1
|
Khan MI, Bertram H, Schmitt AO, Ramzan F, Gültas M. Computational Identification of Milk Trait Regulation Through Transcription Factor Cooperation in Murciano-Granadina Goats. BIOLOGY 2024; 13:929. [PMID: 39596884 PMCID: PMC11591944 DOI: 10.3390/biology13110929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 11/07/2024] [Accepted: 11/12/2024] [Indexed: 11/29/2024]
Abstract
The Murciano-Granadina goat (MUG) is a renowned dairy breed, known for its adaptability and resilience, as well as for its exceptional milk traits characterized by high protein and fat content, along with low somatic cell counts. These traits are governed by complex biological processes, crucial in shaping phenotypic diversity. Thus, it is imperative to explore the factors regulating milk production and lactation for this breed. In this study, we investigated the genetic architecture of seven milk traits in MUGs, employing a two-step computational analysis to examine genotype-phenotype associations. Initially, a random forest algorithm identified the relative importance of each single-nucleotide polymorphism (SNP) in determining the traits of interest. The second step applied an information theory-based approach to exploring the complex genetic architecture of quantitative milk traits, focusing on epistatic interactions that may have been overlooked in the first step. These approaches allowed us to identify an almost distinct set of candidate genes for each trait. In contrast, by analyzing the promoter regions of these genes, we revealed common regulatory networks among the milk traits under study. These findings are crucial for understanding the molecular mechanisms underlying gene regulation, and they highlight the pivotal role of transcription factors (TFs) and their preferential interactions in the development of these traits. Notably, TFs such as DBP, HAND1E47, HOXA4, PPARA, and THAP1 were consistently identified for all traits, highlighting their important roles in immunity within the mammary gland and milk production during lactation.
Collapse
Affiliation(s)
- Muhammad Imran Khan
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany;
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany;
- Department of Livestock Production and Management, Faculty of Veterinary and Animal Sciences, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Hendrik Bertram
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany;
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany;
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany;
- Center for Integrated Breeding Research (CiBreed), Georg-August University, Carl-Sprengel-Weg 1, 37075 Göttingen, Germany
| | - Faisal Ramzan
- Institute of Animal and Dairy Sciences, Faculty of Animal Husbandry, University of Agriculture, Faisalabad 38000, Pakistan;
| | - Mehmet Gültas
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany;
- Center for Integrated Breeding Research (CiBreed), Georg-August University, Carl-Sprengel-Weg 1, 37075 Göttingen, Germany
| |
Collapse
|
2
|
Machold R, Rudy B. Genetic approaches to elucidating cortical and hippocampal GABAergic interneuron diversity. Front Cell Neurosci 2024; 18:1414955. [PMID: 39113758 PMCID: PMC11303334 DOI: 10.3389/fncel.2024.1414955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
GABAergic interneurons (INs) in the mammalian forebrain represent a diverse population of cells that provide specialized forms of local inhibition to regulate neural circuit activity. Over the last few decades, the development of a palette of genetic tools along with the generation of single-cell transcriptomic data has begun to reveal the molecular basis of IN diversity, thereby providing deep insights into how different IN subtypes function in the forebrain. In this review, we outline the emerging picture of cortical and hippocampal IN speciation as defined by transcriptomics and developmental origin and summarize the genetic strategies that have been utilized to target specific IN subtypes, along with the technical considerations inherent to each approach. Collectively, these methods have greatly facilitated our understanding of how IN subtypes regulate forebrain circuitry via cell type and compartment-specific inhibition and thus have illuminated a path toward potential therapeutic interventions for a variety of neurocognitive disorders.
Collapse
Affiliation(s)
- Robert Machold
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, United States
| | - Bernardo Rudy
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Anesthesiology, Perioperative Care and Pain Medicine, New York University Grossman School of Medicine, New York, NY, United States
| |
Collapse
|
3
|
Rubenstein JL, Nord AS, Ekker M. DLX genes and proteins in mammalian forebrain development. Development 2024; 151:dev202684. [PMID: 38819455 PMCID: PMC11190439 DOI: 10.1242/dev.202684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
The vertebrate Dlx gene family encode homeobox transcription factors that are related to the Drosophila Distal-less (Dll) gene and are crucial for development. Over the last ∼35 years detailed information has accrued about the redundant and unique expression and function of the six mammalian Dlx family genes. DLX proteins interact with general transcriptional regulators, and co-bind with other transcription factors to enhancer elements with highly specific activity in the developing forebrain. Integration of the genetic and biochemical data has yielded a foundation for a gene regulatory network governing the differentiation of forebrain GABAergic neurons. In this Primer, we describe the discovery of vertebrate Dlx genes and their crucial roles in embryonic development. We largely focus on the role of Dlx family genes in mammalian forebrain development revealed through studies in mice. Finally, we highlight questions that remain unanswered regarding vertebrate Dlx genes despite over 30 years of research.
Collapse
Affiliation(s)
- John L. Rubenstein
- UCSF Department of Psychiatry and Behavioral Sciences, Department of UCSF Weill Institute for Neurosciences, Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alex S. Nord
- Department of Neurobiology, Physiology, and Behavior and Department of Psychiatry and 20 Behavioral Sciences, Center for Neuroscience, University of California Davis, Davis, CA 95618, USA
| | - Marc Ekker
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| |
Collapse
|
4
|
Gonzalez P, Hauck QC, Baxevanis AD. Conserved Noncoding Elements Evolve Around the Same Genes Throughout Metazoan Evolution. Genome Biol Evol 2024; 16:evae052. [PMID: 38502060 PMCID: PMC10988421 DOI: 10.1093/gbe/evae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024] Open
Abstract
Conserved noncoding elements (CNEs) are DNA sequences located outside of protein-coding genes that can remain under purifying selection for up to hundreds of millions of years. Studies in vertebrate genomes have revealed that most CNEs carry out regulatory functions. Notably, many of them are enhancers that control the expression of homeodomain transcription factors and other genes that play crucial roles in embryonic development. To further our knowledge of CNEs in other parts of the animal tree, we conducted a large-scale characterization of CNEs in more than 50 genomes from three of the main branches of the metazoan tree: Cnidaria, Mollusca, and Arthropoda. We identified hundreds of thousands of CNEs and reconstructed the temporal dynamics of their appearance in each lineage, as well as determining their spatial distribution across genomes. We show that CNEs evolve repeatedly around the same genes across the Metazoa, including around homeodomain genes and other transcription factors; they also evolve repeatedly around genes involved in neural development. We also show that transposons are a major source of CNEs, confirming previous observations from vertebrates and suggesting that they have played a major role in wiring developmental gene regulatory mechanisms since the dawn of animal evolution.
Collapse
Affiliation(s)
- Paul Gonzalez
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Quinn C Hauck
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andreas D Baxevanis
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
5
|
Sowińska-Seidler A, Socha M, Szoszkiewicz A, Materna-Kiryluk A, Jamsheer A. A genotype-phenotype correlation in split-hand/foot malformation type 1: further refinement of the phenotypic subregions within the 7q21.3 locus. Front Mol Biosci 2023; 10:1250714. [PMID: 37916192 PMCID: PMC10616856 DOI: 10.3389/fmolb.2023.1250714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
Background: Split-hand/foot malformation type 1 (SHFM1) refers to the group of rare congenital limb disorders defined by the absence or hypoplasia of the central rays of the autopods with or without accompanying anomalies, such as hearing loss, craniofacial malformation, and ectodermal dysplasia. Consequently, the condition is characterized by clinical variability that hinders diagnostic and counseling procedures. SHFM1 is caused by pathogenic variants affecting the DLX5/6 genes and/or their tissue-specific enhancers at the 7q21.3 locus. Herein, we report on seven patients from five unrelated Polish families affected by variable symptoms of the SHFM1 spectrum, all harboring 7q21.3 or 7q21.2-q21.3 rearrangements, and provide a genotype-phenotype correlation in the studied cohort. Methods: We applied GTG banding, array-based comparative genomic hybridization (aCGH), and whole-genome sequencing (WGS) in order to identify the causative aberrations in all affected patients. Results: The identified pathogenic structural variants included deletions and/or translocations involving the 7q21.3 locus, i.e., t(7;10)(q21.3;q22.2) and t(7;12)(q21.3;q21.2) in all affected individuals. Interestingly, a sporadic carrier of the latter aberration presented the SHFM1 phenotype with additional features overlapping with Baker-Gordon syndrome (BAGOS), which resulted from the translocation breakpoint at chromosome 12 within the SYT1 gene. Conclusion: Clinical variability of the studied cohort reflects the composition of the DLX5/6 regulatory elements that were dislocated from their target genes by chromosomal rearrangements. The correlation of our data with the previously published observations enabled us to update the phenotypic subregions and regulatory units within the SHFM1 locus. In addition, we present the first case of SHFM1 and BAGOS-like phenotype that resulted from translocation breakpoints at chromosomes 7 and 12, both of which were pathogenic, and consequently, we show the first evidence that BAGOS can also result from the regulatory loss-of-function SYT1 mutations. In this paper, we emphasize the utility of sequence-based approaches in molecular diagnostics of disorders caused by regulatory structural variants.
Collapse
Affiliation(s)
- Anna Sowińska-Seidler
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Magdalena Socha
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Anna Szoszkiewicz
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
| |
Collapse
|
6
|
Zoodsma JD, Keegan EJ, Moody GR, Bhandiwad AA, Napoli AJ, Burgess HA, Wollmuth LP, Sirotkin HI. Disruption of grin2B, an ASD-associated gene, produces social deficits in zebrafish. Mol Autism 2022; 13:38. [PMID: 36138431 PMCID: PMC9502958 DOI: 10.1186/s13229-022-00516-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD), like many neurodevelopmental disorders, has complex and varied etiologies. Advances in genome sequencing have identified multiple candidate genes associated with ASD, including dozens of missense and nonsense mutations in the NMDAR subunit GluN2B, encoded by GRIN2B. NMDARs are glutamate-gated ion channels with key synaptic functions in excitatory neurotransmission. How alterations in these proteins impact neurodevelopment is poorly understood, in part because knockouts of GluN2B in rodents are lethal. METHODS Here, we use CRISPR-Cas9 to generate zebrafish lacking GluN2B (grin2B-/-). Using these fish, we run an array of behavioral tests and perform whole-brain larval imaging to assay developmental roles and functions of GluN2B. RESULTS We demonstrate that zebrafish GluN2B displays similar structural and functional properties to human GluN2B. Zebrafish lacking GluN2B (grin2B-/-) surprisingly survive into adulthood. Given the prevalence of social deficits in ASD, we assayed social preference in the grin2B-/- fish. Wild-type fish develop a strong social preference by 3 weeks post fertilization. In contrast, grin2B-/- fish at this age exhibit significantly reduced social preference. Notably, the lack of GluN2B does not result in a broad disruption of neurodevelopment, as grin2B-/- larvae do not show alterations in spontaneous or photic-evoked movements, are capable of prey capture, and exhibit learning. Whole-brain imaging of grin2B-/- larvae revealed reduction of an inhibitory neuron marker in the subpallium, a region linked to ASD in humans, but showed that overall brain size and E/I balance in grin2B-/- is comparable to wild type. LIMITATIONS Zebrafish lacking GluN2B, while useful in studying developmental roles of GluN2B, are unlikely to model nuanced functional alterations of human missense mutations that are not complete loss of function. Additionally, detailed mammalian homologies for larval zebrafish brain subdivisions at the age of whole-brain imaging are not fully resolved. CONCLUSIONS We demonstrate that zebrafish completely lacking the GluN2B subunit of the NMDAR, unlike rodent models, are viable into adulthood. Notably, they exhibit a highly specific deficit in social behavior. As such, this zebrafish model affords a unique opportunity to study the roles of GluN2B in ASD etiologies and establish a disease-relevant in vivo model for future studies.
