1
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Leyva-Díaz E. CUT homeobox genes: transcriptional regulation of neuronal specification and beyond. Front Cell Neurosci 2023; 17:1233830. [PMID: 37744879 PMCID: PMC10515288 DOI: 10.3389/fncel.2023.1233830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
CUT homeobox genes represent a captivating gene class fulfilling critical functions in the development and maintenance of multiple cell types across a wide range of organisms. They belong to the larger group of homeobox genes, which encode transcription factors responsible for regulating gene expression patterns during development. CUT homeobox genes exhibit two distinct and conserved DNA binding domains, a homeodomain accompanied by one or more CUT domains. Numerous studies have shown the involvement of CUT homeobox genes in diverse developmental processes such as body axis formation, organogenesis, tissue patterning and neuronal specification. They govern these processes by exerting control over gene expression through their transcriptional regulatory activities, which they accomplish by a combination of classic and unconventional interactions with the DNA. Intriguingly, apart from their roles as transcriptional regulators, they also serve as accessory factors in DNA repair pathways through protein-protein interactions. They are highly conserved across species, highlighting their fundamental importance in developmental biology. Remarkably, evolutionary analysis has revealed that CUT homeobox genes have experienced an extraordinary degree of rearrangements and diversification compared to other classes of homeobox genes, including the emergence of a novel gene family in vertebrates. Investigating the functions and regulatory networks of CUT homeobox genes provides significant understanding into the molecular mechanisms underlying embryonic development and tissue homeostasis. Furthermore, aberrant expression or mutations in CUT homeobox genes have been associated with various human diseases, highlighting their relevance beyond developmental processes. This review will overview the well known roles of CUT homeobox genes in nervous system development, as well as their functions in other tissues across phylogeny.
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2
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The emerging role of the sympathetic nervous system in skeletal muscle motor innervation and sarcopenia. Ageing Res Rev 2021; 67:101305. [PMID: 33610815 DOI: 10.1016/j.arr.2021.101305] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/06/2021] [Accepted: 02/15/2021] [Indexed: 12/30/2022]
Abstract
Examining neural etiologic factors'role in the decline of neuromuscular function with aging is essential to our understanding of the mechanisms underlying sarcopenia, the age-dependent decline in muscle mass, force and power. Innervation of the skeletal muscle by both motor and sympathetic axons has been established, igniting interest in determining how the sympathetic nervous system (SNS) affect skeletal muscle composition and function throughout the lifetime. Selective expression of the heart and neural crest derivative 2 gene in peripheral SNs increases muscle mass and force regulating skeletal muscle sympathetic and motor innervation; improving acetylcholine receptor stability and NMJ transmission; preventing inflammation and myofibrillar protein degradation; increasing autophagy; and probably enhancing protein synthesis. Elucidating the role of central SNs will help to define the coordinated response of the visceral and neuromuscular system to physiological and pathological challenges across ages. This review discusses the following questions: (1) Does the SNS regulate skeletal muscle motor innervation? (2) Does the SNS regulate presynaptic and postsynaptic neuromuscular junction (NMJ) structure and function? (3) Does sympathetic neuron (SN) regulation of NMJ transmission decline with aging? (4) Does maintenance of SNs attenuate aging sarcopenia? and (5) Do central SN group relays influence sympathetic and motor muscle innervation?
