1
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Aron L, Qiu C, Ngian ZK, Liang M, Drake D, Choi J, Fernandez MA, Roche P, Bunting EL, Lacey EK, Hamplova SE, Yuan M, Wolfe MS, Bennett DA, Lee EA, Yankner BA. A neurodegeneration checkpoint mediated by REST protects against the onset of Alzheimer's disease. Nat Commun 2023; 14:7030. [PMID: 37919281 PMCID: PMC10622455 DOI: 10.1038/s41467-023-42704-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 10/17/2023] [Indexed: 11/04/2023] Open
Abstract
Many aging individuals accumulate the pathology of Alzheimer's disease (AD) without evidence of cognitive decline. Here we describe an integrated neurodegeneration checkpoint response to early pathological changes that restricts further disease progression and preserves cognitive function. Checkpoint activation is mediated by the REST transcriptional repressor, which is induced in cognitively-intact aging humans and AD mouse models at the onset of amyloid β-protein (Aβ) deposition and tau accumulation. REST induction is mediated by the unfolded protein response together with β-catenin signaling. A consequence of this response is the targeting of REST to genes involved in key pathogenic pathways, resulting in downregulation of gamma secretase, tau kinases, and pro-apoptotic proteins. Deletion of REST in the 3xTg and J20 AD mouse models accelerates Aβ deposition and the accumulation of misfolded and phosphorylated tau, leading to neurodegeneration and cognitive decline. Conversely, viral-mediated overexpression of REST in the hippocampus suppresses Aβ and tau pathology. Thus, REST mediates a neurodegeneration checkpoint response with multiple molecular targets that may protect against the onset of AD.
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Affiliation(s)
- Liviu Aron
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Zhen Kai Ngian
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Marianna Liang
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Derek Drake
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jaejoon Choi
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Marty A Fernandez
- Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Perle Roche
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Emma L Bunting
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Ella K Lacey
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Sara E Hamplova
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Monlan Yuan
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Michael S Wolfe
- Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL60612, USA
| | - Eunjung A Lee
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Bruce A Yankner
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
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2
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Yamasaki Y, Lim YM, Minami R, Tsuda L. A splicing variant of Charlatan, a Drosophila REST-like molecule, preferentially localizes to axons. Biochem Biophys Res Commun 2021; 578:35-41. [PMID: 34536827 DOI: 10.1016/j.bbrc.2021.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 10/20/2022]
Abstract
Neuron-restrictive silencing factor (NRSF), also known as RE-1 silencing transcription factor (REST), has pivotal functions in many neuron-specific genes. Previous studies revealed that neuron-specific alternative splicing (AS) of REST produces divergent forms of REST variants and provides regulatory complexity in the nervous system. However, the biological significance of these variants in the regulation of neuronal activities remains to be clarified. Here, we revealed that Charlatan (Chn), a Drosophila REST-like molecule, is also regulated by neuron-specific AS. Neuron-specific AS produced six divergent variants of Chn proteins, one of which preferentially localized to axons. A small sequence of this variant was especially important for the axonal localization. Our data suggest that some variants have roles beyond the transcriptional regulation of neuronal activities.
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Affiliation(s)
- Yasutoyo Yamasaki
- National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
| | - Young-Mi Lim
- National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
| | - Ryunosuke Minami
- Department of Advanced Medical Science, Asahikawa Medical University, Japan
| | - Leo Tsuda
- National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan.
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3
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Ryan KC, Ashkavand Z, Sarasija S, Laboy JT, Samarakoon R, Norman KR. Increased mitochondrial calcium uptake and concomitant mitochondrial activity by presenilin loss promotes mTORC1 signaling to drive neurodegeneration. Aging Cell 2021; 20:e13472. [PMID: 34499406 PMCID: PMC8520713 DOI: 10.1111/acel.13472] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/21/2021] [Accepted: 08/05/2021] [Indexed: 12/21/2022] Open
Abstract
Metabolic dysfunction and protein aggregation are common characteristics that occur in age‐related neurodegenerative disease. However, the mechanisms underlying these abnormalities remain poorly understood. We have found that mutations in the gene encoding presenilin in Caenorhabditis elegans, sel‐12, results in elevated mitochondrial activity that drives oxidative stress and neuronal dysfunction. Mutations in the human presenilin genes are the primary cause of familial Alzheimer's disease. Here, we demonstrate that loss of SEL‐12/presenilin results in the hyperactivation of the mTORC1 pathway. This hyperactivation is caused by elevated mitochondrial calcium influx and, likely, the associated increase in mitochondrial activity. Reducing mTORC1 activity improves proteostasis defects and neurodegenerative phenotypes associated with loss of SEL‐12 function. Consistent with high mTORC1 activity, we find that SEL‐12 loss reduces autophagosome formation, and this reduction is prevented by limiting mitochondrial calcium uptake. Moreover, the improvements of proteostasis and neuronal defects in sel‐12 mutants due to mTORC1 inhibition require the induction of autophagy. These results indicate that mTORC1 hyperactivation exacerbates the defects in proteostasis and neuronal function in sel‐12 mutants and demonstrate a critical role of presenilin in promoting neuronal health.