Collapse
Affiliation(s)
- Josiah D Zoodsma
- Graduate Program in Neuroscience, Stony Brook University, Stony Brook, NY, 11794-5230, USA
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Emma J Keegan
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Gabrielle R Moody
- Graduate Program in Molecular and Cellular Pharmacology, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Ashwin A Bhandiwad
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Amalia J Napoli
- Graduate Program in Neuroscience, Stony Brook University, Stony Brook, NY, 11794-5230, USA
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Harold A Burgess
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Lonnie P Wollmuth
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794-5230, USA
- Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Howard I Sirotkin
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA.
| |
Collapse
|
7
|
Leung RF, George AM, Roussel EM, Faux MC, Wigle JT, Eisenstat DD. Genetic Regulation of Vertebrate Forebrain Development by Homeobox Genes. Front Neurosci 2022; 16:843794. [PMID: 35546872 PMCID: PMC9081933 DOI: 10.3389/fnins.2022.843794] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/14/2022] [Indexed: 01/19/2023] Open
Abstract
Forebrain development in vertebrates is regulated by transcription factors encoded by homeobox, bHLH and forkhead gene families throughout the progressive and overlapping stages of neural induction and patterning, regional specification and generation of neurons and glia from central nervous system (CNS) progenitor cells. Moreover, cell fate decisions, differentiation and migration of these committed CNS progenitors are controlled by the gene regulatory networks that are regulated by various homeodomain-containing transcription factors, including but not limited to those of the Pax (paired), Nkx, Otx (orthodenticle), Gsx/Gsh (genetic screened), and Dlx (distal-less) homeobox gene families. This comprehensive review outlines the integral role of key homeobox transcription factors and their target genes on forebrain development, focused primarily on the telencephalon. Furthermore, links of these transcription factors to human diseases, such as neurodevelopmental disorders and brain tumors are provided.
Collapse
Affiliation(s)
- Ryan F. Leung
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Ankita M. George
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Enola M. Roussel
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Maree C. Faux
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Jeffrey T. Wigle
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
| | - David D. Eisenstat
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
8
|
Duba-Kiss R, Niibori Y, Hampson DR. GABAergic Gene Regulatory Elements Used in Adeno-Associated Viral Vectors. Front Neurol 2021; 12:745159. [PMID: 34671313 PMCID: PMC8521139 DOI: 10.3389/fneur.2021.745159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Several neurological and psychiatric disorders have been associated with impairments in GABAergic inhibitory neurons in the brain. Thus, in the current era of accelerated development of molecular medicine and biologically-based drugs, there is a need to identify gene regulatory sequences that can be utilized for selectively manipulating the expression of nucleic acids and proteins in GABAergic neurons. This is particularly important for the use of viral vectors in gene therapy. In this Mini Review, we discuss the use of various gene regulatory elements for targeting GABAergic neurons, with an emphasis on adeno-associated viral vectors, the most widely used class of viral vectors for treating brain diseases.
Collapse
Affiliation(s)
- Robert Duba-Kiss
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Yosuke Niibori
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - David R Hampson
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
9
|
Fazel Darbandi S, Esau C, Lesage-Pelletier C, Monis S, Poitras L, Yu M, Perin S, Hatch G, Ekker M. Increased Sociability in Mice Lacking Intergenic Dlx Enhancers. Front Neurosci 2021; 15:718948. [PMID: 34671237 PMCID: PMC8520905 DOI: 10.3389/fnins.2021.718948] [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: 06/01/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022] Open
Abstract
The Dlx homeodomain transcription factors play important roles in the differentiation and migration of GABAergic interneuron precursors. The mouse and human genomes each have six Dlx genes organized into three convergently transcribed bigene clusters (Dlx1/2, Dlx3/4, and Dlx5/6) with cis-regulatory elements (CREs) located in the intergenic region of each cluster. Amongst these, the I56i and I12b enhancers from the Dlx1/2 and Dlx5/6 locus, respectively, are active in the developing forebrain. I56i is also a binding site for GTF2I, a transcription factor whose function is associated with increased sociability and Williams-Beuren syndrome. In determining the regulatory roles of these CREs on forebrain development, we have generated mutant mouse-lines where Dlx forebrain intergenic enhancers have been deleted (I56i(-/-), I12b(-/-)). Loss of Dlx intergenic enhancers impairs expression of Dlx genes as well as some of their downstream targets or associated genes including Gad2 and Evf2. The loss of the I56i enhancer resulted in a transient decrease in GABA+ cells in the developing forebrain. The intergenic enhancer mutants also demonstrate increased sociability and learning deficits in a fear conditioning test. Characterizing mice with mutated Dlx intergenic enhancers will help us to further enhance our understanding of the role of these Dlx genes in forebrain development.
Collapse
Affiliation(s)
| | - Crystal Esau
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | | | - Simon Monis
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Luc Poitras
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Man Yu
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Sofia Perin
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Gary Hatch
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Marc Ekker
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| |
Collapse
|
10
|
DLX Genes: Roles in Development and Cancer. Cancers (Basel) 2021; 13:cancers13123005. [PMID: 34203994 PMCID: PMC8232755 DOI: 10.3390/cancers13123005] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary DLX homeobox family genes encode transcription factors that have indispensable roles in embryonic and postnatal development. These genes are critically linked to the morphogenesis of craniofacial structures, branchial arches, forebrain, and sensory organs. DLX genes are also involved in postnatal homeostasis, particularly hematopoiesis and, when dysregulated, oncogenesis. DLX1/2, DLX3/4, and DLX5/6 exist as bigenes on different chromosomes, sharing intergenic enhancers between gene pairs, which allows orchestrated spatiotemporal expression. Genomic alterations of human DLX gene enhancers or coding sequences result in congenital disorders such as split-hand/foot malformation. Aberrant postnatal expression of DLX genes is associated with hematological malignancies, including leukemias and lymphomas. In several mouse models of T-cell lymphoma, Dlx5 has been shown to act as an oncogene by cooperating with activated Akt, Notch1/3, and/or Wnt to drive tumor formation. In humans, DLX5 is aberrantly expressed in lung and ovarian carcinomas and holds promise as a therapeutic target. Abstract Homeobox genes control body patterning and cell-fate decisions during development. The homeobox genes consist of many families, only some of which have been investigated regarding a possible role in tumorigenesis. Dysregulation of HOX family genes have been widely implicated in cancer etiology. DLX homeobox genes, which belong to the NK-like family, exert dual roles in development and cancer. The DLX genes are the key transcription factors involved in regulating the development of craniofacial structures in vertebrates. The three DLX bigenes have overlapping expression in the branchial arches. Disruption of DLX function has destructive consequences in organogenesis and is associated with certain congenital disorders in humans. The role of DLX genes in oncogenesis is only beginning to emerge. DLX2 diminishes cellular senescence by regulating p53 function, whereas DLX4 has been associated with metastasis in breast cancer. In human ovarian cancer cells, DLX5 is essential for regulating AKT signaling, thereby promoting cell proliferation and survival. We previously implicated Dlx5 as an oncogene in murine T-cell lymphoma driven by a constitutively active form of Akt2. In this mouse model, overexpression of Dlx5 was caused by a chromosomal rearrangement that juxtaposed the Tcr-beta promoter region near the Dlx5 locus. Moreover, transgenic mice overexpressing Dlx5, specifically in immature T-cells, develop spontaneous thymic lymphomas. Oncogenesis in this mouse model involves binding of Dlx5 to the Notch1 and Notch3 gene loci to activate their transcription. Dlx5 also cooperates with Akt signaling to accelerate lymphomagenesis by activating Wnt signaling. We also discuss the fact that human DLX5 is aberrantly expressed in several human malignancies.
Collapse
|
11
|
Functional Access to Neuron Subclasses in Rodent and Primate Forebrain. Cell Rep 2020; 26:2818-2832.e8. [PMID: 30840900 PMCID: PMC6509701 DOI: 10.1016/j.celrep.2019.02.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 01/08/2019] [Accepted: 02/04/2019] [Indexed: 12/21/2022] Open
Abstract
Viral vectors enable foreign proteins to be expressed in brains of non-genetic species, including non-human primates. However, viruses targeting specific neuron classes have proved elusive. Here we describe viral promoters and strategies for accessing GABAergic interneurons and their molecularly defined subsets in the rodent and primate. Using a set intersection approach, which relies on two co-active promoters, we can restrict heterologous protein expression to cortical and hippocampal somatostatin-positive and parvalbumin-positive interneurons. With an orthogonal set difference method, we can enrich for subclasses of neuropeptide-Y-positive GABAergic interneurons by effectively subtracting the expression pattern of one promoter from that of another. These methods harness the complexity of gene expression patterns in the brain and significantly expand the number of genetically tractable neuron classes across mammals.
Collapse
|
12
|
Weinschutz Mendes H, Taktek M, Duret T, Ekker M. Expression of dlx genes in the normal and regenerating brain of adult zebrafish. PLoS One 2020; 15:e0229549. [PMID: 32497078 PMCID: PMC7272068 DOI: 10.1371/journal.pone.0229549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/16/2020] [Indexed: 12/12/2022] Open
Abstract
Dysfunctions in the GABAergic system lead to various pathological conditions and impaired inhibitory function is one of the causes behind neuropathies characterized by neuronal hyper excitability. The Dlx homeobox genes are involved in the development of nervous system, neural crest, branchial arches and developing appendages. Dlx genes also take part in neuronal migration and differentiation during development, more precisely, in the migration and differentiation of GABAergic neurons. Functional analysis of dlx genes has mainly been carried out in developing zebrafish embryos and larvae, however information regarding the expression and roles of these genes in the adult zebrafish brain is still lacking. The extensive neurogenesis that takes place in the adult zebrafish brain, makes them a good model for the visualization of mechanisms involving dlx genes during adulthood in physiological conditions and during regeneration of the nervous system. We have identified the adult brain regions where transcripts of dlx1a, dlx2a, dlx5a and dlx6a genes are normally found and have confirmed that within telencephalic domains, there is high overlapping expression of the four dlx paralogs with a marker for GABAergic neurons. Co-localization analyses carried with the Tg(dlx6a-1.4kbdlx5a/dlx6a:GFP) reporter line have also shown that in some areas of the diencephalon, cells expressing the dlx5a/6a bigene may have a neural stem cell identity. Furthermore, investigations in a response to stab wound lesions, have demonstrated a possible participation of the dlx5a/6a bigene, most likely of dlx5a, during regeneration of the adult zebrafish brain. These observations suggest a possible participation of dlx-expressing cells during brain regeneration in adult zebrafish and also provide information on the role of dlx genes under normal physiological conditions in adults.
Collapse
Affiliation(s)
| | - Mariam Taktek
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Thomas Duret
- Faculté des Sciences Fondamentales et Appliquées, Université de Poitiers, Poitiers, France
| | - Marc Ekker
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
13
|
Sumiyama K, Tanave A. The regulatory landscape of the
Dlx
gene system in branchial arches: Shared characteristics among
Dlx
bigene clusters and evolution. Dev Growth Differ 2020; 62:355-362. [DOI: 10.1111/dgd.12671] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/18/2020] [Accepted: 04/28/2020] [Indexed: 01/09/2023]
Affiliation(s)
- Kenta Sumiyama
- Laboratory for Mouse Genetic EngineeringRIKEN Center for Biosystems Dynamics Research Suita Osaka Japan
| | - Akira Tanave
- Laboratory for Mouse Genetic EngineeringRIKEN Center for Biosystems Dynamics Research Suita Osaka Japan
| |
Collapse
|
14
|
László ZI, Bercsényi K, Mayer M, Lefkovics K, Szabó G, Katona I, Lele Z. N-cadherin (Cdh2) Maintains Migration and Postmitotic Survival of Cortical Interneuron Precursors in a Cell-Type-Specific Manner. Cereb Cortex 2020; 30:1318-1329. [PMID: 31402374 PMCID: PMC7219024 DOI: 10.1093/cercor/bhz168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 12/14/2022] Open
Abstract
The multiplex role of cadherin-based adhesion complexes during development of pallial excitatory neurons has been thoroughly characterized. In contrast, much less is known about their function during interneuron development. Here, we report that conditional removal of N-cadherin (Cdh2) from postmitotic neuroblasts of the subpallium results in a decreased number of Gad65-GFP-positive interneurons in the adult cortex. We also found that interneuron precursor migration into the pallium was already delayed at E14. Using immunohistochemistry and TUNEL assay in the embryonic subpallium, we excluded decreased mitosis and elevated cell death as possible sources of this defect. Moreover, by analyzing the interneuron composition of the adult somatosensory cortex, we uncovered an unexpected interneuron-type-specific defect caused by Cdh2-loss. This was not due to a fate-switch between interneuron populations or altered target selection during migration. Instead, potentially due to the migration delay, part of the precursors failed to enter the cortical plate and consequently got eliminated at early postnatal stages. In summary, our results indicate that Cdh2-mediated interactions are necessary for migration and survival during the postmitotic phase of interneuron development. Furthermore, we also propose that unlike in pallial glutamatergic cells, Cdh2 is not universal, rather a cell type-specific factor during this process.