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3
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Rodrigues ACZ, Wang ZM, Messi ML, Bonilla HJ, Liu L, Freeman WM, Delbono O. Heart and neural crest derivative 2-induced preservation of sympathetic neurons attenuates sarcopenia with aging. J Cachexia Sarcopenia Muscle 2021; 12:91-108. [PMID: 33258279 PMCID: PMC7890150 DOI: 10.1002/jcsm.12644] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 10/02/2020] [Accepted: 10/12/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Sarcopenia, or age-dependent decline in muscle force and power, impairs mobility, increasing the risk of falls, institutionalization, co-morbidity, and premature death. The discovery of adrenoceptors, which mediate the effects of the sympathetic nervous system (SNS) neurotransmitter norepinephrine on specific tissues, sparked the development of sympathomimetics that have profound influence on skeletal muscle mass. However, chronic administration has serious side effects that preclude their use for muscle-wasting conditions. Interventions that can adjust neurotransmitter release to changing physiological demands depend on understanding how the SNS affects neuromuscular transmission, muscle motor innervation, and muscle mass. METHODS We examined age-dependent expression of the heart and neural crest derivative 2 (Hand2), a critical transcription factor for SN maintenance, and we tested the possibility that inducing its expression exclusively in sympathetic neurons (SN) will prevent (i) motor denervation, (ii) impaired neuromuscular junction (NMJ) transmission, and (iii) loss of muscle mass and function in old mice. To test this hypothesis, we delivered a viral vector carrying Hand2 expression or an empty vector exclusively in SNs by vein injection in 16-month-old C57BL/6 mice that were sacrificed 6 months later. Techniques include RNA-sequencing, real-time PCR, genomic DNA methylation, viral vector construct, tissue immunohistochemistry, immunoblot, confocal microscopy, electrophysiology, and in vivo mouse physical performance. RESULTS Hand2 expression declines throughout life, but inducing its expression increased (i) the number and size of SNs, (ii) muscle sympathetic innervation, (iii) muscle weight and force and whole-body strength, (iv) myofiber size but not muscle fibre-type composition, (v) NMJ transmission and nerve-evoked muscle force, and (vi) motor innervation in old mice. Additionally, the SN controls a set of genes to reduce inflammation and to promote transcription factor activity, cell signalling, and synapse in the skeletal muscle. Hand2 DNA methylation may contribute, at least partially, to gene silencing. CONCLUSIONS Selective expression of Hand2 in the mouse SNs from middle age through old age increases muscle mass and force by (i) regulating skeletal muscle sympathetic and motor innervation; (ii) improving acetylcholine receptor stability and NMJ transmission; (iii) preventing inflammation and myofibrillar protein degradation; (iv) increasing autophagy; and (v) probably enhancing protein synthesis.
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Affiliation(s)
- Anna Carolina Zaia Rodrigues
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Neuroscience Program, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Zhong-Min Wang
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - María Laura Messi
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Henry Jacob Bonilla
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Liang Liu
- Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | - Osvaldo Delbono
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Neuroscience Program, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Sticht Center for Healthy Aging and Alzheimer's Prevention, Wake Forest School of Medicine, Winston-Salem, NC, USA
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4
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Visualizing the Synaptic and Cellular Ultrastructure in Neurons Differentiated from Human Induced Neural Stem Cells-An Optimized Protocol. Int J Mol Sci 2020; 21:ijms21051708. [PMID: 32131546 PMCID: PMC7084184 DOI: 10.3390/ijms21051708] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/23/2020] [Accepted: 02/28/2020] [Indexed: 11/29/2022] Open
Abstract
The size of the synaptic subcomponents falls below the limits of visible light microscopy. Despite new developments in advanced microscopy techniques, the resolution of transmission electron microscopy (TEM) remains unsurpassed. The requirements of tissue preservation are very high, and human post mortem material often does not offer adequate quality. However, new reprogramming techniques that generate human neurons in vitro provide samples that can easily fulfill these requirements. The objective of this study was to identify the culture technique with the best ultrastructural preservation in combination with the best embedding and contrasting technique for visualizing neuronal elements. Two induced neural stem cell lines derived from healthy control subjects underwent differentiation either adherent on glass coverslips, embedded in a droplet of highly concentrated Matrigel, or as a compact neurosphere. Afterward, they were fixed using a combination of glutaraldehyde (GA) and paraformaldehyde (PFA) followed by three approaches (standard stain, Ruthenium red stain, high contrast en-bloc stain) using different combinations of membrane enhancing and contrasting steps before ultrathin sectioning and imaging by TEM. The compact free-floating neurospheres exhibited the best ultrastructural preservation. High-contrast en-bloc stain offered particularly sharp staining of membrane structures and the highest quality visualization of neuronal structures. In conclusion, compact neurospheres growing under free-floating conditions in combination with a high contrast en-bloc staining protocol, offer the optimal preservation and contrast with a particular focus on visualizing membrane structures as required for analyzing synaptic structures.
