovaries after chronic waterborne exposure. Metallomics 2017; 9:525-534. [DOI: 10.1039/c6mt00291a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
14
|
Cnbp ameliorates Treacher Collins Syndrome craniofacial anomalies through a pathway that involves redox-responsive genes. Cell Death Dis 2016; 7:e2397. [PMID: 27711076 PMCID: PMC5133970 DOI: 10.1038/cddis.2016.299] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/28/2016] [Accepted: 08/25/2016] [Indexed: 11/08/2022]
Abstract
Treacher Collins Syndrome (TCS) is a rare congenital disease (1:50 000 live births) characterized by craniofacial defects, including hypoplasia of facial bones, cleft palate and palpebral fissures. Over 90% of the cases are due to mutations in the TCOF1 gene, which codifies the nucleolar protein Treacle. Here we report a novel TCS-like zebrafish model displaying features that fully recapitulate the spectrum of craniofacial abnormalities observed in patients. As it was reported for a Tcof1+/- mouse model, Treacle depletion in zebrafish caused reduced rRNA transcription, stabilization of Tp53 and increased cell death in the cephalic region. An increase of ROS along with the overexpression of redox-responsive genes was detected; furthermore, treatment with antioxidants ameliorated the phenotypic defects of craniofacial anomalies in TCS-like larvae. On the other hand, Treacle depletion led to a lowering in the abundance of Cnbp, a protein required for proper craniofacial development. Tcof1 knockdown in transgenic zebrafish overexpressing cnbp resulted in barely affected craniofacial cartilage development, reinforcing the notion that Cnbp has a role in the pathogenesis of TCS. The cnbp overexpression rescued the TCS phenotype in a dose-dependent manner by a ROS-cytoprotective action that prevented the redox-responsive genes' upregulation but did not normalize the synthesis of rRNAs. Finally, a positive correlation between the expression of CNBP and TCOF1 in mesenchymal cells from both control and TCS subjects was found. Based on this, we suggest CNBP as an additional target for new alternative therapeutic treatments to reduce craniofacial defects not only in TCS but also in other neurocristopathies.
Collapse
|
15
|
A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage. Mol Cell 2016; 64:37-50. [PMID: 27618485 DOI: 10.1016/j.molcel.2016.08.010] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/21/2016] [Accepted: 08/05/2016] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) are an emerging class of transcripts that can modulate gene expression; however, their mechanisms of action remain poorly understood. Here, we experimentally determine the secondary structure of Braveheart (Bvht) using chemical probing methods and show that this ∼590 nt transcript has a modular fold. Using CRISPR/Cas9-mediated editing of mouse embryonic stem cells, we find that deletion of 11 nt in a 5' asymmetric G-rich internal loop (AGIL) of Bvht (bvhtdAGIL) dramatically impairs cardiomyocyte differentiation. We demonstrate a specific interaction between AGIL and cellular nucleic acid binding protein (CNBP/ZNF9), a zinc-finger protein known to bind single-stranded G-rich sequences. We further show that CNBP deletion partially rescues the bvhtdAGIL mutant phenotype by restoring differentiation capacity. Together, our work shows that Bvht functions with CNBP through a well-defined RNA motif to regulate cardiovascular lineage commitment, opening the door for exploring broader roles of RNA structure in development and disease.
Collapse
|
16
|
CNBP modulates the transcription of Wnt signaling pathway components. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1151-60. [DOI: 10.1016/j.bbagrm.2014.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 08/01/2014] [Accepted: 08/14/2014] [Indexed: 01/15/2023]
|
17
|
Challier E, Lisa MN, Nerli BB, Calcaterra NB, Armas P. Novel high-performance purification protocol of recombinant CNBP suitable for biochemical and biophysical characterization. Protein Expr Purif 2013; 93:23-31. [PMID: 24161561 DOI: 10.1016/j.pep.2013.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/13/2013] [Indexed: 12/21/2022]
Abstract
Cellular nucleic acid binding protein (CNBP) is a highly conserved multi-zinc knuckle protein that enhances c-MYC expression, is related to certain human muscular diseases and is required for proper rostral head development. CNBP binds to single-stranded DNA (ssDNA) and RNA and acts as nucleic acid chaperone. Despite the advances made concerning CNBP biological roles, a full knowledge about the structure-function relationship has not yet been achieved, likely due to difficulty in obtaining pure and tag-free CNBP. Here, we report a fast, simple, reproducible, and high-performance expression and purification protocol that provides recombinant tag-free CNBP from Escherichia coli cultures. We determined that tag-free CNBP binds its molecular targets with higher affinity than tagged-CNBP. Furthermore, fluorescence spectroscopy revealed the presence of a unique and conserved tryptophan, which is exposed to the solvent and involved, directly or indirectly, in nucleic acid binding. Size-exclusion HPLC revealed that CNBP forms homodimers independently of nucleic acid binding and coexist with monomers as non-interconvertible forms or in slow equilibrium. Circular dichroism spectroscopy showed that CNBP has a secondary structure dominated by random-coil and β-sheet coincident with the sequence-predicted repetitive zinc knuckles motifs, which folding is required for CNBP structural stability and biochemical activity. CNBP structural stability increased in the presence of single-stranded nucleic acid targets similar to other unstructured nucleic acid chaperones. Altogether, data suggest that CNBP is a flexible protein with interspersed structured zinc knuckles, and acquires a more rigid structure upon nucleic acid binding.