Collapse
Affiliation(s)
- Zsófia I László
- Momentum Laboratory of Molecular Neurobiology, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
- Szentágothai János Doctoral School of Neuroscience, Semmelweis University, Budapest, Hungary
| | - Kinga Bercsényi
- Laboratory of Molecular Biology and Genetics, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, and Medical Research Council Centre for Neurodevelopmental Disorders, King’s College London, London, UK
| | - Mátyás Mayer
- Laboratory of Molecular Biology and Genetics, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
| | - Kornél Lefkovics
- Laboratory of Molecular Biology and Genetics, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gábor Szabó
- Laboratory of Molecular Biology and Genetics, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
| | - István Katona
- Momentum Laboratory of Molecular Neurobiology, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
| | - Zsolt Lele
- Momentum Laboratory of Molecular Neurobiology, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
- Laboratory of Molecular Biology and Genetics, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
| |
Collapse
|
15
|
Parcellation of the striatal complex into dorsal and ventral districts. Proc Natl Acad Sci U S A 2020; 117:7418-7429. [PMID: 32170006 DOI: 10.1073/pnas.1921007117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The striatal complex of basal ganglia comprises two functionally distinct districts. The dorsal district controls motor and cognitive functions. The ventral district regulates the limbic function of motivation, reward, and emotion. The dorsoventral parcellation of the striatum also is of clinical importance as differential striatal pathophysiologies occur in Huntington's disease, Parkinson's disease, and drug addiction disorders. Despite these striking neurobiologic contrasts, it is largely unknown how the dorsal and ventral divisions of the striatum are set up. Here, we demonstrate that interactions between the two key transcription factors Nolz-1 and Dlx1/2 control the migratory paths of striatal neurons to the dorsal or ventral striatum. Moreover, these same transcription factors control the cell identity of striatal projection neurons in both the dorsal and the ventral striata including the D1-direct and D2-indirect pathways. We show that Nolz-1, through the I12b enhancer, represses Dlx1/2, allowing normal migration of striatal neurons to dorsal and ventral locations. We demonstrate that deletion, up-regulation, and down-regulation of Nolz-1 and Dlx1/2 can produce a striatal phenotype characterized by a withered dorsal striatum and an enlarged ventral striatum and that we can rescue this phenotype by manipulating the interactions between Nolz-1 and Dlx1/2 transcription factors. Our study indicates that the two-tier system of striatal complex is built by coupling of cell-type identity and migration and suggests that the fundamental basis for divisions of the striatum known to be differentially vulnerable at maturity is already encoded by the time embryonic striatal neurons begin their migrations into developing striata.
Collapse
|
16
|
Nair RR, Blankvoort S, Lagartos MJ, Kentros C. Enhancer-Driven Gene Expression (EDGE) Enables the Generation of Viral Vectors Specific to Neuronal Subtypes. iScience 2020; 23:100888. [PMID: 32087575 PMCID: PMC7033522 DOI: 10.1016/j.isci.2020.100888] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/03/2019] [Accepted: 02/03/2020] [Indexed: 12/19/2022] Open
Abstract
Although a variety of remarkable molecular tools for studying neural circuits have recently been developed, the ability to deploy them in particular neuronal subtypes is limited by the fact that native promoters are almost never specific enough. We recently showed that one can generate transgenic mice with anatomical specificity surpassing that of native promoters by combining enhancers uniquely active in particular brain regions with a heterologous minimal promoter, an approach we call EDGE (Enhancer-Driven Gene Expression). Here we extend this strategy to the generation of viral (rAAV) vectors, showing that some EDGE rAAVs can recapitulate the specificity of the corresponding transgenic lines in wild-type animals, even of another species. This approach thus holds the promise of enabling circuit-specific manipulations in wild-type animals, not only enhancing our understanding of brain function, but perhaps one day even providing novel therapeutic avenues to approach disorders of the brain. rAAVs with enhancers unique to a brain region specify cell types of that brain region This requires viral constructs optimized to express only with enhancers One rAAV distinguishes distinct subtypes of excitatory neurons in a cortical layer The same specificity is seen in wild-type animals of at least two species
Collapse
Affiliation(s)
| | - Stefan Blankvoort
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Norway
| | - Maria Jose Lagartos
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Norway
| | - Cliff Kentros
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Norway; Institute of Neuroscience, University of Oregon, Eugene OR, USA.
| |
Collapse
|
17
|
Enhancer Trapping and Annotation in Zebrafish Mediated with Sleeping Beauty, piggyBac and Tol2 Transposons. Genes (Basel) 2018; 9:genes9120630. [PMID: 30551672 PMCID: PMC6316676 DOI: 10.3390/genes9120630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 12/18/2022] Open
Abstract
Although transposon-mediated enhancer trapping (ET) is successfully applied in diverse models, the efficiency of various transposon systems varies significantly, and little information is available regarding efficiency of enhancer trapping by various transposons in zebrafish. Most potential enhancers (Ens) still lack evidence of actual En activity. Here, we compared the differences in ET efficiency between sleeping beauty (SB), piggyBac (PB) and Tol2 transposons. Tol2 represented the highest germline transfer efficiencies at 55.56% (NF0 = 165), followed by SB (38.36%, NF0 = 151) and PB (32.65%, NF0 = 149). ET lines generated by the Tol2 transposon tended to produce offspring with a single expression pattern per line, while PB and SB tended to generate embryos with multiple expression patterns. In our tests, 10 putative Ens (En1–10) were identified by splinkerette PCR and comparative genomic analysis. Combining the GFP expression profiles and mRNA expression patterns revealed that En1 and En2 may be involved in regulation of the expression of dlx1a and dlx2a, while En6 may be involved in regulation of the expression of line TK4 transgene and rps26, and En7 may be involved in the regulation of the expression of wnt1 and wnt10b. Most identified Ens were found to be transcribed in zebrafish embryos, and their regulatory function may involve eRNAs.
Collapse
|
18
|
De Backer JF, Monlezun S, Detraux B, Gazan A, Vanopdenbosch L, Cheron J, Cannazza G, Valverde S, Cantacorps L, Nassar M, Venance L, Valverde O, Faure P, Zoli M, De Backer O, Gall D, Schiffmann SN, de Kerchove d'Exaerde A. Deletion of Maged1 in mice abolishes locomotor and reinforcing effects of cocaine. EMBO Rep 2018; 19:embr.201745089. [PMID: 30002119 DOI: 10.15252/embr.201745089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 06/20/2018] [Accepted: 06/21/2018] [Indexed: 12/21/2022] Open
Abstract
Melanoma antigen genes (Mage) were first described as tumour markers. However, some of Mage are also expressed in healthy cells where their functions remain poorly understood. Here, we describe an unexpected role for one of these genes, Maged1, in the control of behaviours related to drug addiction. Mice lacking Maged1 are insensitive to the behavioural effects of cocaine as assessed by locomotor sensitization, conditioned place preference (CPP) and drug self-administration. Electrophysiological experiments in brain slices and conditional knockout mice demonstrate that Maged1 is critical for cortico-accumbal neurotransmission. Further, expression of Maged1 in the prefrontal cortex (PFC) and the amygdala, but not in dopaminergic or striatal and other GABAergic neurons, is necessary for cocaine-mediated behavioural sensitization, and its expression in the PFC is also required for cocaine-induced extracellular dopamine (DA) release in the nucleus accumbens (NAc). This work identifies Maged1 as a critical molecule involved in cellular processes and behaviours related to addiction.
Collapse
Affiliation(s)
- Jean-François De Backer
- Laboratoire de Neurophysiologie, ULB Neuroscience Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Stéphanie Monlezun
- Laboratoire de Neurophysiologie, ULB Neuroscience Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Bérangère Detraux
- Laboratoire de Neurophysiologie, ULB Neuroscience Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Adeline Gazan
- Laboratoire de Neurophysiologie, ULB Neuroscience Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Laura Vanopdenbosch
- Laboratoire de Neurophysiologie, ULB Neuroscience Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Julian Cheron
- Laboratoire de Neurophysiologie, ULB Neuroscience Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Giuseppe Cannazza
- Dipartimento di Scienze della Vita, Centro di Neuroscienze e Neurotecnologie, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Sébastien Valverde
- INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), UPMC Univ Paris 06 Sorbonne Universités, Paris, France
| | - Lídia Cantacorps
- Departament de Ciències Experimentals i de la Salut, Grup de Recerca en Neurobiologia del Comportament (GReNeC), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Pompeu Fabra, Barcelone, Spain
| | - Mérie Nassar
- Center for Interdisciplinary Research in Biology, Collège de France, INSERM U1050, CNRS UMR7241, Labex Memolife, Paris, France
| | - Laurent Venance
- Center for Interdisciplinary Research in Biology, Collège de France, INSERM U1050, CNRS UMR7241, Labex Memolife, Paris, France
| | - Olga Valverde
- Departament de Ciències Experimentals i de la Salut, Grup de Recerca en Neurobiologia del Comportament (GReNeC), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Pompeu Fabra, Barcelone, Spain
| | - Philippe Faure
- INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS), UPMC Univ Paris 06 Sorbonne Universités, Paris, France
| | - Michele Zoli
- Dipartimento di Scienze Biomediche, Metaboliche e Neuroscienze, Centro di Neuroscienze e Neurotecnologie, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Olivier De Backer
- URPHYM (Unité de Recherche en Physiologie Moléculaire), NARILIS (Namur Research Institute for Life Sciences), Université de Namur, Namur, Belgium
| | - David Gall
- Laboratoire de Neurophysiologie, ULB Neuroscience Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Serge N Schiffmann
- Laboratoire de Neurophysiologie, ULB Neuroscience Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Alban de Kerchove d'Exaerde
- Laboratoire de Neurophysiologie, ULB Neuroscience Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium .,WELBIO, Brussels, Belgium
| |
Collapse
|
19
|
Fernandez JP, Moreno-Mateos MA, Gohr A, Miao L, Chan SH, Irimia M, Giraldez AJ. RES complex is associated with intron definition and required for zebrafish early embryogenesis. PLoS Genet 2018; 14:e1007473. [PMID: 29969449 PMCID: PMC6047831 DOI: 10.1371/journal.pgen.1007473] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 07/16/2018] [Accepted: 06/06/2018] [Indexed: 12/16/2022] Open
Abstract
Pre-mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome-wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA-binding proteins. The retention and splicing (RES) complex is formed by three different proteins (Bud13p, Pml1p and Snu17p) and is involved in splicing in yeast. However, the importance of the RES complex for vertebrate splicing, the intronic features associated with its activity, and its role in development are unknown. In this study, we have generated loss-of-function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13, snip1 (pml1) and rbmx2 (snu17) mutants revealed a global defect in intron splicing, with strong mis-splicing of a subset of introns. We found these RES-dependent introns were short, rich in GC and flanked by GC depleted exons, all of which are features associated with intron definition. Using these features, we developed and validated a predictive model that classifies RES dependent introns. Altogether, our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.