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5
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Homan AE, Meriney SD. Active zone structure-function relationships at the neuromuscular junction. Synapse 2018; 72:e22057. [PMID: 29956366 DOI: 10.1002/syn.22057] [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: 04/16/2018] [Revised: 06/15/2018] [Accepted: 06/26/2018] [Indexed: 11/08/2022]
Abstract
The impact of presynaptic transmitter release site organization on synaptic function has been a vibrant area of research for synaptic physiologists. Because there is a highly nonlinear relationship between presynaptic calcium influx and subsequent neurotransmitter release at synapses, the organization and density of calcium sources (voltage-gated calcium channels [VGCCs]) relative to calcium sensors located on synaptic vesicles is predicted to play a major role in shaping the dynamics of neurotransmitter release at a synapse. Here we review the history of structure-function studies within transmitter release sites at the neuromuscular junction across three model preparations in an effort to discern the relationship between VGCC organization and synaptic function, and whether that organizational structure imparts evolutionary advantages for each species.
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Affiliation(s)
- Anne E Homan
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Stephen D Meriney
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania
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6
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Wang A, Wang J, Liu Y, Zhou Y. Mechanisms of Long Non-Coding RNAs in the Assembly and Plasticity of Neural Circuitry. Front Neural Circuits 2017; 11:76. [PMID: 29109677 PMCID: PMC5660110 DOI: 10.3389/fncir.2017.00076] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/28/2017] [Indexed: 12/31/2022] Open
Abstract
The mechanisms underlying development processes and functional dynamics of neural circuits are far from understood. Long non-coding RNAs (lncRNAs) have emerged as essential players in defining identities of neural cells, and in modulating neural activities. In this review, we summarized latest advances concerning roles and mechanisms of lncRNAs in assembly, maintenance and plasticity of neural circuitry, as well as lncRNAs' implications in neurological disorders. We also discussed technical advances and challenges in studying functions and mechanisms of lncRNAs in neural circuitry. Finally, we proposed that lncRNA studies would advance our understanding on how neural circuits develop and function in physiology and disease conditions.
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Affiliation(s)
- Andi Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Junbao Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ying Liu
- Medical Research Institute, Wuhan University, Wuhan, China
| | - Yan Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.,Medical Research Institute, Wuhan University, Wuhan, China
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7
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Zhou L, McInnes J, Wierda K, Holt M, Herrmann AG, Jackson RJ, Wang YC, Swerts J, Beyens J, Miskiewicz K, Vilain S, Dewachter I, Moechars D, De Strooper B, Spires-Jones TL, De Wit J, Verstreken P. Tau association with synaptic vesicles causes presynaptic dysfunction. Nat Commun 2017; 8:15295. [PMID: 28492240 PMCID: PMC5437271 DOI: 10.1038/ncomms15295] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 03/17/2017] [Indexed: 12/18/2022] Open
Abstract
Tau is implicated in more than 20 neurodegenerative diseases, including Alzheimer's disease. Under pathological conditions, Tau dissociates from axonal microtubules and missorts to pre- and postsynaptic terminals. Patients suffer from early synaptic dysfunction prior to Tau aggregate formation, but the underlying mechanism is unclear. Here we show that pathogenic Tau binds to synaptic vesicles via its N-terminal domain and interferes with presynaptic functions, including synaptic vesicle mobility and release rate, lowering neurotransmission in fly and rat neurons. Pathological Tau mutants lacking the vesicle binding domain still localize to the presynaptic compartment but do not impair synaptic function in fly neurons. Moreover, an exogenously applied membrane-permeable peptide that competes for Tau-vesicle binding suppresses Tau-induced synaptic toxicity in rat neurons. Our work uncovers a presynaptic role of Tau that may be part of the early pathology in various Tauopathies and could be exploited therapeutically.