Collapse
Affiliation(s)
- Emilse Challier
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CCT-Rosario, Ocampo y Esmeralda, S2000FHQ Rosario, Argentina
| | | | | | | | | |
Collapse
|
18
|
Guan R, El-Rass S, Spillane D, Lam S, Wang Y, Wu J, Chen Z, Wang A, Jia Z, Keating A, Hu J, Wen XY. rbm47, a novel RNA binding protein, regulates zebrafish head development. Dev Dyn 2013; 242:1395-404. [PMID: 24038582 DOI: 10.1002/dvdy.24039] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 08/02/2013] [Accepted: 08/14/2013] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Vertebrate trunk induction requires inhibition of bone morphogenetic protein (BMP) signaling, whereas vertebrate head induction requires concerted inhibition of both Wnt and BMP signaling. RNA binding proteins play diverse roles in embryonic development and their roles in vertebrate head development remain to be elucidated. RESULTS We first characterized the human RBM47 as an RNA binding protein that specifically binds RNA but not single-stranded DNA. Next, we knocked down rbm47 gene function in zebrafish using morpholinos targeting the start codon and exon-1/intron-1 splice junction. Down-regulation of rbm47 resulted in headless and small head phenotypes, which can be rescued by a wnt8a blocking morpholino. To further reveal the mechanism of rbm47's role in head development, microarrays were performed to screen genes differentially expressed in normal and knockdown embryos. epcam and a2ml were identified as the most significantly up- and down-regulated genes, respectively. The microarrays also confirmed up-regulation of several genes involved in head development, including gsk3a, otx2, and chordin, which are important regulators of Wnt signaling. CONCLUSIONS Altogether, our findings reveal that Rbm47 is a novel RNA-binding protein critical for head formation and embryonic patterning during zebrafish embryogenesis which may act through a Wnt8a signaling pathway.
Collapse
Affiliation(s)
- Rui Guan
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Medicine, Physiology and Institute of Medical Science, University of Toronto, Canada; Department of Laboratory Medicine and Pathology, University of Toronto & Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, Canada; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital and Cancer Research Institute, Central South, Hunan Province, China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Armas P, Margarit E, Mouguelar VS, Allende ML, Calcaterra NB. Beyond the binding site: in vivo identification of tbx2, smarca5 and wnt5b as molecular targets of CNBP during embryonic development. PLoS One 2013; 8:e63234. [PMID: 23667590 PMCID: PMC3646763 DOI: 10.1371/journal.pone.0063234] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 04/01/2013] [Indexed: 12/30/2022] Open
Abstract
CNBP is a nucleic acid chaperone implicated in vertebrate craniofacial development, as well as in myotonic dystrophy type 2 (DM2) and sporadic inclusion body myositis (sIBM) human muscle diseases. CNBP is highly conserved among vertebrates and has been implicated in transcriptional regulation; however, its DNA binding sites and molecular targets remain elusive. The main goal of this work was to identify CNBP DNA binding sites that might reveal target genes involved in vertebrate embryonic development. To accomplish this, we used a recently described yeast one-hybrid assay to identify DNA sequences bound in vivo by CNBP. Bioinformatic analyses revealed that these sequences are G-enriched and show high frequency of putative G-quadruplex DNA secondary structure. Moreover, an in silico approach enabled us to establish the CNBP DNA-binding site and to predict CNBP putative targets based on gene ontology terms and synexpression with CNBP. The direct interaction between CNBP and candidate genes was proved by EMSA and ChIP assays. Besides, the role of CNBP upon the identified genes was validated in loss-of-function experiments in developing zebrafish. We successfully confirmed that CNBP up-regulates tbx2b and smarca5, and down-regulates wnt5b gene expression. The highly stringent strategy used in this work allowed us to identify new CNBP target genes functionally important in different contexts of vertebrate embryonic development. Furthermore, it represents a novel approach toward understanding the biological function and regulatory networks involving CNBP in the biology of vertebrates.
Collapse
Affiliation(s)
- Pablo Armas
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, (S2000FHQ) Rosario, Argentina
| | - Ezequiel Margarit
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, (S2000FHQ) Rosario, Argentina
| | - Valeria S. Mouguelar
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, (S2000FHQ) Rosario, Argentina
| | - Miguel L. Allende
- FONDAP Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Nora B. Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, (S2000FHQ) Rosario, Argentina
- * E-mail:
| |
Collapse
|
20
|
Abstract
Treacher Collins syndrome (TCS) is an autosomal dominant disorder of craniofacial development, and mutations in the TCOF1 gene are responsible for over 90% of TCS cases. The knowledge about the molecular mechanisms responsible for this syndrome is relatively scant, probably due to the difficulty of reproducing the pathology in experimental animals. Zebrafish is an emerging model for human disease studies, and we therefore assessed it as a model for studying TCS. We identified in silico the putative zebrafish TCOF1 ortholog and cloned the corresponding cDNA. The derived polypeptide shares the main structural domains found in mammals and amphibians. Tcof1 expression is restricted to the anterior-most regions of zebrafish developing embryos, similar to what happens in mouse embryos. Tcof1 loss-of-function resulted in fish showing phenotypes similar to those observed in TCS patients, and enabled a further characterization of the mechanisms underlying craniofacial malformation. Besides, we initiated the identification of potential molecular targets of treacle in zebrafish. We found that Tcof1 loss-of-function led to a decrease in the expression of cellular proliferation and craniofacial development. Together, results presented here strongly suggest that it is possible to achieve fish with TCS-like phenotype by knocking down the expression of the TCOF1 ortholog in zebrafish. This experimental condition may facilitate the study of the disease etiology during embryonic development.
Collapse
|