Collapse
Affiliation(s)
- Juan Pablo Fernandez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
| | | | - Andre Gohr
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Liyun Miao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
| | - Shun Hang Chan
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, United States of America
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, United States of America
| |
Collapse
|
20
|
Visual Experience Facilitates BDNF-Dependent Adaptive Recruitment of New Neurons in the Postembryonic Optic Tectum. J Neurosci 2018; 38:2000-2014. [PMID: 29363581 DOI: 10.1523/jneurosci.1962-17.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 01/08/2018] [Accepted: 01/15/2018] [Indexed: 01/11/2023] Open
Abstract
Postembryonic brain development is sensitive to environmental input and sensory experience, but the mechanisms underlying healthy adaptive brain growth are poorly understood. Here, we tested the importance of visual experience on larval zebrafish (Danio rerio) postembryonic development of the optic tectum (OT), a midbrain structure involved in visually guided behavior. We first characterized postembryonic neurogenic growth in OT, in which new neurons are generated along the caudal tectal surface and contribute appositionally to anatomical growth. Restricting visual experience during development by rearing larvae in dim light impaired OT anatomical and neurogenic growth, specifically by reducing the survival of new neurons in the medial periventricular gray zone. Neuronal survival in the OT was reduced only when visual experience was restricted for the first 5 d following new neuron generation, suggesting that tectal neurons exhibit an early sensitive period in which visual experience protects these cells from subsequent neuronal loss. The effect of dim rearing on neuronal survival was mimicked by treatment with an NMDA receptor antagonist early, but not later, in a new neuron's life. Both dim rearing and antagonist treatment reduced BDNF production in the OT, and supplementing larvae with exogenous BDNF during dim rearing prevented neuronal loss, suggesting that visual experience protects new tectal neurons through neural activity-dependent BDNF expression. Collectively, we present evidence for a sensitive period of neurogenic adaptive growth in the larval zebrafish OT that relies on visual experience-dependent mechanisms.SIGNIFICANCE STATEMENT Early brain development is shaped by environmental factors via sensory input; however, this form of experience-dependent neuroplasticity is traditionally studied as structural and functional changes within preexisting neurons. Here, we found that restricting visual experience affects development of the larval zebrafish optic tectum, a midbrain structure involved in visually guided behavior, by limiting the survival of newly generated neurons. We found that new tectal neurons exhibit a sensitive period soon after cell birth in which adequate visual experience, likely mediated by neuronal activity driving BDNF production within the tectum, would protect them from subsequent neuronal loss over the following week. Collectively, we present evidence for neurogenic adaptive tectal growth under different environmental lighting conditions.
Collapse
|
21
|
Loss of Intercalated Cells (ITCs) in the Mouse Amygdala of Tshz1 Mutants Correlates with Fear, Depression, and Social Interaction Phenotypes. J Neurosci 2017; 38:1160-1177. [PMID: 29255003 DOI: 10.1523/jneurosci.1412-17.2017] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/10/2017] [Accepted: 12/10/2017] [Indexed: 01/17/2023] Open
Abstract
The intercalated cells (ITCs) of the amygdala have been shown to be critical regulatory components of amygdalar circuits, which control appropriate fear responses. Despite this, the molecular processes guiding ITC development remain poorly understood. Here we establish the zinc finger transcription factor Tshz1 as a marker of ITCs during their migration from the dorsal lateral ganglionic eminence through maturity. Using germline and conditional knock-out (cKO) mouse models, we show that Tshz1 is required for the proper migration and differentiation of ITCs. In the absence of Tshz1, migrating ITC precursors fail to settle in their stereotypical locations encapsulating the lateral amygdala and BLA. Furthermore, they display reductions in the ITC marker Foxp2 and ectopic persistence of the dorsal lateral ganglionic eminence marker Sp8. Tshz1 mutant ITCs show increased cell death at postnatal time points, leading to a dramatic reduction by 3 weeks of age. In line with this, Foxp2-null mutants also show a loss of ITCs at postnatal time points, suggesting that Foxp2 may function downstream of Tshz1 in the maintenance of ITCs. Behavioral analysis of male Tshz1 cKOs revealed defects in fear extinction as well as an increase in floating during the forced swim test, indicative of a depression-like phenotype. Moreover, Tshz1 cKOs display significantly impaired social interaction (i.e., increased passivity) regardless of partner genetics. Together, these results suggest that Tshz1 plays a critical role in the development of ITCs and that fear, depression-like and social behavioral deficits arise in their absence.SIGNIFICANCE STATEMENT We show here that the zinc finger transcription factor Tshz1 is expressed during development of the intercalated cells (ITCs) within the mouse amygdala. These neurons have previously been shown to play a crucial role in fear extinction. Tshz1 mouse mutants exhibit severely reduced numbers of ITCs as a result of abnormal migration, differentiation, and survival of these neurons. Furthermore, the loss of ITCs in mouse Tshz1 mutants correlates well with defects in fear extinction as well as the appearance of depression-like and abnormal social interaction behaviors reminiscent of depressive disorders observed in human patients with distal 18q deletions, including the Tshz1 locus.
Collapse
|
22
|
Behavioral Comorbidities and Drug Treatments in a Zebrafish scn1lab Model of Dravet Syndrome. eNeuro 2017; 4:eN-NWR-0066-17. [PMID: 28812061 PMCID: PMC5555352 DOI: 10.1523/eneuro.0066-17.2017] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/11/2017] [Accepted: 07/30/2017] [Indexed: 12/15/2022] Open
Abstract
Loss-of-function mutations in SCN1A cause Dravet syndrome (DS), a catastrophic childhood epilepsy in which patients experience comorbid behavioral conditions, including movement disorders, sleep abnormalities, anxiety, and intellectual disability. To study the functional consequences of voltage-gated sodium channel mutations, we use zebrafish with a loss-of-function mutation in scn1lab, a zebrafish homolog of human SCN1A. Homozygous scn1labs552/s552 mutants exhibit early-life seizures, metabolic deficits, and early death. Here, we developed in vivo assays using scn1labs552 mutants between 3 and 6 d postfertilization (dpf). To evaluate sleep disturbances, we monitored larvae for 24 h with locomotion tracking software. Locomotor activity during dark (night phase) was significantly higher in mutants than in controls. Among anticonvulsant drugs, clemizole and diazepam, but not trazodone or valproic acid, decreased distance moved at night for scn1labs552 mutant larvae. To monitor exploratory behavior in an open field, we tracked larvae in a novel arena. Mutant larvae exhibited impaired exploratory behavior, with increased time spent near the edge of the arena and decreased mobility, suggesting greater anxiety. Both clemizole and diazepam, but not trazodone or valproic acid, decreased distance moved and increased time spent in the center of the arena. Counting inhibitory neurons in vivo revealed no differences between scn1labs552 mutants and siblings. Taken together, our results demonstrate conserved features of sleep, anxiety, and movement disorders in scn1lab mutant zebrafish, and provide evidence that a zebrafish model allows effective tests of treatments for behavioral comorbidities associated with DS.
Collapse
|
23
|
Xie Y, Kaufmann D, Moulton MJ, Panahi S, Gaynes JA, Watters HN, Zhou D, Xue HH, Fung CM, Levine EM, Letsou A, Brennan KC, Dorsky RI. Lef1-dependent hypothalamic neurogenesis inhibits anxiety. PLoS Biol 2017; 15:e2002257. [PMID: 28837622 PMCID: PMC5570277 DOI: 10.1371/journal.pbio.2002257] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 07/21/2017] [Indexed: 11/19/2022] Open
Abstract
While innate behaviors are conserved throughout the animal kingdom, it is unknown whether common signaling pathways regulate the development of neuronal populations mediating these behaviors in diverse organisms. Here, we demonstrate that the Wnt/ß-catenin effector Lef1 is required for the differentiation of anxiolytic hypothalamic neurons in zebrafish and mice, although the identity of Lef1-dependent genes and neurons differ between these 2 species. We further show that zebrafish and Drosophila have common Lef1-dependent gene expression in their respective neuroendocrine organs, consistent with a conserved pathway that has diverged in the mouse. Finally, orthologs of Lef1-dependent genes from both zebrafish and mouse show highly correlated hypothalamic expression in marmosets and humans, suggesting co-regulation of 2 parallel anxiolytic pathways in primates. These findings demonstrate that during evolution, a transcription factor can act through multiple mechanisms to generate a common behavioral output, and that Lef1 regulates circuit development that is fundamentally important for mediating anxiety in a wide variety of animal species.
Collapse
Affiliation(s)
- Yuanyuan Xie
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, Utah, United States of America
| | - Dan Kaufmann
- Department of Neurology, University of Utah, Salt Lake City, Utah, United States of America
| | - Matthew J. Moulton
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Samin Panahi
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, Utah, United States of America
| | - John A. Gaynes
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, Utah, United States of America
| | - Harrison N. Watters
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, Utah, United States of America
| | - Dingxi Zhou
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, Utah, United States of America
- School of Life Sciences, Peking University, Beijing, China
| | - Hai-Hui Xue
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Camille M. Fung
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Edward M. Levine
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
| | - Anthea Letsou
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - K. C. Brennan
- Department of Neurology, University of Utah, Salt Lake City, Utah, United States of America
| | - Richard I. Dorsky
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, Utah, United States of America
| |
Collapse
|
24
|
Solek CM, Feng S, Perin S, Weinschutz Mendes H, Ekker M. Lineage tracing of dlx1a/2a and dlx5a/6a expressing cells in the developing zebrafish brain. Dev Biol 2017; 427:131-147. [PMID: 28479339 DOI: 10.1016/j.ydbio.2017.04.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 04/28/2017] [Accepted: 04/29/2017] [Indexed: 02/06/2023]
Abstract
Lineage tracing of specific populations of progenitor cells provides crucial information about developmental programs. Four members of the Dlx homeobox gene family, Dlx1,2, 5 and 6, are involved in the specification of γ-aminobutyric acid (GABA)ergic neurons in the vertebrate forebrain. Orthologous genes in mammals and teleost show similarities in expression patterns and transcriptional regulation mechanisms. We have used lineage tracing to permanently label dlx-expressing cells in the zebrafish and have characterized the progeny of these cells in the larva and in the juvenile and adult brain. We have found that dlx1a/2a and dlx5a/6a expressing progenitors give rise, for the most part, to small populations of cells which constitute only a small proportion of GABAergic cells in the adult brain tissue. Moreover, some of the cells do not acquire a neuronal phenotype suggesting that, regardless of the time a cell expresses dlx genes in the brain, it can potentially give rise to cells other than neurons. In some instances, labeling larval dlx5a/6a-expressing cells, but not dlx1a/2a-expressing cells, results in massively expanding, widespread clonal expansion throughout the adult brain. Our data provide a detailed lineage analysis of the dlx1a/2a and dlx5a/6a expressing progenitors in the zebrafish brain and lays the foundation for further characterization of the role of these transcription factors beyond the specification of GABAergic neurons.