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Affiliation(s)
- Kerry C. Ryan
- Department of Regenerative and Cancer Cell Biology Albany Medical College Albany New York USA
| | - Zahra Ashkavand
- Department of Regenerative and Cancer Cell Biology Albany Medical College Albany New York USA
| | - Shaarika Sarasija
- Department of Regenerative and Cancer Cell Biology Albany Medical College Albany New York USA
| | - Jocelyn T. Laboy
- Department of Regenerative and Cancer Cell Biology Albany Medical College Albany New York USA
| | - Rohan Samarakoon
- Department of Regenerative and Cancer Cell Biology Albany Medical College Albany New York USA
| | - Kenneth R. Norman
- Department of Regenerative and Cancer Cell Biology Albany Medical College Albany New York USA
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4
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Chamberlin HM, Jain IM, Corchado-Sonera M, Kelley LH, Sharanya D, Jama A, Pabla R, Dawes AT, Gupta BP. Evolution of Transcriptional Repressors Impacts Caenorhabditis Vulval Development. Mol Biol Evol 2021; 37:1350-1361. [PMID: 31960924 DOI: 10.1093/molbev/msaa009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Comparative genomic sequence analysis has found that the genes for many chromatin-associated proteins are poorly conserved, but the biological consequences of these sequence changes are not understood. Here, we show that four genes identified for an Inappropriate Vulval cell Proliferation (ivp) phenotype in the nematode Caenorhabditis briggsae exhibit distinct functions and genetic interactions when compared with their orthologs in C. elegans. Specifically, we show that the four C. briggsae ivp genes encode the noncanonical histone HTZ-1/H2A.z and three nematode-specific proteins predicted to function in the nucleus. The mutants exhibit ectopic vulval precursor cell proliferation (the multivulva [Muv] phenotype) due to inappropriate expression of the lin-3/EGF gene, and RNAseq analysis suggests a broad role for these ivp genes in transcriptional repression. Importantly, although the C. briggsae phenotypes have parallels with those seen in the C. elegans synMuv system, except for the highly conserved HTZ-1/H2A.z, comparable mutations in C. elegans ivp orthologs do not exhibit synMuv gene interactions or phenotypes. These results demonstrate the evolutionary changes that can underlie conserved biological outputs and argue that proteins critical to repress inappropriate expression from the genome participate in a rapidly evolving functional landscape.
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Affiliation(s)
| | - Ish M Jain
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | | | - Leanne H Kelley
- Department of Molecular Genetics, Ohio State University, Columbus, OH
| | - Devika Sharanya
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Abdulrahman Jama
- Department of Molecular Genetics, Ohio State University, Columbus, OH
| | - Romy Pabla
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Adriana T Dawes
- Department of Molecular Genetics, Ohio State University, Columbus, OH.,Department of Mathematics, Ohio State University, Columbus, OH
| | - Bhagwati P Gupta
- Department of Biology, McMaster University, Hamilton, ON, Canada
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5
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Caldwell KA, Willicott CW, Caldwell GA. Modeling neurodegeneration in Caenorhabditis elegans. Dis Model Mech 2020; 13:13/10/dmm046110. [PMID: 33106318 PMCID: PMC7648605 DOI: 10.1242/dmm.046110] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The global burden of neurodegenerative diseases underscores the urgent need for innovative strategies to define new drug targets and disease-modifying factors. The nematode Caenorhabditis elegans has served as the experimental subject for multiple transformative discoveries that have redefined our understanding of biology for ∼60 years. More recently, the considerable attributes of C. elegans have been applied to neurodegenerative diseases, including amyotrophic lateral sclerosis, Alzheimer's disease, Parkinson's disease and Huntington's disease. Transgenic nematodes with genes encoding normal and disease variants of proteins at the single- or multi-copy level under neuronal-specific promoters limits expression to select neuronal subtypes. The anatomical transparency of C. elegans affords the use of co-expressed fluorescent proteins to follow the progression of neurodegeneration as the animals age. Significantly, a completely defined connectome facilitates detailed understanding of the impact of neurodegeneration on organismal health and offers a unique capacity to accurately link cell death with behavioral dysfunction or phenotypic variation in vivo. Moreover, chemical treatments, as well as forward and reverse genetic screening, hasten the identification of modifiers that alter neurodegeneration. When combined, these chemical-genetic analyses establish critical threshold states to enhance or reduce cellular stress for dissecting associated pathways. Furthermore, C. elegans can rapidly reveal whether lifespan or healthspan factor into neurodegenerative processes. Here, we outline the methodologies employed to investigate neurodegeneration in C. elegans and highlight numerous studies that exemplify its utility as a pre-clinical intermediary to expedite and inform mammalian translational research. Summary: While unsurpassed as an experimental system for fundamental biology, Caenorhabditis elegans remains undervalued for its translational potential. Here, we highlight significant outcomes from, and resources available for, C. elegans-based research into neurodegenerative disorders.