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Affiliation(s)
- Lujia Zhou
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- KU Leuven, Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), Leuven 3000, Belgium
| | - Joseph McInnes
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- KU Leuven, Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), Leuven 3000, Belgium
| | - Keimpe Wierda
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- KU Leuven, Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), Leuven 3000, Belgium
| | - Matthew Holt
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- KU Leuven, Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), Leuven 3000, Belgium
| | - Abigail G. Herrmann
- University of Edinburgh, Centre for Cognitive and Neural Systems, Center for Dementia Prevention and Euan MacDonald Centre, Edinburgh EH8 9JZ, UK
| | - Rosemary J. Jackson
- University of Edinburgh, Centre for Cognitive and Neural Systems, Center for Dementia Prevention and Euan MacDonald Centre, Edinburgh EH8 9JZ, UK
| | - Yu-Chun Wang
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- KU Leuven, Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), Leuven 3000, Belgium
| | - Jef Swerts
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- KU Leuven, Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), Leuven 3000, Belgium
| | - Jelle Beyens
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- KU Leuven, Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), Leuven 3000, Belgium
| | - Katarzyna Miskiewicz
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- KU Leuven, Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), Leuven 3000, Belgium
| | - Sven Vilain
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- KU Leuven, Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), Leuven 3000, Belgium
| | - Ilse Dewachter
- Catholic University of Louvain, Alzheimer Dementia Group, Institute of Neuroscience, Brussels 1200, Belgium
- University of Hasselt, Biomedical Research Institute, Hasselt 3500, Belgium
| | - Diederik Moechars
- A Division of Janssen Pharmaceutica NV, Neuroscience Department, Janssen Research and Development, Beerse 2340, Belgium
| | - Bart De Strooper
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- KU Leuven, Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), Leuven 3000, Belgium
| | - Tara L. Spires-Jones
- University of Edinburgh, Centre for Cognitive and Neural Systems, Center for Dementia Prevention and Euan MacDonald Centre, Edinburgh EH8 9JZ, UK
| | - Joris De Wit
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- KU Leuven, Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), Leuven 3000, Belgium
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- KU Leuven, Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), Leuven 3000, Belgium
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8
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Piccolo paralogs and orthologs display conserved patterns of alternative splicing within the C2A and C2B domains. Genes Genomics 2016. [DOI: 10.1007/s13258-015-0383-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Sancho-Knapik S, Guillén N, Osada J. Cloning and expression of hepatic synaptotagmin 1 in mouse. Gene 2015; 562:236-43. [PMID: 25735570 DOI: 10.1016/j.gene.2015.02.074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 02/17/2015] [Accepted: 02/27/2015] [Indexed: 11/29/2022]
Abstract
Mouse hepatic synaptotagmin 1 (SYT1) cDNA was cloned, characterized and compared to the brain one. The hepatic transcript was 1807 bp in length, smaller than the brain, and only encoded by 9 of 11 gene exons. In this regard, 5'-and 3'-untranslated regions were 66 and 476 bp, respectively; the open reading frame of 1266 bp codified for a protein of 421 amino acids, identical to the brain, with a predicted molecular mass of 47.4 kDa and highly conserved across different species. Immunoblotting of protein showed two isoforms of higher molecular masses than the theoretical prediction based on amino acid sequence suggesting posttranslational modifications. Subcellular distribution of protein isoforms corresponded to plasma membrane, lysosomes and microsomes and was identical between the brain and liver. Nonetheless, the highest molecular weight isoform was smaller in the liver, irrespective of subcellular location. Quantitative mRNA tissue distribution showed that it was widely expressed and that the highest values corresponded to the brain, followed by the liver, spleen, abdominal fat, intestine and skeletal muscle. These findings indicate tissue-specific splicing of the gene and posttranslational modification and the variation in expression in the different tissues might suggest a different requirement of SYT1 for the specific function in each organ.
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Affiliation(s)
- Sara Sancho-Knapik
- Departamento Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón (IIS), Universidad de Zaragoza, Spain
| | - Natalia Guillén
- Departamento de Toxicología, Facultad de Veterinaria, Universidad de Zaragoza, Spain
| | - Jesús Osada
- Departamento Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón (IIS), Universidad de Zaragoza, Spain; CIBER de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Spain.
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10
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Ha T, Swanson D, Larouche M, Glenn R, Weeden D, Zhang P, Hamre K, Langston M, Phillips C, Song M, Ouyang Z, Chesler E, Duvvurru S, Yordanova R, Cui Y, Campbell K, Ricker G, Phillips C, Homayouni R, Goldowitz D. CbGRiTS: cerebellar gene regulation in time and space. Dev Biol 2014; 397:18-30. [PMID: 25446528 DOI: 10.1016/j.ydbio.2014.09.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 08/23/2014] [Accepted: 09/27/2014] [Indexed: 01/09/2023]
Abstract
The mammalian CNS is one of the most complex biological systems to understand at the molecular level. The temporal information from time series transcriptome analysis can serve as a potent source of associative information between developmental processes and regulatory genes. Here, we introduce a new transcriptome database called, Cerebellar Gene Regulation in Time and Space (CbGRiTS). This dataset is populated with transcriptome data across embryonic and postnatal development from two standard mouse strains, C57BL/6J and DBA/2J, several recombinant inbred lines and cerebellar mutant strains. Users can evaluate expression profiles across cerebellar development in a deep time series with graphical interfaces for data exploration and link-out to anatomical expression databases. We present three analytical approaches that take advantage of specific aspects of the time series for transcriptome analysis. We demonstrate the use of CbGRiTS dataset as a community resource to explore patterns of gene expression and develop hypotheses concerning gene regulatory networks in brain development.