Collapse
Affiliation(s)
- Cynthia M Solek
- CAREG, Department of Biology, University of Ottawa, 20 Marie-Curie Private, Ottawa, ON, Canada K1N 6N5; Montreal Neurological Institute, McGill University, 3801 University Street, Montreal, QC, Canada H3A 2B4
| | - Shengrui Feng
- CAREG, Department of Biology, University of Ottawa, 20 Marie-Curie Private, Ottawa, ON, Canada K1N 6N5; Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, ON, Canada M5G 2M9
| | - Sofia Perin
- CAREG, Department of Biology, University of Ottawa, 20 Marie-Curie Private, Ottawa, ON, Canada K1N 6N5
| | - Hellen Weinschutz Mendes
- CAREG, Department of Biology, University of Ottawa, 20 Marie-Curie Private, Ottawa, ON, Canada K1N 6N5
| | - Marc Ekker
- CAREG, Department of Biology, University of Ottawa, 20 Marie-Curie Private, Ottawa, ON, Canada K1N 6N5.
| |
Collapse
|
25
|
Thomas-Jinu S, Gordon PM, Fielding T, Taylor R, Smith BN, Snowden V, Blanc E, Vance C, Topp S, Wong CH, Bielen H, Williams KL, McCann EP, Nicholson GA, Pan-Vazquez A, Fox AH, Bond CS, Talbot WS, Blair IP, Shaw CE, Houart C. Non-nuclear Pool of Splicing Factor SFPQ Regulates Axonal Transcripts Required for Normal Motor Development. Neuron 2017; 94:322-336.e5. [PMID: 28392072 PMCID: PMC5405110 DOI: 10.1016/j.neuron.2017.03.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/02/2017] [Accepted: 03/17/2017] [Indexed: 12/12/2022]
Abstract
Recent progress revealed the complexity of RNA processing and its association to human disorders. Here, we unveil a new facet of this complexity. Complete loss of function of the ubiquitous splicing factor SFPQ affects zebrafish motoneuron differentiation cell autonomously. In addition to its nuclear localization, the protein unexpectedly localizes to motor axons. The cytosolic version of SFPQ abolishes motor axonal defects, rescuing key transcripts, and restores motility in the paralyzed sfpq null mutants, indicating a non-nuclear processing role in motor axons. Novel variants affecting the conserved coiled-coil domain, so far exclusively found in fALS exomes, specifically affect the ability of SFPQ to localize in axons. They broadly rescue morphology and motility in the zebrafish mutant, but alter motor axon morphology, demonstrating functional requirement for axonal SFPQ. Altogether, we uncover the axonal function of the splicing factor SFPQ in motor development and highlight the importance of the coiled-coil domain in this process. Video Abstract
SFPQ splicing factor is present in motor axons Non-nuclear SFPQ is able to drive axon maturation and connectivity Loss of axonal SFPQ affects axonal morphology Coiled-coil domain of the protein is important for non-nuclear localization
Collapse
Affiliation(s)
- Swapna Thomas-Jinu
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Patricia M Gordon
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Triona Fielding
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Richard Taylor
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Bradley N Smith
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Victoria Snowden
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Eric Blanc
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Caroline Vance
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Simon Topp
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Chun-Hao Wong
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Holger Bielen
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Kelly L Williams
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Emily P McCann
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Garth A Nicholson
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia; ANZAC Research Institute, University of Sydney, Concord Hospital, Sydney, NSW 2139, Australia
| | - Alejandro Pan-Vazquez
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Archa H Fox
- School of Anatomy, Physiology, and Human Biology, University of Western Australia, Crawley, WA 6009, Australia; Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; Centre for Medical Research, University of Western Australia, Crawley, WA 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA 6009, Australia
| | - William S Talbot
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian P Blair
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Corinne Houart
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK.
| |
Collapse
|
26
|
Zhang Q, Zagozewski J, Cheng S, Dixit R, Zhang S, de Melo J, Mu X, Klein WH, Brown NL, Wigle JT, Schuurmans C, Eisenstat DD. Regulation of Brn3b by DLX1 and DLX2 is required for retinal ganglion cell differentiation in the vertebrate retina. Development 2017; 144:1698-1711. [PMID: 28356311 PMCID: PMC5450843 DOI: 10.1242/dev.142042] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 03/17/2017] [Indexed: 12/24/2022]
Abstract
Regulated retinal ganglion cell (RGC) differentiation and axonal guidance is required for a functional visual system. Homeodomain and basic helix-loop-helix transcription factors are required for retinogenesis, as well as patterning, differentiation and maintenance of specific retinal cell types. We hypothesized that Dlx1, Dlx2 and Brn3b homeobox genes function in parallel intrinsic pathways to determine RGC fate and therefore generated Dlx1/Dlx2/Brn3b triple-knockout mice. A more severe retinal phenotype was found in the Dlx1/Dlx2/Brn3b-null retinas than was predicted by combining features of the Brn3b single- and Dlx1/Dlx2 double-knockout retinas, including near total RGC loss with a marked increase in amacrine cells in the ganglion cell layer. Furthermore, we discovered that DLX1 and DLX2 function as direct transcriptional activators of Brn3b expression. Knockdown of Dlx2 expression in primary embryonic retinal cultures and Dlx2 gain of function in utero strongly support that DLX2 is both necessary and sufficient for Brn3b expression in vivo. We suggest that ATOH7 specifies RGC-committed progenitors and that Dlx1 and Dlx2 function both downstream of ATOH7 and in parallel, but cooperative, pathways that involve regulation of Brn3b expression to determine RGC fate. Summary:Dlx1/2 homeobox genes regulate retinal ganglion cell (RGC) differentiation by directly activating Brn3b expression; accordingly, Dlx1/Dlx2/Brn3b triple-knockout mice exhibit near complete RGC loss.
Collapse
Affiliation(s)
- Qi Zhang
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, Canada R3E 0J9
| | - Jamie Zagozewski
- Department of Medical Genetics, University of Alberta, Edmonton, Canada T6G 2H7
| | - Shaohong Cheng
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Canada R3A 1S1
| | - Rajiv Dixit
- Hotchkiss Brain Institute, University of Calgary, Canada T2N 4N1
| | - Shunzhen Zhang
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada R3E 3J7
| | - Jimmy de Melo
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, Canada R3E 0J9
| | - Xiuqian Mu
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - William H Klein
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Nadean L Brown
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA 95616, Canada
| | - Jeffrey T Wigle
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada R3E 3J7
| | - Carol Schuurmans
- Hotchkiss Brain Institute, University of Calgary, Canada T2N 4N1
| | - David D Eisenstat
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, Canada R3E 0J9 .,Department of Medical Genetics, University of Alberta, Edmonton, Canada T6G 2H7.,Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Canada R3A 1S1.,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada R3E 3J7.,Department of Ophthalmology, University of Manitoba, Winnipeg, Canada R3T 2N2
| |
Collapse
|
27
|
The genome of the Gulf pipefish enables understanding of evolutionary innovations. Genome Biol 2016; 17:258. [PMID: 27993155 PMCID: PMC5168715 DOI: 10.1186/s13059-016-1126-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/05/2016] [Indexed: 11/10/2022] Open
Abstract
Background Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuing these molecular phenomena underlying phenotypic evolution. We explored the genome of the Gulf pipefish (Syngnathus scovelli), which belongs to family Syngnathidae (pipefishes, seahorses, and seadragons). These fishes have dramatically derived bodies and a remarkable novelty among vertebrates, the male brood pouch. Results We produce a reference genome, condensed into chromosomes, for the Gulf pipefish. Gene losses and other changes have occurred in pipefish hox and dlx clusters and in the tbx and pitx gene families, candidate mechanisms for the evolution of syngnathid traits, including an elongated axis and the loss of ribs, pelvic fins, and teeth. We measure gene expression changes in pregnant versus non-pregnant brood pouch tissue and characterize the genomic organization of duplicated metalloprotease genes (patristacins) recruited into the function of this novel structure. Phylogenetic inference using ultraconserved sequences provides an alternative hypothesis for the relationship between orders Syngnathiformes and Scombriformes. Comparisons of chromosome structure among percomorphs show that chromosome number in a pipefish ancestor became reduced via chromosomal fusions. Conclusions The collected findings from this first syngnathid reference genome open a window into the genomic underpinnings of highly derived morphologies, demonstrating that de novo production of high quality and useful reference genomes is within reach of even small research groups. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1126-6) contains supplementary material, which is available to authorized users.
Collapse
|
28
|
Dimidschstein J, Chen Q, Tremblay R, Rogers SL, Saldi GA, Guo L, Xu C, Liu R, Lu C, Chu J, Avery MC, Rashid SM, Baek M, Jacob AL, Smith GB, Wilson DE, Kosche G, Kruglikov I, Rusielewicz T, Kotak VC, Mowery TM, Anderson SA, Callaway EM, Dasen JS, Fitzpatrick D, Fossati V, Long MA, Noggle S, Reynolds JH, Sanes DH, Rudy B, Feng G, Fishell G. A viral strategy for targeting and manipulating interneurons across vertebrate species. Nat Neurosci 2016; 19:1743-1749. [PMID: 27798629 PMCID: PMC5348112 DOI: 10.1038/nn.4430] [Citation(s) in RCA: 342] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/27/2016] [Indexed: 12/11/2022]
Abstract
A fundamental impediment to understanding the brain is the availability of inexpensive and robust methods for targeting and manipulating specific neuronal populations. The need to overcome this barrier is pressing because there are considerable anatomical, physiological, cognitive and behavioral differences between mice and higher mammalian species in which it is difficult to specifically target and manipulate genetically defined functional cell types. In particular, it is unclear the degree to which insights from mouse models can shed light on the neural mechanisms that mediate cognitive functions in higher species, including humans. Here we describe a novel recombinant adeno-associated virus that restricts gene expression to GABAergic interneurons within the telencephalon. We demonstrate that the viral expression is specific and robust, allowing for morphological visualization, activity monitoring and functional manipulation of interneurons in both mice and non-genetically tractable species, thus opening the possibility to study GABAergic function in virtually any vertebrate species.
Collapse
Affiliation(s)
- J Dimidschstein
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
- Center for Genomics & Systems Biology, New York University, Abu Dhabi, UAE
| | - Q Chen
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - R Tremblay
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - SL Rogers
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - GA Saldi
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - L Guo
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
- Center for Genomics & Systems Biology, New York University, Abu Dhabi, UAE
| | - C Xu
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
- Center for Genomics & Systems Biology, New York University, Abu Dhabi, UAE
| | - R Liu
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - C Lu
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - J Chu
- Department of Psychiatry, Children’s Hospital of Philadelphia and UPenn School of Medicine, Philadelphia, PA 19104, USA
| | - MC Avery
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - SM Rashid
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - M Baek
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - AL Jacob
- Department of Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA
| | - GB Smith
- Department of Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA
| | - DE Wilson
- Department of Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA
| | - G Kosche
- NYU Neuroscience Institute and the Department of Otolaryngology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - I Kruglikov
- New York Stem Cell Foundation, New York, NY10023, USA
| | - T Rusielewicz
- New York Stem Cell Foundation, New York, NY10023, USA
| | - VC Kotak
- NYU Center for Neural Science, New York University, New York, NY 10003, USA
| | - TM Mowery
- NYU Center for Neural Science, New York University, New York, NY 10003, USA
| | - SA Anderson
- Department of Psychiatry, Children’s Hospital of Philadelphia and UPenn School of Medicine, Philadelphia, PA 19104, USA
| | - EM Callaway
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - JS Dasen
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - D Fitzpatrick
- Department of Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, Jupiter, FL 33458, USA
| | - V Fossati
- New York Stem Cell Foundation, New York, NY10023, USA
| | - MA Long
- NYU Neuroscience Institute and the Department of Otolaryngology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - S Noggle
- New York Stem Cell Foundation, New York, NY10023, USA
| | - JH Reynolds
- Systems Neurobiology Laboratories, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - DH Sanes
- NYU Center for Neural Science, New York University, New York, NY 10003, USA
| | - B Rudy
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - G Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - G Fishell
- NYU Neuroscience Institute and the Department of Neuroscience and Physiology, Smilow Research Center, New York University Langone Medical Center, New York, NY 10016, USA
- Center for Genomics & Systems Biology, New York University, Abu Dhabi, UAE
| |
Collapse
|
29
|
Fazel Darbandi S, Poitras L, Monis S, Lindtner S, Yu M, Hatch G, Rubenstein JL, Ekker M. Functional consequences of I56ii Dlx enhancer deletion in the developing mouse forebrain. Dev Biol 2016; 420:S0012-1606(16)30263-9. [PMID: 27983964 DOI: 10.1016/j.ydbio.2016.10.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 09/22/2016] [Accepted: 10/24/2016] [Indexed: 12/12/2022]
Abstract
Dlx homeobox genes encode a group of transcription factors that play an essential role during developmental processes including maintaining the differentiation, proliferation and migration of GABAergic interneurons. The Dlx1/2 and Dlx5/6 genes are expressed in the forebrain and are arranged in convergently transcribed bigene clusters, with I12a/I12b and I56i/I56ii cis-regulatory elements (CREs) located in the intergenic region of each cluster respectively. We have characterized the phenotypic consequences of deleting I56ii on forebrain development and spatial patterning of corridor cells that are involved in guiding thalamocortical projections. Here we report that deletion of I56ii impairs expression of Dlx genes and that of potential targets including Gad2 as well as striatal markers Islet1, Meis2, and Ebf1. In addition, I56ii deletion reduces both the binding of DLX2 in the Dlx5/Dlx6 intergenic region and the presence of H3K9Ac at the Dlx5/Dlx6 locus, consistent with the reduced expression of these genes. Deletion of I56ii reduces the expression of the ISLET1 and CTIP2 in the striatum and disrupts the number of parvalbumin and calretinin expressing cells in the adult somatosensory cortex of the ΔI56ii mice. These data suggest an important regulatory role for I56ii in the developing forebrain by means of a potential regulatory mechanism which may regulate the expression of Dlx genes, notably Dlx6 as well as the spatial patterning of the ventral telencephalon, including possibly corridor cells.