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Affiliation(s)
- Kim A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA .,Departments of Neurobiology, Neurology, Center for Neurodegeneration and Experimental Therapeutics, and Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Corey W Willicott
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Guy A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA.,Departments of Neurobiology, Neurology, Center for Neurodegeneration and Experimental Therapeutics, and Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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6
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Zullo JM, Drake D, Aron L, O'Hern P, Dhamne SC, Davidsohn N, Mao CA, Klein WH, Rotenberg A, Bennett DA, Church GM, Colaiácovo MP, Yankner BA. Regulation of lifespan by neural excitation and REST. Nature 2019; 574:359-364. [PMID: 31619788 PMCID: PMC6893853 DOI: 10.1038/s41586-019-1647-8] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 09/18/2019] [Indexed: 12/27/2022]
Abstract
The mechanisms that extend lifespan in humans are poorly understood. Here we show that extended longevity in humans is associated with a distinct transcriptome signature in the cerebral cortex that is characterized by downregulation of genes related to neural excitation and synaptic function. In Caenorhabditis elegans, neural excitation increases with age and inhibition of excitation globally, or in glutamatergic or cholinergic neurons, increases longevity. Furthermore, longevity is dynamically regulated by the excitatory-inhibitory balance of neural circuits. The transcription factor REST is upregulated in humans with extended longevity and represses excitation-related genes. Notably, REST-deficient mice exhibit increased cortical activity and neuronal excitability during ageing. Similarly, loss-of-function mutations in the C. elegans REST orthologue genes spr-3 and spr-4 elevate neural excitation and reduce the lifespan of long-lived daf-2 mutants. In wild-type worms, overexpression of spr-4 suppresses excitation and extends lifespan. REST, SPR-3, SPR-4 and reduced excitation activate the longevity-associated transcription factors FOXO1 and DAF-16 in mammals and worms, respectively. These findings reveal a conserved mechanism of ageing that is mediated by neural circuit activity and regulated by REST.
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Affiliation(s)
- Joseph M Zullo
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Derek Drake
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Liviu Aron
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Patrick O'Hern
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sameer C Dhamne
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Noah Davidsohn
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chai-An Mao
- Department of Ophthalmology and Visual Science, The University of Texas McGovern Medical School, Houston, TX, USA
| | - William H Klein
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander Rotenberg
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Bruce A Yankner
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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7
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Wu S, Lei L, Song Y, Liu M, Lu S, Lou D, Shi Y, Wang Z, He D. Mutation of hop-1 and pink-1 attenuates vulnerability of neurotoxicity in C. elegans: the role of mitochondria-associated membrane proteins in Parkinsonism. Exp Neurol 2018; 309:67-78. [PMID: 30076829 DOI: 10.1016/j.expneurol.2018.07.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 07/04/2018] [Accepted: 07/31/2018] [Indexed: 12/22/2022]
Abstract
Mitochondrial dysfunction is considered as a critical mechanism in the pathogenesis of Parkinson's disease (PD). Increasing evidence supports the notion of mitochondria-associated membranes (MAMs) in mitochondrial dysfunction; yet little is known about the role of MAMs-related proteins in the pathogenesis of PD. Herein we exposed the nematode Caenorhabditis elegans to 0.5-10.0 μM rotenone (RO) or 0.2-1.6 mM paraquat (PQ) for 3 days. Our results showed that both RO and PQ induced similar Parkinsonism including motor deficits and dopaminergic degeneration. RO/PQ caused mitochondrial damages characterized by the increase of vacuole areas and autophagy vesicles, but the decrease of mitochondrial cristae. RO/PQ-impacted mitochondrial function was also demonstrated by the decrease of ATP level and mitochondrial membrane potential. Additionally, the attachment or surrounding of endoplasmic reticulum to the damaged mitochondria indicates ultrastructural alterations in MAMs. Using fluorescently labeled transgenic nematodes, we further found that the expression of tomm-7 and genes of Complex I, II and III was reduced, whereas the expression of pink-1 was increased in the exposed animals. To determine MAMs in toxicity toward PD, we investigated the mutants of hop-1 and pink-1, encoding presenilin and PTEN-induced putative kinase 1 (PINK1) in mitochondria-associated membranes, respectively. Results demonstrated that the mutation of both hop-1 and pink-1 reduced the vulnerability of lethal, behavioral, and mitochondrial toxicity induced by RO/PQ. These findings suggest that presenilin and PINK1 play important roles in the RO/PQ-induced neurotoxicity through the mechanisms involved in mitochondria-associated membranes.
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Affiliation(s)
- Siyu Wu
- Laboratory of Toxicology, School of Ecological and Environmental Sciences, East China Normal University, 500# DongChuan RD, Shanghai 200241, China
| | - Lili Lei
- Laboratory of Toxicology, School of Ecological and Environmental Sciences, East China Normal University, 500# DongChuan RD, Shanghai 200241, China
| | - Yang Song
- Laboratory of Toxicology, School of Ecological and Environmental Sciences, East China Normal University, 500# DongChuan RD, Shanghai 200241, China
| | - Mengting Liu
- Laboratory of Toxicology, School of Ecological and Environmental Sciences, East China Normal University, 500# DongChuan RD, Shanghai 200241, China
| | - Shibo Lu
- Laboratory of Toxicology, School of Ecological and Environmental Sciences, East China Normal University, 500# DongChuan RD, Shanghai 200241, China
| | - Dan Lou
- Department of Environmental Health & Engineering, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St., Baltimore 21205, USA
| | - Yonghong Shi
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518# Ziyue RD, Shanghai 200241, China
| | - Zhibin Wang
- Department of Environmental Health & Engineering, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St., Baltimore 21205, USA.
| | - Defu He
- Laboratory of Toxicology, School of Ecological and Environmental Sciences, East China Normal University, 500# DongChuan RD, Shanghai 200241, China; Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai 200241, China.