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Affiliation(s)
- Thomas Ha
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - Douglas Swanson
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - Matt Larouche
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - Randy Glenn
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - Dave Weeden
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - Peter Zhang
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - Kristin Hamre
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Michael Langston
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, USA
| | - Charles Phillips
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, USA
| | - Mingzhou Song
- Department of Computer Science, New Mexico State University, Las Cruces, NM, USA
| | - Zhengyu Ouyang
- Department of Computer Science, New Mexico State University, Las Cruces, NM, USA
| | | | | | | | - Yan Cui
- Department of Molecular Science, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kate Campbell
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - Greg Ricker
- Department of Biology, Bowdoin College, Brunswick, ME, USA
| | - Carey Phillips
- Department of Biology, Bowdoin College, Brunswick, ME, USA
| | - Ramin Homayouni
- Bioinformatics Program, Department of Biology, University of Memphis, Memphis, TN, USA
| | - Dan Goldowitz
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada V5Z 4H4.
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11
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Hadley D, Wu ZL, Kao C, Kini A, Mohamed-Hadley A, Thomas K, Vazquez L, Qiu H, Mentch F, Pellegrino R, Kim C, Connolly J, Glessner J, Hakonarson H. The impact of the metabotropic glutamate receptor and other gene family interaction networks on autism. Nat Commun 2014; 5:4074. [PMID: 24927284 PMCID: PMC4059929 DOI: 10.1038/ncomms5074] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 05/07/2014] [Indexed: 01/19/2023] Open
Abstract
Although multiple reports show that defective genetic networks underlie the aetiology
of autism, few have translated into pharmacotherapeutic opportunities. Since drugs
compete with endogenous small molecules for protein binding, many successful drugs
target large gene families with multiple drug binding sites. Here we search for
defective gene family interaction networks (GFINs) in 6,742 patients with the ASDs
relative to 12,544 neurologically normal controls, to find potentially druggable
genetic targets. We find significant enrichment of structural defects
(P≤2.40E−09, 1.8-fold enrichment) in the metabotropic
glutamate receptor (GRM) GFIN, previously observed to impact attention deficit
hyperactivity disorder (ADHD) and schizophrenia. Also, the MXD-MYC-MAX network of genes, previously implicated in cancer, is
significantly enriched (P≤3.83E−23, 2.5-fold
enrichment), as is the calmodulin 1
(CALM1) gene interaction
network (P≤4.16E−04, 14.4-fold enrichment), which
regulates voltage-independent calcium-activated action potentials at the neuronal
synapse. We find that multiple defective gene family interactions underlie autism,
presenting new translational opportunities to explore for therapeutic
interventions. The autism spectrum disorders are complex genetic traits characterized
by various neurodevelopmental deficits. Here, the authors analyse defective gene family
interaction networks in autism cases and healthy controls and identify potential gene
family interactions that may contribute to autism aetiology.
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Affiliation(s)
- Dexter Hadley
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Zhi-Liang Wu
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Charlly Kao
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Akshata Kini
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Alisha Mohamed-Hadley
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Kelly Thomas
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Lyam Vazquez
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Haijun Qiu
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Frank Mentch
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Renata Pellegrino
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Cecilia Kim
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - John Connolly
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | | | - Joseph Glessner
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Hakon Hakonarson
- 1] The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA [2] Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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12
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Ahmed M, Liang P. Study of Modern Human Evolution via Comparative Analysis with the Neanderthal Genome. Genomics Inform 2013; 11:230-8. [PMID: 24465235 PMCID: PMC3897851 DOI: 10.5808/gi.2013.11.4.230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 11/20/2013] [Accepted: 11/21/2013] [Indexed: 12/11/2022] Open
Abstract
Many other human species appeared in evolution in the last 6 million years that have not been able to survive to modern times and are broadly known as archaic humans, as opposed to the extant modern humans. It has always been considered fascinating to compare the modern human genome with that of archaic humans to identify modern human-specific sequence variants and figure out those that made modern humans different from their predecessors or cousin species. Neanderthals are the latest humans to become extinct, and many factors made them the best representatives of archaic humans. Even though a number of comparisons have been made sporadically between Neanderthals and modern humans, mostly following a candidate gene approach, the major breakthrough took place with the sequencing of the Neanderthal genome. The initial genome-wide comparison, based on the first draft of the Neanderthal genome, has generated some interesting inferences regarding variations in functional elements that are not shared by the two species and the debated admixture question. However, there are certain other genetic elements that were not included or included at a smaller scale in those studies, and they should be compared comprehensively to better understand the molecular make-up of modern humans and their phenotypic characteristics. Besides briefly discussing the important outcomes of the comparative analyses made so far between modern humans and Neanderthals, we propose that future comparative studies may include retrotransposons, pseudogenes, and conserved non-coding regions, all of which might have played significant roles during the evolution of modern humans.