Collapse
Affiliation(s)
- S Fazel Darbandi
- Department of Biology, University of Ottawa, 20 Marie Curie, Ottawa, ON Canada K1N 6N5; Department of Psychiatry, School of Medicine, Rock Hall, University of California, San Francisco (UCSF), San Francisco, CA 94158-2324, USA
| | - L Poitras
- Department of Biology, University of Ottawa, 20 Marie Curie, Ottawa, ON Canada K1N 6N5
| | - S Monis
- Department of Biology, University of Ottawa, 20 Marie Curie, Ottawa, ON Canada K1N 6N5
| | - S Lindtner
- Department of Psychiatry, School of Medicine, Rock Hall, University of California, San Francisco (UCSF), San Francisco, CA 94158-2324, USA
| | - M Yu
- Department of Biology, University of Ottawa, 20 Marie Curie, Ottawa, ON Canada K1N 6N5
| | - G Hatch
- Department of Biology, University of Ottawa, 20 Marie Curie, Ottawa, ON Canada K1N 6N5
| | - J L Rubenstein
- Department of Psychiatry, School of Medicine, Rock Hall, University of California, San Francisco (UCSF), San Francisco, CA 94158-2324, USA
| | - M Ekker
- Department of Biology, University of Ottawa, 20 Marie Curie, Ottawa, ON Canada K1N 6N5.
| |
Collapse
|
30
|
Marques F, Tenney J, Duran I, Martin J, Nevarez L, Pogue R, Krakow D, Cohn DH, Li B. Altered mRNA Splicing, Chondrocyte Gene Expression and Abnormal Skeletal Development due to SF3B4 Mutations in Rodriguez Acrofacial Dysostosis. PLoS Genet 2016; 12:e1006307. [PMID: 27622494 PMCID: PMC5021280 DOI: 10.1371/journal.pgen.1006307] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/17/2016] [Indexed: 02/04/2023] Open
Abstract
The acrofacial dysostoses (AFD) are a genetically heterogeneous group of inherited disorders with craniofacial and limb abnormalities. Rodriguez syndrome is a severe, usually perinatal lethal AFD, characterized by severe retrognathia, oligodactyly and lower limb abnormalities. Rodriguez syndrome has been proposed to be a severe form of Nager syndrome, a non-lethal AFD that results from mutations in SF3B4, a component of the U2 small nuclear ribonucleoprotein particle (U2 snRNP). Furthermore, a case with a phenotype intermediate between Rodriguez and Nager syndromes has been shown to have an SF3B4 mutation. We identified heterozygosity for SF3B4 mutations in Rodriguez syndrome, confirming that the phenotype is a dominant disorder that is allelic with Nager syndrome. The mutations led to reduced SF3B4 synthesis and defects in mRNA splicing, primarily exon skipping. The mutations also led to reduced expression in growth plate chondrocytes of target genes, including the DLX5, DLX6, SOX9, and SOX6 transcription factor genes, which are known to be important for skeletal development. These data provide mechanistic insight toward understanding how SF3B4 mutations lead to the skeletal abnormalities observed in the acrofacial dysostoses. The acrofacial dysostoses (AFD) are inherited disorders with abnormalities of the facial and limb bones. Rodriguez syndrome is a severe type of AFD that is usually lethal in the immediate perinatal period. Rodriguez syndrome has been proposed to be a severe form of Nager syndrome, a non-lethal AFD that results from mutations in SF3B4, a component of mRNA splicing machinery needed for proper maturation of primary transcripts. Furthermore, a case with a phenotype intermediate between Rodriguez and Nager syndromes has been shown to have an SF3B4 mutation. We found that mutations in SF3B4 produce Rodriguez syndrome, further demonstrating that it is allelic with Nager syndrome. The consequences of the mutations include abnormal splicing and reduced expression in growth plate chondrocytes of genes that are important for proper development of the skeleton, providing mechanistic insight toward understanding how SF3B4 mutations lead to the skeletal abnormalities observed in the acrofacial dysostoses.
Collapse
Affiliation(s)
- Felipe Marques
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
- Laboratório de Biotecnologia, Universidade CEUMA, Campus Renascença, São Luís-MA, Brazil
| | - Jessica Tenney
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Department of Pediatrics, Division of Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Ivan Duran
- Department of Orthopaedic Surgery, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jorge Martin
- Department of Orthopaedic Surgery, University of California Los Angeles, Los Angeles, California, United States of America
| | - Lisette Nevarez
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Robert Pogue
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Deborah Krakow
- Department of Orthopaedic Surgery, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California, United States of America
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (DK); (DHC)
| | - Daniel H. Cohn
- Department of Orthopaedic Surgery, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (DK); (DHC)
| | - Bing Li
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| |
Collapse
|
31
|
Measuring inputs to a common function: The case of Dlx5 and Dlx6. Biochem Biophys Res Commun 2016; 478:371-377. [DOI: 10.1016/j.bbrc.2016.07.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 07/08/2016] [Indexed: 11/23/2022]
|
32
|
Hoffman EJ, Turner KJ, Fernandez JM, Cifuentes D, Ghosh M, Ijaz S, Jain RA, Kubo F, Bill BR, Baier H, Granato M, Barresi MJF, Wilson SW, Rihel J, State MW, Giraldez AJ. Estrogens Suppress a Behavioral Phenotype in Zebrafish Mutants of the Autism Risk Gene, CNTNAP2. Neuron 2016; 89:725-33. [PMID: 26833134 PMCID: PMC4766582 DOI: 10.1016/j.neuron.2015.12.039] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/16/2015] [Accepted: 12/21/2015] [Indexed: 12/20/2022]
Abstract
Autism spectrum disorders (ASDs) are a group of devastating neurodevelopmental syndromes that affect up to 1 in 68 children. Despite advances in the identification of ASD risk genes, the mechanisms underlying ASDs remain unknown. Homozygous loss-of-function mutations in Contactin Associated Protein-like 2 (CNTNAP2) are strongly linked to ASDs. Here we investigate the function of Cntnap2 and undertake pharmacological screens to identify phenotypic suppressors. We find that zebrafish cntnap2 mutants display GABAergic deficits, particularly in the forebrain, and sensitivity to drug-induced seizures. High-throughput behavioral profiling identifies nighttime hyperactivity in cntnap2 mutants, while pharmacological testing reveals dysregulation of GABAergic and glutamatergic systems. Finally, we find that estrogen receptor agonists elicit a behavioral fingerprint anti-correlative to that of cntnap2 mutants and show that the phytoestrogen biochanin A specifically reverses the mutant behavioral phenotype. These results identify estrogenic compounds as phenotypic suppressors and illuminate novel pharmacological pathways with relevance to autism.
Collapse
Affiliation(s)
- Ellen J Hoffman
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Katherine J Turner
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Joseph M Fernandez
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Daniel Cifuentes
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Marcus Ghosh
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Sundas Ijaz
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Roshan A Jain
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Biology, Haverford College, Haverford, PA 19041, USA
| | - Fumi Kubo
- Department Genes - Circuits - Behavior, Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Brent R Bill
- Center for Autism Research and Treatment, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biology, The University of Texas at Tyler, Tyler, TX 75799, USA
| | - Herwig Baier
- Department Genes - Circuits - Behavior, Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Michael Granato
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Michael J F Barresi
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Jason Rihel
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.
| | - Matthew W State
- Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Program on Neurogenetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
| |
Collapse
|
33
|
Rasmussen MB, Kreiborg S, Jensen P, Bak M, Mang Y, Lodahl M, Budtz-Jørgensen E, Tommerup N, Tranebjærg L, Rendtorff ND. Phenotypic subregions within the split-hand/foot malformation 1 locus. Hum Genet 2016; 135:345-57. [DOI: 10.1007/s00439-016-1635-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/13/2016] [Indexed: 11/29/2022]
|
34
|
Zhao N, Han D, Liu Y, Li Y, Zeng L, Wang Y, Feng H. DLX3 negatively regulates osteoclastic differentiation through microRNA-124. Exp Cell Res 2016; 341:166-76. [DOI: 10.1016/j.yexcr.2016.01.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 01/21/2016] [Accepted: 01/29/2016] [Indexed: 11/26/2022]
|
35
|
Zapilko V, Korsching SI. Tetrapod V1R-like ora genes in an early-diverging ray-finned fish species: the canonical six ora gene repertoire of teleost fish resulted from gene loss in a larger ancestral repertoire. BMC Genomics 2016; 17:83. [PMID: 26818853 PMCID: PMC4728799 DOI: 10.1186/s12864-016-2399-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chemical senses serve a multitude of essential functions across the animal kingdom. Vertebrates employ four GPCR families to detect odors, among them the v1r/ora gene family. The V1R family is known to evolve rapidly in the lobe-finned lineage giving rise to tetrapods, but the homologous ORA family consists of just six highly conserved genes in teleost fish, with direct orthologs in the lobe-finned fish coelacanth. Thus, the teleost repertoire of six canonical ora genes was assumed to be the ancestral feature before the divergence of ray-finned and lobe-finned fish. So far, this hypothesis has not been tested with earlier diverging ray-finned fish. RESULTS We have newly identified the complete ora gene repertoires of five teleost species, and of spotted gar, a basal ray-finned fish, using thorough data mining and extensive phylogenetic analysis. The genomes of eight further teleost species were re-analyzed for their ORA repertoires. We report that direct orthologs of the six canonical ora genes (ora1-6) were present in all newly analyzed species, with faithfully preserved exon/intron structure and mostly preserved genomic arrangement in symmetric pairs for ora1-4. In four teleost species including medaka and cave fish we observe species-specific gene duplication events. Thus, the ora gene repertoire in teleost fish is not quite as strictly conserved as previously assumed. In fact, the examination of non-synonymous vs. synonymous substitution rates (dN/dS) shows pronounced negative selection in five of the six ora genes, but also rare occurrence of positive selection in ora3 and ora6. Surprisingly, spotted gar possesses beyond the six canonical genes three additional genes, ora7-8b, orthologous to coelacanth genes v1r07-10. No orthologs for these genes were found in teleosts and cartilaginous fish. CONCLUSIONS Early diverging ray-finned fish such as the spotted gar possess several v1r-like genes previously assumed to be restricted to the lobe-finned lineage, but now found to be already present in the most recent common ancestor of lobe- and ray-finned fish. Thus, the presence of just six canonical ora genes in many teleost species is not the ancestral feature of the ray-finned lineage, but caused by loss of two ancestral genes in teleosts.