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8
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Lopez CI, Saud KE, Aguilar R, Berndt FA, Cánovas J, Montecino M, Kukuljan M. The chromatin modifying complex CoREST/LSD1 negatively regulates notch pathway during cerebral cortex development. Dev Neurobiol 2016; 76:1360-1373. [PMID: 27112428 DOI: 10.1002/dneu.22397] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/19/2016] [Accepted: 04/22/2016] [Indexed: 12/22/2022]
Abstract
The development of the cerebral cortex is a dynamic and coordinated process in which cell division, cell death, migration, and differentiation must be highly regulated to acquire the final architecture and functional competence of the mature organ. Notch pathway is an important regulator of differentiation and it is essential to maintain neural stem cell (NSC) pool. Here, we studied the role of epigenetic modulators such as lysine-specific demethylase 1 (LSD1) and its interactor CoREST in the regulation of the Notch pathway activity during the development of the cerebral cortex. We found that CoREST and LSD1 interact in vitro with RBPJ-κ in the repressor complex and these proteins are released upon overexpression of Notch intracellular domain (NICD). We corroborated LSD1 and RBPJ-κ interaction in developing cerebral cortex and also found that LSD1 binds to the hes1 promoter. Knock-down of CoREST and LSD1 by in utero electroporation increases Hes1 expression in vivo and decreases Ngn2. Interestingly, we found a functional interaction between CoREST and LSD1 with Notch pathway. This conclusion is based on the observation that both the defects in neuronal migration and the increase in the number of cells expressing Sox2 and Tbr2 were associated to the knock-down of either CoREST or LSD1 and were reversed by the loss of Notch. These results demonstrate that CoREST and LSD1 downregulate the Notch pathway in the developing cerebral cortex, thus suggesting a role of epigenetic regulation in the fine tuning of cell differentiation. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 76: 1360-1373, 2016.
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Affiliation(s)
- Cecilia I Lopez
- Faculty of Medicine, Program in Physiology and Biophysics, Institute for Biomedical Sciences, Universidad de Chile, Santiago, Chile.,Faculty of Medicine, Biomedical Neuroscience Institute (BNI), Universidad de Chile, Santiago, Chile
| | - Katherine E Saud
- Faculty of Medicine, Program in Physiology and Biophysics, Institute for Biomedical Sciences, Universidad de Chile, Santiago, Chile.,Faculty of Medicine, Biomedical Neuroscience Institute (BNI), Universidad de Chile, Santiago, Chile
| | - Rodrigo Aguilar
- Faculty of Biological Sciences and Faculty of Medicine, Center for Biomedical Research and FONDAP Center for Genome Regulation, Universidad Andre's Bello, Santiago, Chile
| | - F Andrés Berndt
- Faculty of Medicine, Program in Physiology and Biophysics, Institute for Biomedical Sciences, Universidad de Chile, Santiago, Chile.,Faculty of Medicine, Biomedical Neuroscience Institute (BNI), Universidad de Chile, Santiago, Chile
| | - José Cánovas
- Faculty of Medicine, Program in Physiology and Biophysics, Institute for Biomedical Sciences, Universidad de Chile, Santiago, Chile.,Faculty of Medicine, Biomedical Neuroscience Institute (BNI), Universidad de Chile, Santiago, Chile
| | - Martín Montecino
- Faculty of Biological Sciences and Faculty of Medicine, Center for Biomedical Research and FONDAP Center for Genome Regulation, Universidad Andre's Bello, Santiago, Chile
| | - Manuel Kukuljan
- Faculty of Medicine, Program in Physiology and Biophysics, Institute for Biomedical Sciences, Universidad de Chile, Santiago, Chile.,Faculty of Medicine, Biomedical Neuroscience Institute (BNI), Universidad de Chile, Santiago, Chile
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9
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Stefanakis N, Carrera I, Hobert O. Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans. Neuron 2015; 87:733-50. [PMID: 26291158 DOI: 10.1016/j.neuron.2015.07.031] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/01/2015] [Accepted: 07/20/2015] [Indexed: 01/03/2023]
Abstract
While neuronal cell types display an astounding degree of phenotypic diversity, most if not all neuron types share a core panel of terminal features. However, little is known about how pan-neuronal expression patterns are genetically programmed. Through an extensive analysis of the cis-regulatory control regions of a battery of pan-neuronal C. elegans genes, including genes involved in synaptic vesicle biology and neuropeptide signaling, we define a common organizational principle in the regulation of pan-neuronal genes in the form of a surprisingly complex array of seemingly redundant, parallel-acting cis-regulatory modules that direct expression to broad, overlapping domains throughout the nervous system. These parallel-acting cis-regulatory modules are responsive to a multitude of distinct trans-acting factors. Neuronal gene expression programs therefore fall into two fundamentally distinct classes. Neuron-type-specific genes are generally controlled by discrete and non-redundantly acting regulatory inputs, while pan-neuronal gene expression is controlled by diverse, coincident and seemingly redundant regulatory inputs.