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Affiliation(s)
- Musaddeque Ahmed
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
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Georgi B, Voight BF, Bućan M. From mouse to human: evolutionary genomics analysis of human orthologs of essential genes. PLoS Genet 2013; 9:e1003484. [PMID: 23675308 PMCID: PMC3649967 DOI: 10.1371/journal.pgen.1003484] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/15/2013] [Indexed: 02/01/2023] Open
Abstract
Understanding the core set of genes that are necessary for basic developmental functions is one of the central goals in biology. Studies in model organisms identified a significant fraction of essential genes through the analysis of null-mutations that lead to lethality. Recent large-scale next-generation sequencing efforts have provided unprecedented data on genetic variation in human. However, evolutionary and genomic characteristics of human essential genes have never been directly studied on a genome-wide scale. Here we use detailed phenotypic resources available for the mouse and deep genomics sequencing data from human populations to characterize patterns of genetic variation and mutational burden in a set of 2,472 human orthologs of known essential genes in the mouse. Consistent with the action of strong, purifying selection, these genes exhibit comparatively reduced levels of sequence variation, skew in allele frequency towards more rare, and exhibit increased conservation across the primate and rodent lineages relative to the remainder of genes in the genome. In individual genomes we observed ∼12 rare mutations within essential genes predicted to be damaging. Consistent with the hypothesis that mutations in essential genes are risk factors for neurodevelopmental disease, we show that de novo variants in patients with Autism Spectrum Disorder are more likely to occur in this collection of genes. While incomplete, our set of human orthologs shows characteristics fully consistent with essential function in human and thus provides a resource to inform and facilitate interpretation of sequence data in studies of human disease. Essential genes are necessary for fundamental processes in an organism and lead to pre- or neonatal lethality when disrupted. In this work, we characterize 2,472 human orthologs of mouse essential genes in terms of their evolutionary and population genetics properties using data from recent deep sequencing initiatives in human populations. We find a signature of strong, purifying selection and a reduced load of sequence variants within the putative essential genes when compared to a control-group of non-essential genes. We also show a significant enrichment of variants within essential genes across a set of four recent studies of de novo variants in patients with Autism Spectrum Disorder. Our results establish the catalogue of putative essential genes as an important resource for analysis and interpretation of sequencing studies for human disease.
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Affiliation(s)
- Benjamin Georgi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Benjamin F. Voight
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (MB); (BFV)
| | - Maja Bućan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (MB); (BFV)
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Regulation of gene expression during early neuronal differentiation: evidence for patterns conserved across neuron populations and vertebrate classes. Cell Tissue Res 2012; 348:1-27. [PMID: 22437873 DOI: 10.1007/s00441-012-1367-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 02/08/2012] [Indexed: 12/19/2022]
Abstract
Analysis of transcription factor function during neurogenesis has provided a huge amount of data on the generation and specification of diverse neuron populations in the central and peripheral nervous systems of vertebrates. However, an understanding of the induction of key neuron functions including electrical information processing and synaptic transmission lags seriously behind. Whereas pan-neuronal markers such as neurofilaments, neuron-specific tubulin and RNA-binding proteins have often been included in developmental analysis, the molecular players underlying electrical activity and transmitter release have been neglected in studies addressing gene expression during neuronal induction. Here, I summarize the evidence for a distinct accumulation pattern of mRNAs for synaptic proteins, a pattern that is delayed compared with pan-neuronal gene expression during neurogenesis. The conservation of this pattern across diverse avian and mammalian neuron populations suggests a common mechanism for the regulation of various sets of neuronal genes during initial neuronal differentiation. The co-regulation of genes coding for synaptic proteins from embryonic to postnatal development indicates that the expression of the players required for synaptic transmission shares common regulatory features. For the ion channels involved in neuronal electrical activity, such as voltage-gated sodium channels, the situation is less clear because of the lack of comparative studies early during neurogenesis. Transcription factors have been characterized that regulate the expression of synaptic proteins in vitro and in vivo. They currently do not explain the co-regulation of these genes across different neuron populations. The neuron-restrictive silencing factor NRSF/REST targets a large gene set, but not all of the genes coding for pan-neuronal, synaptic and ion channel proteins. The discrepancy between NRSF/REST loss-of-function and silencer-to-activator-switch studies leaves the full functional implications of this factor open. Together with microRNAs, splicing regulators, chromatin remodellers and an increasing list of transcriptional regulators, the factor is embedded in feedback circuits with the potential to orchestrate neuronal differentiation. The precise regulation of the coordinated expression of proteins underlying key neuronal functions by these circuits during neuronal induction is a major emerging topic.