Collapse
Affiliation(s)
- Veronika Zapilko
- Institute of Genetics, University of Cologne, 50674, Cologne, Germany
| | | |
Collapse
|
36
|
Qadir AS, Um S, Lee H, Baek K, Seo BM, Lee G, Kim GS, Woo KM, Ryoo HM, Baek JH. miR-124 Negatively Regulates Osteogenic Differentiation and In vivo Bone Formation of Mesenchymal Stem Cells. J Cell Biochem 2015; 116:730-42. [DOI: 10.1002/jcb.25026] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 11/21/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Abdul S. Qadir
- Department of Molecular Genetics; School of Dentistry and Dental Research Institute; Seoul National University; Seoul 110-744 Korea
| | - Soyoun Um
- Department of Dental Science; School of Dentistry and Dental Research Institute; Seoul National University; Seoul 110-744 Korea
| | - Heesu Lee
- Department of Oral Anatomy; Research Institute of Oral Science; College of Dentistry; Gangneung-Wonju National University; Gangwondo 210-702 Korea
| | - Kyunghwa Baek
- Department of Pharmacology; Research Institute of Oral Science; College of Dentistry, Gangneung-Wonju National University; Gangwondo 210-702 Korea
| | - Byoung Moo Seo
- Department of Oral and Maxillofacial Surgery; School of Dentistry and Dental Research Institute; Seoul National University; Seoul 110-744 Korea
| | - Gene Lee
- Department of Molecular Genetics; School of Dentistry and Dental Research Institute; Seoul National University; Seoul 110-744 Korea
| | - Gwan-Shik Kim
- Department of Molecular Genetics; School of Dentistry and Dental Research Institute; Seoul National University; Seoul 110-744 Korea
| | - Kyung Mi Woo
- Department of Molecular Genetics; School of Dentistry and Dental Research Institute; Seoul National University; Seoul 110-744 Korea
| | - Hyun-Mo Ryoo
- Department of Molecular Genetics; School of Dentistry and Dental Research Institute; Seoul National University; Seoul 110-744 Korea
| | - Jeong-Hwa Baek
- Department of Molecular Genetics; School of Dentistry and Dental Research Institute; Seoul National University; Seoul 110-744 Korea
| |
Collapse
|
37
|
Song H, Lee B, Pyun D, Guimera J, Son Y, Yoon J, Baek K, Wurst W, Jeong Y. Ascl1 and Helt act combinatorially to specify thalamic neuronal identity by repressing Dlxs activation. Dev Biol 2015; 398:280-91. [DOI: 10.1016/j.ydbio.2014.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/02/2014] [Accepted: 12/04/2014] [Indexed: 11/25/2022]
|
38
|
Zagozewski JL, Zhang Q, Pinto VI, Wigle JT, Eisenstat DD. The role of homeobox genes in retinal development and disease. Dev Biol 2014; 393:195-208. [PMID: 25035933 DOI: 10.1016/j.ydbio.2014.07.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/02/2014] [Accepted: 07/08/2014] [Indexed: 11/18/2022]
Abstract
Homeobox genes are an evolutionarily conserved class of transcription factors that are critical for development of many organ systems, including the brain and eye. During retinogenesis, homeodomain-containing transcription factors, which are encoded by homeobox genes, play essential roles in the regionalization and patterning of the optic neuroepithelium, specification of retinal progenitors and differentiation of all seven of the retinal cell classes that derive from a common progenitor. Homeodomain transcription factors control retinal cell fate by regulating the expression of target genes required for retinal progenitor cell fate decisions and for terminal differentiation of specific retinal cell types. The essential role of homeobox genes during retinal development is demonstrated by the number of human eye diseases, including colobomas and anophthalmia, which are attributed to homeobox gene mutations. In the following review, we highlight the role of homeodomain transcription factors during retinogenesis and regulation of their gene targets. Understanding the complexities of vertebrate retina development will enhance our ability to drive differentiation of specific retinal cell types towards novel cell-based replacement therapies for retinal degenerative diseases.
Collapse
Affiliation(s)
- Jamie L Zagozewski
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Qi Zhang
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB, Canada R3E 0J9
| | - Vanessa I Pinto
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada R3E 0J9
| | - Jeffrey T Wigle
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada R3E 0J9; Institute of Cardiovascular Sciences, St. Boniface Hospital Research Institute, Winnipeg, MB, Canada R2H 2A6
| | - David D Eisenstat
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada T6G 2H7; Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada R3E 0J9; Department of Pediatrics, University of Alberta, Edmonton, AB, Canada T6G 1C9.
| |
Collapse
|
39
|
Vogt D, Hunt RF, Mandal S, Sandberg M, Silberberg SN, Nagasawa T, Yang Z, Baraban SC, Rubenstein JLR. Lhx6 directly regulates Arx and CXCR7 to determine cortical interneuron fate and laminar position. Neuron 2014; 82:350-64. [PMID: 24742460 DOI: 10.1016/j.neuron.2014.02.030] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2014] [Indexed: 12/13/2022]
Abstract
Cortical GABAergic interneurons have essential roles for information processing and their dysfunction is implicated in neuropsychiatric disorders. Transcriptional codes are elucidating mechanisms of interneuron specification in the MGE (a subcortical progenitor zone), which regulate their migration, integration, and function within cortical circuitry. Lhx6, a LIM-homeodomain transcription factor, is essential for specification of MGE-derived somatostatin and parvalbumin interneurons. Here, we demonstrate that some Lhx6⁻/⁻ MGE cells acquire a CGE-like fate. Using an in vivo MGE complementation/transplantation assay, we show that Lhx6-regulated genes Arx and CXCR7 rescue divergent aspects of Lhx6⁻/⁻ cell-fate and laminar mutant phenotypes and provide insight into a neonatal role for CXCR7 in MGE-derived interneuron lamination. Finally, Lhx6 directly binds in vivo to an Arx enhancer and to an intronic CXCR7 enhancer that remains active in mature interneurons. These data define the molecular identity of Lhx6 mutants and introduce technologies to test mechanisms in GABAergic interneuron differentiation.
Collapse
Affiliation(s)
- Daniel Vogt
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Robert F Hunt
- Epilepsy Research Laboratory, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Shyamali Mandal
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cancer Biology and Pharmacology University of Illinois, Peoria, IL 61656, USA
| | - Magnus Sandberg
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Shanni N Silberberg
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Takashi Nagasawa
- Department of Immunology and Hematology, Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Zhengang Yang
- Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Scott C Baraban
- Epilepsy Research Laboratory, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John L R Rubenstein
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
40
|
Silbereis JC, Nobuta H, Tsai HH, Heine VM, McKinsey GL, Meijer DH, Howard MA, Petryniak MA, Potter GB, Alberta JA, Baraban SC, Stiles CD, Rubenstein JLR, Rowitch DH. Olig1 function is required to repress dlx1/2 and interneuron production in Mammalian brain. Neuron 2014; 81:574-87. [PMID: 24507192 DOI: 10.1016/j.neuron.2013.11.024] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2013] [Indexed: 12/21/2022]
Abstract
Abnormal GABAergic interneuron density, and imbalance of excitatory versus inhibitory tone, is thought to result in epilepsy, neurodevelopmental disorders, and psychiatric disease. Recent studies indicate that interneuron cortical density is determined primarily by the size of the precursor pool in the embryonic telencephalon. However, factors essential for regulating interneuron allocation from telencephalic multipotent precursors are poorly understood. Here we report that Olig1 represses production of GABAergic interneurons throughout the mouse brain. Olig1 deletion in mutant mice results in ectopic expression and upregulation of Dlx1/2 genes in the ventral medial ganglionic eminences and adjacent regions of the septum, resulting in an ∼30% increase in adult cortical interneuron numbers. We show that Olig1 directly represses the Dlx1/2 I12b intergenic enhancer and that Dlx1/2 functions genetically downstream of Olig1. These findings establish Olig1 as an essential repressor of Dlx1/2 and interneuron production in developing mammalian brain.
Collapse
Affiliation(s)
- John C Silbereis
- Department of Pediatrics, Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurosurgery, University of California, San Francisco, San Francisco, CA 94143, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Hiroko Nobuta
- Department of Pediatrics, Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurosurgery, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Hui-Hsin Tsai
- Department of Pediatrics, Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurosurgery, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Vivi M Heine
- Department of Pediatrics, Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurosurgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gabriel L McKinsey
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dimphna H Meijer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Mackenzie A Howard
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Magda A Petryniak
- Department of Pediatrics, Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gregory B Potter
- Department of Pediatrics, Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John A Alberta
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Scott C Baraban
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charles D Stiles
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - John L R Rubenstein
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David H Rowitch
- Department of Pediatrics, Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurosurgery, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| |
Collapse
|
41
|
Yang G, Yuan G, Li X, Liu P, Chen Z, Fan M. BMP-2 Induction of Dlx3 Expression Is Mediated by p38/Smad5 Signaling Pathway in Osteoblastic MC3T3-E1 Cells. J Cell Physiol 2014; 229:943-54. [PMID: 24647893 DOI: 10.1002/jcp.24525] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/04/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Guobin Yang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory of Oral Biomedicine Ministry of Education; School and Hospital of Stomatology; Wuhan University; Wuhan China
| | - Guohua Yuan
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory of Oral Biomedicine Ministry of Education; School and Hospital of Stomatology; Wuhan University; Wuhan China
| | - Xiaoyan Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory of Oral Biomedicine Ministry of Education; School and Hospital of Stomatology; Wuhan University; Wuhan China
| | - Pingxian Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory of Oral Biomedicine Ministry of Education; School and Hospital of Stomatology; Wuhan University; Wuhan China
| | - Zhi Chen
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory of Oral Biomedicine Ministry of Education; School and Hospital of Stomatology; Wuhan University; Wuhan China
| | - Mingwen Fan
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory of Oral Biomedicine Ministry of Education; School and Hospital of Stomatology; Wuhan University; Wuhan China
| |
Collapse
|
42
|
Maeso I, Irimia M, Tena JJ, Casares F, Gómez-Skarmeta JL. Deep conservation of cis-regulatory elements in metazoans. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130020. [PMID: 24218633 DOI: 10.1098/rstb.2013.0020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Despite the vast morphological variation observed across phyla, animals share multiple basic developmental processes orchestrated by a common ancestral gene toolkit. These genes interact with each other building complex gene regulatory networks (GRNs), which are encoded in the genome by cis-regulatory elements (CREs) that serve as computational units of the network. Although GRN subcircuits involved in ancient developmental processes are expected to be at least partially conserved, identification of CREs that are conserved across phyla has remained elusive. Here, we review recent studies that revealed such deeply conserved CREs do exist, discuss the difficulties associated with their identification and describe new approaches that will facilitate this search.
Collapse
Affiliation(s)
- Ignacio Maeso
- Department of Zoology, University of Oxford, , Oxford, UK
| | | | | | | | | |
Collapse
|
43
|
Irvine SQ. Study of Cis-regulatory Elements in the Ascidian Ciona intestinalis. Curr Genomics 2013; 14:56-67. [PMID: 23997651 PMCID: PMC3580780 DOI: 10.2174/138920213804999192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 12/30/2012] [Accepted: 01/01/2013] [Indexed: 01/31/2023] Open
Abstract
The ascidian (sea squirt) C. intestinalis has become an important model organism for the study of cis-regulation. This is largely due to the technology that has been developed for assessing cis-regulatory activity through the use of transient reporter transgenes introduced into fertilized eggs. This technique allows the rapid and inexpensive testing of endogenous or altered DNA for regulatory activity in vivo. This review examines evidence that C. intestinaliscis-regulatory elements are located more closely to coding regions than in other model organisms. I go on to compare the organization of cis-regulatory elements and conserved non-coding sequences in Ciona, mammals, and other deuterostomes for three representative C.intestinalis genes, Pax6, FoxAa, and the DlxA-B cluster, along with homologs in the other species. These comparisons point out some of the similarities and differences between cis-regulatory elements and their study in the various model organisms. Finally, I provide illustrations of how C. intestinalis lends itself to detailed study of the structure of cis-regulatory elements, which have led, and promise to continue to lead, to important insights into the fundamentals of transcriptional regulation.