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Affiliation(s)
- Nikolaos Stefanakis
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY, USA
| | - Ines Carrera
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY, USA
| | - Oliver Hobert
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY, USA.
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10
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Vandamme J, Sidoli S, Mariani L, Friis C, Christensen J, Helin K, Jensen ON, Salcini AE. H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans. Nucleic Acids Res 2015; 43:9694-710. [PMID: 26476455 PMCID: PMC4787770 DOI: 10.1093/nar/gkv1063] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/01/2015] [Indexed: 12/05/2022] Open
Abstract
Genome-wide analyses in Caenorhabditis elegans show that post-translational modifications (PTMs) of histones are evolutionary conserved and distributed along functionally distinct genomic domains. However, a global profile of PTMs and their co-occurrence on the same histone tail has not been described in this organism. We used mass spectrometry based middle-down proteomics to analyze histone H3 N-terminal tails from C. elegans embryos for the presence, the relative abundance and the potential cross-talk of co-existing PTMs. This analysis highlighted that the lysine 23 of histone H3 (H3K23) is extensively modified by methylation and that tri-methylated H3K9 (H3K9me3) is exclusively detected on histone tails with di-methylated H3K23 (H3K23me2). Chromatin immunoprecipitation approaches revealed a positive correlation between H3K23me2 and repressive marks. By immunofluorescence analyses, H3K23me2 appears differentially regulated in germ and somatic cells, in part by the action of the histone demethylase JMJD-1.2. H3K23me2 is enriched in heterochromatic regions, localizing in H3K9me3 and heterochromatin protein like-1 (HPL-1)-positive foci. Biochemical analyses indicated that HPL-1 binds to H3K23me2 and interacts with a conserved CoREST repressive complex. Thus, our study suggests that H3K23me2 defines repressive domains and contributes to organizing the genome in distinct heterochromatic regions during embryogenesis.
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Affiliation(s)
- Julien Vandamme
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Simone Sidoli
- Centre for Epigenetics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Luca Mariani
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Carsten Friis
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Jesper Christensen
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Kristian Helin
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark The Danish Stem Cell Centre (Danstem), University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Ole N Jensen
- Centre for Epigenetics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Anna Elisabetta Salcini
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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11
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Alexander AG, Marfil V, Li C. Use of Caenorhabditis elegans as a model to study Alzheimer's disease and other neurodegenerative diseases. Front Genet 2014; 5:279. [PMID: 25250042 PMCID: PMC4155875 DOI: 10.3389/fgene.2014.00279] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 07/31/2014] [Indexed: 12/12/2022] Open
Abstract
Advances in research and technology has increased our quality of life, allowed us to combat diseases, and achieve increased longevity. Unfortunately, increased longevity is accompanied by a rise in the incidences of age-related diseases such as Alzheimer’s disease (AD). AD is the sixth leading cause of death, and one of the leading causes of dementia amongst the aged population in the USA. It is a progressive neurodegenerative disorder, characterized by the prevalence of extracellular Aβ plaques and intracellular neurofibrillary tangles, derived from the proteolysis of the amyloid precursor protein (APP) and the hyperphosphorylation of microtubule-associated protein tau, respectively. Despite years of extensive research, the molecular mechanisms that underlie the pathology of AD remain unclear. Model organisms, such as the nematode, Caenorhabditis elegans, present a complementary approach to addressing these questions. C. elegans has many advantages as a model system to study AD and other neurodegenerative diseases. Like their mammalian counterparts, they have complex biochemical pathways, most of which are conserved. Genes in which mutations are correlated with AD have counterparts in C. elegans, including an APP-related gene, apl-1, a tau homolog, ptl-1, and presenilin homologs, such as sel-12 and hop-1. Since the neuronal connectivity in C. elegans has already been established, C. elegans is also advantageous in modeling learning and memory impairments seen during AD. This article addresses the insights C. elegans provide in studying AD and other neurodegenerative diseases. Additionally, we explore the advantages and drawbacks associated with using this model.