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Abstract
The generation of individual neuron types in the nervous system is a multistep process whose endpoint is the expression of neuron type-specific batteries of terminal differentiation genes that determine the functional properties of a neuron. This review focuses on the regulatory mechanisms that are involved in controlling the terminally differentiated state of a neuron. I review several case studies from invertebrate and vertebrate nervous systems that reveal that many terminal differentiation features of a neuron are coregulated via terminal selector transcription factors that initiate and maintain terminal differentiation programs.
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Affiliation(s)
- Oliver Hobert
- Howard Hughes Medical Institute, New York, NY 10032, USA.
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Abstract
Understanding the evolutionary origins of behaviour is a central aim in the study of biology and may lead to insights into human disorders. Synaptic transmission is observed in a wide range of invertebrate and vertebrate organisms and underlies their behaviour. Proteomic studies of the molecular components of the highly complex mammalian postsynaptic machinery point to an ancestral molecular machinery in unicellular organisms--the protosynapse--that existed before the evolution of metazoans and neurons, and hence challenges existing views on the origins of the brain. The phylogeny of the molecular components of the synapse provides a new model for studying synapse diversity and complexity, and their implications for brain evolution.
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Liu R, Hannenhalli S, Bucan M. Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons. Genome Biol 2009; 10:R72. [PMID: 19570198 PMCID: PMC2728526 DOI: 10.1186/gb-2009-10-7-r72] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 06/11/2009] [Accepted: 07/01/2009] [Indexed: 12/19/2022] Open
Abstract
An integrative strategy of comparative genomics, experimental and computational approaches reveals aspects of a regulatory network controlling neuronal-specific expression in presynaptic neurons. Background Hundreds of proteins modulate neurotransmitter release and synaptic plasticity during neuronal development and in response to synaptic activity. The expression of genes in the pre- and post-synaptic neurons is under stringent spatio-temporal control, but the mechanism underlying the neuronal expression of these genes remains largely unknown. Results Using unbiased in vivo and in vitro screens, we characterized the cis elements regulating the Rab3A gene, which is expressed abundantly in presynaptic neurons. A set of identified regulatory elements of the Rab3A gene corresponded to the defined Rab3A multi-species conserved elements. In order to identify clusters of enriched transcription factor binding sites, for example, cis-regulatory modules, we analyzed intergenic multi-species conserved elements in the vicinity of nine presynaptic genes, including Rab3A, that are highly and specifically expressed in brain regions. Sixteen transcription factor binding motifs were over-represented in these multi-species conserved elements. Based on a combined occurrence for these enriched motifs, multi-species conserved elements in the vicinity of 107 previously identified presynaptic genes were scored and ranked. We then experimentally validated the scoring strategy by showing that 12 of 16 (75%) high-scoring multi-species conserved elements functioned as neuronal enhancers in a cell-based assay. Conclusions This work introduces an integrative strategy of comparative genomics, experimental, and computational approaches to reveal aspects of a regulatory network controlling neuronal-specific expression of genes in presynaptic neurons.