Collapse
Affiliation(s)
- Steven Q Irvine
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| |
Collapse
|
44
|
MacDonald RB, Pollack JN, Debiais-Thibaud M, Heude E, Talbot JC, Ekker M. The ascl1a and dlx genes have a regulatory role in the development of GABAergic interneurons in the zebrafish diencephalon. Dev Biol 2013; 381:276-85. [PMID: 23747543 DOI: 10.1016/j.ydbio.2013.05.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 05/08/2013] [Accepted: 05/25/2013] [Indexed: 11/28/2022]
Abstract
During development of the mouse forebrain interneurons, the Dlx genes play a key role in a gene regulatory network (GRN) that leads to the GABAergic phenotype. Here, we have examined the regulatory relationships between the ascl1a, dlx, and gad1b genes in the zebrafish forebrain. Expression of ascl1a overlaps with dlx1a in the telencephalon and diencephalon during early forebrain development. The loss of Ascl1a function results in a loss of dlx expression, and subsequent losses of dlx5a and gad1b expression in the diencephalic prethalamus and hypothalamus. Loss of Dlx1a and Dlx2a function, and, to a lesser extent, of Dlx5a and Dlx6a, impairs gad1b expression in the prethalamus and hypothalamus. We conclude that dlx1a/2a act downstream of ascl1a but upstream of dlx5a/dlx6a and gad1b to activate GABAergic specification. This pathway is conserved in the diencephalon, but has diverged between mammals and teleosts in the telencephalon.
Collapse
Affiliation(s)
- Ryan B MacDonald
- Center for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, ON, Canada, K1N 6N5
| | | | | | | | | | | |
Collapse
|
45
|
Compagnucci C, Debiais-Thibaud M, Coolen M, Fish J, Griffin JN, Bertocchini F, Minoux M, Rijli FM, Borday-Birraux V, Casane D, Mazan S, Depew MJ. Pattern and polarity in the development and evolution of the gnathostome jaw: both conservation and heterotopy in the branchial arches of the shark, Scyliorhinus canicula. Dev Biol 2013; 377:428-48. [PMID: 23473983 DOI: 10.1016/j.ydbio.2013.02.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 01/26/2013] [Accepted: 02/18/2013] [Indexed: 10/27/2022]
Abstract
The acquisition of jaws constitutes a landmark event in vertebrate evolution, one that in large part potentiated their success and diversification. Jaw development and patterning involves an intricate spatiotemporal series of reciprocal inductive and responsive interactions between the cephalic epithelia and the cranial neural crest (CNC) and cephalic mesodermal mesenchyme. The coordinated regulation of these interactions is critical for both the ontogenetic registration of the jaws and the evolutionary elaboration of variable jaw morphologies and designs. Current models of jaw development and evolution have been built on molecular and cellular evidence gathered mostly in amniotes such as mice, chicks and humans, and augmented by a much smaller body of work on the zebrafish. These have been partnered by essential work attempting to understand the origins of jaws that has focused on the jawless lamprey. Chondrichthyans (cartilaginous fish) are the most distant group to amniotes within extant gnathostomes, and comprise the crucial clade uniting amniotes and agnathans; yet despite their critical phylogenetic position, evidence of the molecular and cellular underpinnings of jaw development in chondrichthyans is still lacking. Recent advances in genome and molecular developmental biology of the lesser spotted dogfish shark, Scyliorhinus canicula, make it ideal for the molecular study of chondrichthyan jaw development. Here, following the 'Hinge and Caps' model of jaw development, we have investigated evidence of heterotopic (relative changes in position) and heterochronic (relative changes in timing) shifts in gene expression, relative to amniotes, in the jaw primordia of S. canicula embryos. We demonstrate the presence of clear proximo-distal polarity in gene expression patterns in the shark embryo, thus establishing a baseline molecular baüplan for branchial arch-derived jaw development and further validating the utility of the 'Hinge and Caps' model in comparative studies of jaw development and evolution. Moreover, we correlate gene expression patterns with the absence of a lambdoidal junction (formed where the maxillary first arch meets the frontonasal processes) in chondrichthyans, further highlighting the importance of this region for the development and evolution of jaw structure in advanced gnathostomes.
Collapse
Affiliation(s)
- Claudia Compagnucci
- Department of Craniofacial Development, King's College London, Floor 27, Guy's Hospital, London Bridge, London SE1 9RT, UK
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Kraus P, Sivakamasundari V, Lim SL, Xing X, Lipovich L, Lufkin T. Making sense of Dlx1 antisense RNA. Dev Biol 2013; 376:224-35. [PMID: 23415800 DOI: 10.1016/j.ydbio.2013.01.035] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 01/27/2013] [Accepted: 01/29/2013] [Indexed: 12/13/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been recently recognized as a major class of regulators in mammalian systems. LncRNAs function by diverse and heterogeneous mechanisms in gene regulation, and are key contributors to development, neurological disorders, and cancer. This emerging importance of lncRNAs, along with recent reports of a functional lncRNA encoded by the mouse Dlx5-Dlx6 locus, led us to interrogate the biological significance of another distal-less antisense lncRNA, the previously uncharacterized Dlx1 antisense (Dlx1as) transcript. We have functionally ablated this antisense RNA via a highly customized gene targeting approach in vivo. Mice devoid of Dlx1as RNA are viable and fertile, and display a mild skeletal and neurological phenotype reminiscent of a Dlx1 gain-of function phenotype, suggesting a role for this non-coding antisense RNA in modulating Dlx1 transcript levels and stability. The reciprocal relationship between Dlx1as and Dlx1 places this sense-antisense pair into a growing class of mammalian lncRNA-mRNA pairs characterized by inverse regulation.
Collapse
Affiliation(s)
- Petra Kraus
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | | | | | | | | | | |
Collapse
|
47
|
Fujimoto S, Oisi Y, Kuraku S, Ota KG, Kuratani S. Non-parsimonious evolution of hagfish Dlx genes. BMC Evol Biol 2013; 13:15. [PMID: 23331926 PMCID: PMC3552724 DOI: 10.1186/1471-2148-13-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 01/11/2013] [Indexed: 11/28/2022] Open
Abstract
Background The number of members of the Dlx gene family increased during the two rounds of whole-genome duplication that occurred in the common ancestor of the vertebrates. Because the Dlx genes are involved in the development of the cranial skeleton, brain, and sensory organs, their expression patterns have been analysed in various organisms in the context of evolutionary developmental biology. Six Dlx genes have been isolated in the lampreys, a group of living jawless vertebrates (cyclostomes), and their expression patterns analysed. However, little is known about the Dlx genes in the hagfish, the other cyclostome group, mainly because the embryological analysis of this animal is difficult. Results To identify the hagfish Dlx genes and describe their expression patterns, we cloned the cDNA from embryos of the Japanese inshore hagfish Eptatretus burgeri. Our results show that the hagfish has at least six Dlx genes and one pseudogene. In a phylogenetic analysis, the hagfish Dlx genes and those of the lampreys tended to be excluded from the clade of the gnathostome Dlx genes. In several cases, the lamprey Dlx genes clustered with the clade consisting of two hagfish genes, suggesting that independent gene duplications have occurred in the hagfish lineage. Analysis of the expression of these genes showed distinctive overlapping expression patterns in the cranial mesenchymal cells and the inner ear. Conclusions Independent duplication, pseudogenization, and loss of the Dlx genes probably occurred in the hagfish lineage after its split from the other vertebrate lineages. This pattern is reminiscent of the non-parsimonious evolution of its morphological traits, including its inner ear and vertebrae, which indicate that this group is an early-branching lineage that diverged before those characters evolved.
Collapse
Affiliation(s)
- Satoko Fujimoto
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | | | | | | | | |
Collapse
|
48
|
Takechi M, Adachi N, Hirai T, Kuratani S, Kuraku S. The Dlx genes as clues to vertebrate genomics and craniofacial evolution. Semin Cell Dev Biol 2013; 24:110-8. [PMID: 23291259 DOI: 10.1016/j.semcdb.2012.12.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 12/25/2012] [Indexed: 11/25/2022]
Abstract
The group of Dlx genes belongs to the homeobox-containing superfamily, and its members are involved in various morphogenetic processes. In vertebrate genomes, Dlx genes exist as multiple paralogues generated by tandem duplication followed by whole genome duplications. In this review, we provide an overview of the Dlx gene phylogeny with an emphasis on the chordate lineage. Referring to the Dlx gene repertoire, we discuss the establishment and conservation of the nested expression patterns of the Dlx genes in craniofacial development. Despite the accumulating genomic sequence resources in diverse vertebrates, embryological analyses of Dlx gene expression and function remain limited in terms of species diversity. By supplementing our original analysis of shark embryos with previous data from other osteichthyans, such as mice and zebrafish, we support the previous speculation that the nested Dlx expression in the pharyngeal arch is likely a shared feature among all the extant jawed vertebrates. Here, we highlight several hitherto unaddressed issues regarding the evolution and function of Dlx genes, with special reference to the craniofacial development of vertebrates.
Collapse
Affiliation(s)
- Masaki Takechi
- Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe 650-0047, Japan
| | | | | | | | | |
Collapse
|
49
|
The Rb/E2F pathway modulates neurogenesis through direct regulation of the Dlx1/Dlx2 bigene cluster. J Neurosci 2012; 32:8219-30. [PMID: 22699903 DOI: 10.1523/jneurosci.1344-12.2012] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
During brain morphogenesis, the mechanisms through which the cell cycle machinery integrates with differentiation signals remain elusive. Here we show that the Rb/E2F pathway regulates key aspects of differentiation and migration through direct control of the Dlx1 and Dlx2 homeodomain proteins, required for interneuron specification. Rb deficiency results in a dramatic reduction of Dlx1 and Dlx2 gene expression manifested by loss of interneuron subtypes and severe migration defects in the mouse brain. The Rb/E2F pathway modulates Dlx1/Dlx2 regulation through direct interaction with a Dlx forebrain-specific enhancer, I12b, and the Dlx1/Dlx2 proximal promoter regions, through repressor E2F sites both in vitro and in vivo. In the absence of Rb, we demonstrate that repressor E2Fs inhibit Dlx transcription at the Dlx1/Dlx2 promoters and Dlx1/2-I12b enhancer to suppress differentiation. Our findings support a model whereby the cell cycle machinery not only controls cell division but also modulates neuronal differentiation and migration through direct regulation of the Dlx1/Dlx2 bigene cluster during embryonic development.
Collapse
|
50
|
Sumiyama K, Miyake T, Grimwood J, Stuart A, Dickson M, Schmutz J, Ruddle FH, Myers RM, Amemiya CT. Theria-specific homeodomain and cis-regulatory element evolution of the Dlx3-4 bigene cluster in 12 different mammalian species. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2012; 318:639-50. [PMID: 22951979 DOI: 10.1002/jez.b.22469] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/06/2012] [Accepted: 07/10/2012] [Indexed: 11/11/2022]
Abstract
The mammalian Dlx3 and Dlx4 genes are configured as a bigene cluster, and their respective expression patterns are controlled temporally and spatially by cis-elements that largely reside within the intergenic region of the cluster. Previous work revealed that there are conspicuously conserved elements within the intergenic region of the Dlx3-4 bigene clusters of mouse and human. In this paper we have extended these analyses to include 12 additional mammalian taxa (including a marsupial and a monotreme) in order to better define the nature and molecular evolutionary trends of the coding and non-coding functional elements among morphologically divergent mammals. Dlx3-4 regions were fully sequenced from 12 divergent taxa of interest. We identified three theria-specific amino acid replacements in homeodomain of Dlx4 gene that functions in placenta. Sequence analyses of constrained nucleotide sites in the intergenic non-coding region showed that many of the intergenic conserved elements are highly conserved and have evolved slowly within the mammals. In contrast, a branchial arch/craniofacial enhancer I37-2 exhibited accelerated evolution at the branch between the monotreme and therian common ancestor despite being highly conserved among therian species. Functional analysis of I37-2 in transgenic mice has shown that the equivalent region of the platypus fails to drive transcriptional activity in branchial arches. These observations, taken together with our molecular evolutionary data, suggest that theria-specific episodic changes in the I37-2 element may have contributed to craniofacial innovation at the base of the mammalian lineage.
Collapse
Affiliation(s)
- Kenta Sumiyama
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|