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Affiliation(s)
- Adanna G Alexander
- Department of Biology, City College of New York New York, NY, USA ; Department of Biology, The Graduate Center, City University of New York New York, NY, USA
| | - Vanessa Marfil
- Department of Biology, City College of New York New York, NY, USA
| | - Chris Li
- Department of Biology, City College of New York New York, NY, USA ; Department of Biology, The Graduate Center, City University of New York New York, NY, USA
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Lu T, Aron L, Zullo J, Pan Y, Kim H, Chen Y, Yang TH, Kim HM, Drake D, Liu XS, Bennett DA, Colaiácovo MP, Yankner BA. REST and stress resistance in ageing and Alzheimer's disease. Nature 2014; 507:448-54. [PMID: 24670762 PMCID: PMC4110979 DOI: 10.1038/nature13163] [Citation(s) in RCA: 520] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 02/21/2014] [Indexed: 12/13/2022]
Abstract
Human neurons are functional over an entire lifetime, yet the mechanisms that preserve function and protect against neurodegeneration during aging are unknown. Here we show that induction of the repressor element 1-silencing transcription/neuron-restrictive silencer factor (REST/NRSF) is a universal feature of normal aging in human cortical and hippocampal neurons. REST is lost, however, in mild cognitive impairment (MCI) and Alzheimer’s disease (AD). Chromatin immunoprecipitation with deep sequencing (ChIP-seq) and expression analysis show that REST represses genes that promote cell death and AD pathology, and induces the expression of stress response genes. Moreover, REST potently protects neurons from oxidative stress and amyloid β-protein (Aβ) toxicity, and conditional deletion of REST in the mouse brain leads to age-related neurodegeneration. A functional ortholog of REST, C. elegans SPR-4, also protects against oxidative stress and Aβ toxicity. During normal aging, REST is induced in part by cell non-autonomous Wnt signaling. However, in AD, frontotemporal dementia and dementia with Lewy bodies, REST is lost from the nucleus and appears in autophagosomes together with pathologic misfolded proteins. Finally, REST levels during aging are closely correlated with cognitive preservation and longevity. Thus, the activation state of REST may distinguish neuroprotection from neurodegeneration in the aging brain.
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Affiliation(s)
- Tao Lu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Liviu Aron
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph Zullo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ying Pan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Haeyoung Kim
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yiwen Chen
- Department of Biostatistics and Computational Biology, Dana-Faber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Tun-Hsiang Yang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hyun-Min Kim
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Derek Drake
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Faber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612, USA
| | - Monica P Colaiácovo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Bruce A Yankner
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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13
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Yang P, Sun R, Yao M, Chen W, Wang Z, Fei J. A C-terminal truncated mutation of spr-3 gene extends lifespan in Caenorhabditis elegans. Acta Biochim Biophys Sin (Shanghai) 2013; 45:540-8. [PMID: 23692984 DOI: 10.1093/abbs/gmt048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The lifespan of Caenorhabditis elegans is determined by various genetic and environmental factors. In this paper, spr-3, a C. elegans homologous gene of the mammalian neural restrictive silencing factor (NRSF/REST), is reported to be an important gene regulating lifespan of C. elegans. A deletion mutation of spr-3, spr-3(ok2525), or RNAi inhibition of spr-3 expression led to the short lifespan phenotype in C. elegans. However, a nonsense mutation of spr-3, spr-3(by108), increased the lifespan by 26% when compared with that of wild-type nematode. The spr-3(by108) also showed increased resistance to environmental stress. The spr-3(by108) mutated gene encodes a C-terminal truncated protein with a structure comparable with the REST4, a splice variant of the NRSF/REST in mammalian. The long lifespan phenotype of spr-3(by108) mutant is confirmed as a gain of function and dependent on normal functions of daf-16 and glp-1. The lifespan of the spr-3(by108) can be synergistically enhanced by inducing a mutation in daf-2. Quantitative polymerase chain reaction results showed that the expression of daf-16 as well as its target gene sod-3, mtl-1, and sip-1 was up-regulated in the spr-3(by108) mutant. These results would be helpful to further understand the complex function of NRSF/REST gene in mammalian, especially in the aging process and longevity determination.
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Affiliation(s)
- Ping Yang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
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14
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Craig HL, Wirtz J, Bamps S, Dolphin CT, Hope IA. The significance of alternative transcripts for Caenorhabditis elegans transcription factor genes, based on expression pattern analysis. BMC Genomics 2013; 14:249. [PMID: 23586691 PMCID: PMC3685541 DOI: 10.1186/1471-2164-14-249] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 04/09/2013] [Indexed: 11/30/2022] Open
Abstract
Background Sequence-specific DNA-binding proteins, with their paramount importance in the regulation of expression of the genetic material, are encoded by approximately 5% of the genes in an animal’s genome. But it is unclear to what extent alternative transcripts from these genes may further increase the complexity of the transcription factor complement. Results Of the 938 potential C. elegans transcription factor genes, 197 were annotated in WormBase as encoding at least two distinct isoforms. Evaluation of prior evidence identified, with different levels of confidence, 50 genes with alternative transcript starts, 23 with alternative transcript ends, 35 with alternative splicing and 34 with alternative transcripts generated by a combination of mechanisms, leaving 55 that were discounted. Expression patterns were determined for transcripts for a sample of 29 transcription factor genes, concentrating on those with alternative transcript starts for which the evidence was strongest. Seamless fosmid recombineering was used to generate reporter gene fusions with minimal modification to assay expression of specific transcripts while maintaining the broad genomic DNA context and alternative transcript production. Alternative transcription factor gene transcripts were typically expressed with identical or substantially overlapping distributions rather than in distinct domains. Conclusions Increasingly sensitive sequencing technologies will reveal rare transcripts but many of these are clearly non-productive. The majority of the transcription factor gene alternative transcripts that are productive may represent tolerable noise rather than encoding functionally distinct isoforms.