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Affiliation(s)
- Rui Liu
- Department of Genetics and Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
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Yanay C, Morpurgo N, Linial M. Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle. Genome Biol 2008; 9:R27. [PMID: 18257909 PMCID: PMC2374702 DOI: 10.1186/gb-2008-9-2-r27] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 12/06/2007] [Accepted: 02/07/2008] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The molecular components in synapses that are essential to the life cycle of synaptic vesicles are well characterized. Nonetheless, many aspects of synaptic processes, in particular how they relate to complex behaviour, remain elusive. The genomes of flies, mosquitoes, the honeybee and the beetle are now fully sequenced and span an evolutionary breadth of about 350 million years; this provides a unique opportunity to conduct a comparative genomics study of the synapse. RESULTS We compiled a list of 120 gene prototypes that comprise the core of presynaptic structures in insects. Insects lack several scaffolding proteins in the active zone, such as bassoon and piccollo, and the most abundant protein in the mammalian synaptic vesicle, namely synaptophysin. The pattern of evolution of synaptic protein complexes is analyzed. According to this analysis, the components of presynaptic complexes as well as proteins that take part in organelle biogenesis are tightly coordinated. Most synaptic proteins are involved in rich protein interaction networks. Overall, the number of interacting proteins and the degrees of sequence conservation between human and insects are closely correlated. Such a correlation holds for exocytotic but not for endocytotic proteins. CONCLUSION This comparative study of human with insects sheds light on the composition and assembly of protein complexes in the synapse. Specifically, the nature of the protein interaction graphs differentiate exocytotic from endocytotic proteins and suggest unique evolutionary constraints for each set. General principles in the design of proteins of the presynaptic site can be inferred from a comparative study of human and insect genomes.
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Affiliation(s)
- Chava Yanay
- Department of Biological Chemistry, Institute of Life Sciences, Givat Ram Campus, Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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St. Laurent G, Wahlestedt C. Noncoding RNAs: couplers of analog and digital information in nervous system function? Trends Neurosci 2007; 30:612-21. [DOI: 10.1016/j.tins.2007.10.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 10/03/2007] [Accepted: 10/04/2007] [Indexed: 12/14/2022]
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Craxton M. Evolutionary genomics of plant genes encoding N-terminal-TM-C2 domain proteins and the similar FAM62 genes and synaptotagmin genes of metazoans. BMC Genomics 2007; 8:259. [PMID: 17672888 PMCID: PMC1976326 DOI: 10.1186/1471-2164-8-259] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Accepted: 07/31/2007] [Indexed: 11/28/2022] Open
Abstract
Background Synaptotagmin genes are found in animal genomes and are known to function in the nervous system. Genes with a similar domain architecture as well as sequence similarity to synaptotagmin C2 domains have also been found in plant genomes. The plant genes share an additional region of sequence similarity with a group of animal genes named FAM62. FAM62 genes also have a similar domain architecture. Little is known about the functions of the plant genes and animal FAM62 genes. Indeed, many members of the large and diverse Syt gene family await functional characterization. Understanding the evolutionary relationships among these genes will help to realize the full implications of functional studies and lead to improved genome annotation. Results I collected and compared plant Syt-like sequences from the primary nucleotide sequence databases at NCBI. The collection comprises six groups of plant genes conserved in embryophytes: NTMC2Type1 to NTMC2Type6. I collected and compared metazoan FAM62 sequences and identified some similar sequences from other eukaryotic lineages. I found evidence of RNA editing and alternative splicing. I compared the intron patterns of Syt genes. I also compared Rabphilin and Doc2 genes. Conclusion Genes encoding proteins with N-terminal-transmembrane-C2 domain architectures resembling synaptotagmins, are widespread in eukaryotes. A collection of these genes is presented here. The collection provides a resource for studies of intron evolution. I have classified the collection into homologous gene families according to distinctive patterns of sequence conservation and intron position. The evolutionary histories of these gene families are traceable through the appearance of family members in different eukaryotic lineages. Assuming an intron-rich eukaryotic ancestor, the conserved intron patterns distinctive of individual gene families, indicate independent origins of Syt, FAM62 and NTMC2 genes. Resemblances among these large, multi-domain proteins are due not only to shared ancestry (homology) but also to convergent evolution (analogy). During the evolution of these gene families, duplications and other gene rearrangements affecting domain composition, have occurred along with sequence divergence, leading to complex family relationships with accordingly complex functional implications. The functional homologies and analogies among these genes remain to be established empirically.
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Affiliation(s)
- Molly Craxton
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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