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Affiliation(s)
- Hannah L Craig
- School of Biology, Faculty of Biological Sciences, The University of Leeds, Leeds LS2 9JT, UK
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15
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Kok FO, Taibi A, Wanner SJ, Xie X, Moravec CE, Love CE, Prince VE, Mumm JS, Sirotkin HI. Zebrafish rest regulates developmental gene expression but not neurogenesis. Development 2012; 139:3838-48. [PMID: 22951640 DOI: 10.1242/dev.080994] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The transcriptional repressor Rest (Nrsf) recruits chromatin-modifying complexes to RE1 'silencer elements', which are associated with hundreds of neural genes. However, the requirement for Rest-mediated transcriptional regulation of embryonic development and cell fate is poorly understood. Conflicting views of the role of Rest in controlling cell fate have emerged from recent studies. To address these controversies, we examined the developmental requirement for Rest in zebrafish using zinc-finger nuclease-mediated gene targeting. We discovered that germ layer specification progresses normally in rest mutants despite derepression of target genes during embryogenesis. This analysis provides the first evidence that maternal rest is essential for repression of target genes during blastula stages. Surprisingly, neurogenesis proceeds largely normally in rest mutants, although abnormalities are observed within the nervous system, including defects in oligodendrocyte precursor cell development and a partial loss of facial branchiomotor neuron migration. Mutants progress normally through embryogenesis but many die as larvae (after 12 days). However, some homozygotes reach adulthood and are viable. We utilized an RE1/NRSE transgenic reporter system to dynamically monitor Rest activity. This analysis revealed that Rest is required to repress gene expression in mesodermal derivatives including muscle and notochord, as well as within the nervous system. Finally, we demonstrated that Rest is required for long-term repression of target genes in non-neural tissues in adult zebrafish. Our results point to a broad role for Rest in fine-tuning neural gene expression, rather than as a widespread regulator of neurogenesis or cell fate.
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Affiliation(s)
- Fatma O Kok
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY 11794, USA
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16
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SACY-1 DEAD-Box helicase links the somatic control of oocyte meiotic maturation to the sperm-to-oocyte switch and gamete maintenance in Caenorhabditis elegans. Genetics 2012; 192:905-28. [PMID: 22887816 PMCID: PMC3522166 DOI: 10.1534/genetics.112.143271] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In sexually reproducing animals, oocytes arrest at diplotene or diakinesis and resume meiosis (meiotic maturation) in response to hormones. In Caenorhabditis elegans, major sperm protein triggers meiotic resumption through a mechanism involving somatic Gαs–adenylate cyclase signaling and soma-to-germline gap-junctional communication. Using genetic mosaic analysis, we show that the major effector of Gαs–adenylate cyclase signaling, protein kinase A (PKA), is required in gonadal sheath cells for oocyte meiotic maturation and dispensable in the germ line. This result rules out a model in which cyclic nucleotides must transit through sheath-oocyte gap junctions to activate PKA in the germ line, as proposed in vertebrate systems. We conducted a genetic screen to identify regulators of oocyte meiotic maturation functioning downstream of Gαs–adenylate cyclase–PKA signaling. We molecularly identified 10 regulatory loci, which include essential and nonessential factors. sacy-1, which encodes a highly conserved DEAD-box helicase, is an essential germline factor that negatively regulates meiotic maturation. SACY-1 is a multifunctional protein that establishes a mechanistic link connecting the somatic control of meiotic maturation to germline sex determination and gamete maintenance. Modulatory factors include multiple subunits of a CoREST-like complex and the TWK-1 two-pore potassium channel. These factors are not absolutely required for meiotic maturation or its negative regulation in the absence of sperm, but function cumulatively to enable somatic control of meiotic maturation. This work provides insights into the genetic control of meiotic maturation signaling in C. elegans, and the conserved factors identified here might inform analysis in other systems through either homology or analogy.
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17
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Liu Q, Jones TI, Bachmann RA, Meghpara M, Rogowski L, Williams BD, Jones PL. C. elegans PAT-9 is a nuclear zinc finger protein critical for the assembly of muscle attachments. Cell Biosci 2012; 2:18. [PMID: 22616817 PMCID: PMC3419604 DOI: 10.1186/2045-3701-2-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 05/22/2012] [Indexed: 11/28/2022] Open
Abstract
Background Caenorhabditis elegans sarcomeres have been studied extensively utilizing both forward and reverse genetic techniques to provide insight into muscle development and the mechanisms behind muscle contraction. A previous genetic screen investigating early muscle development produced 13 independent mutant genes exhibiting a Pat (paralyzed and arrested elongation at the two-fold length of embryonic development) muscle phenotype. This study reports the identification and characterization of one of those genes, pat-9. Results Positional cloning, reverse genetics, and plasmid rescue experiments were used to identify the predicted C. elegans gene T27B1.2 (recently named ztf-19) as the pat-9 gene. Analysis of pat-9 showed it is expressed early in development and within body wall muscle lineages, consistent with a role in muscle development and producing a Pat phenotype. However, unlike most of the other known Pat gene family members, which encode structural components of muscle attachment sites, PAT-9 is an exclusively nuclear protein. Analysis of the predicted PAT-9 amino acid sequence identified one putative nuclear localization domain and three C2H2 zinc finger domains. Both immunocytochemistry and PAT-9::GFP fusion expression confirm that PAT-9 is primarily a nuclear protein and chromatin immunoprecipitation (ChIP) experiments showed that PAT-9 is present on certain gene promoters. Conclusions We have shown that the T27B1.2 gene is pat-9. Considering the Pat-9 mutant phenotype shows severely disrupted muscle attachment sites despite PAT-9 being a nuclear zinc finger protein and not a structural component of muscle attachment sites, we propose that PAT-9 likely functions in the regulation of gene expression for some necessary structural or regulatory component(s) of the muscle attachment sites.
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Affiliation(s)
- Qian Liu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S, Goodwin Ave, B107 Chemical and Life Sciences Laboratory, Urbana, IL, 61801, USA.
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18
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Verghese E, Schocken J, Jacob S, Wimer AM, Royce R, Nesmith JE, Baer GM, Clever S, McCain E, Lakowski B, Wightman B. The tailless ortholog nhr-67 functions in the development of the C. elegans ventral uterus. Dev Biol 2011; 356:516-28. [DOI: 10.1016/j.ydbio.2011.06.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 05/13/2011] [Accepted: 06/04/2011] [Indexed: 12/14/2022]
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19
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Wenzel D, Palladino F, Jedrusik-Bode M. Epigenetics in C. elegans: facts and challenges. Genesis 2011; 49:647-61. [PMID: 21538806 DOI: 10.1002/dvg.20762] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 04/14/2011] [Accepted: 04/15/2011] [Indexed: 12/31/2022]
Abstract
Epigenetics is defined as the study of heritable changes in gene expression that are not accompanied by changes in the DNA sequence. Epigenetic mechanisms include histone post-translational modifications, histone variant incorporation, non-coding RNAs, and nucleosome remodeling and exchange. In addition, the functional compartmentalization of the nucleus also contributes to epigenetic regulation of gene expression. Studies on the molecular mechanisms underlying epigenetic phenomena and their biological function have relied on various model systems, including yeast, plants, flies, and cultured mammalian cells. Here we will expose the reader to the current understanding of epigenetic regulation in the roundworm C. elegans. We will review recent models of nuclear organization and its impact on gene expression, the biological role of enzymes modifying core histones, and the function of chromatin-associated factors, with special emphasis on Polycomb (PcG) and Trithorax (Trx-G) group proteins. We will discuss how the C. elegans model has provided novel insight into mechanisms of epigenetic regulation as well as suggest directions for future research.
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Affiliation(s)
- Dirk Wenzel
- Electron Microscopy Group 3 Epigenetics in C. elegans Group, Max Planck Institute for Biophysical Chemistry, Am Faβberg 11, 37077 Göttingen, Germany
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Gontijo AM, Aubert S, Roelens I, Lakowski B. Mutations in genes involved in nonsense mediated decay ameliorate the phenotype of sel-12 mutants with amber stop mutations in Caenorhabditis elegans. BMC Genet 2009; 10:14. [PMID: 19302704 PMCID: PMC2678165 DOI: 10.1186/1471-2156-10-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Accepted: 03/20/2009] [Indexed: 11/29/2022] Open
Abstract
Background Presenilin proteins are part of a complex of proteins that can cleave many type I transmembrane proteins, including Notch Receptors and the Amyloid Precursor Protein, in the middle of the transmembrane domain. Dominant mutations in the human presenilin genes PS1 and PS2 lead to Familial Alzheimer's disease. Mutations in the Caenorhabditis elegans sel-12 presenilin gene cause a highly penetrant egg-laying defect due to reduction of signalling through the lin-12/Notch receptor. Mutations in six spr genes (for suppressor of presenilin) are known to strongly suppress sel-12. Mutations in most strong spr genes suppress sel-12 by de-repressing the transcription of the largely functionally equivalent hop-1 presenilin gene. However, how mutations in the spr-2 gene suppress sel-12 is unknown. Results We show that spr-2 mutations increase the levels of sel-12 transcripts with Premature translation Termination Codons (PTCs) in embryos and L1 larvae. mRNA transcripts from sel-12 alleles with PTCs undergo degradation by a process known as Nonsense Mediated Decay (NMD). However, spr-2 mutations do not appear to affect NMD. Mutations in the smg genes, which are required for NMD, can restore sel-12(PTC) transcript levels and ameliorate the phenotype of sel-12 mutants with amber PTCs. However, the phenotypic suppression of sel-12 by smg genes is nowhere near as strong as the effect of previously characterized spr mutations including spr-2. Consistent with this, we have identified only two mutations in smg genes among the more than 100 spr mutations recovered in genetic screens. Conclusion spr-2 mutations do not suppress sel-12 by affecting NMD of sel-12(PTC) transcripts and appear to have a novel mechanism of suppression. The fact that mutations in smg genes can ameliorate the phenotype of sel-12 alleles with amber PTCs suggests that some read-through of sel-12(amber) alleles occurs in smg backgrounds.
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Cunliffe VT. Eloquent silence: developmental functions of Class I histone deacetylases. Curr Opin Genet Dev 2008; 18:404-10. [PMID: 18929655 PMCID: PMC2671034 DOI: 10.1016/j.gde.2008.10.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 09/16/2008] [Accepted: 10/02/2008] [Indexed: 11/10/2022]
Abstract
Histone deacetylases (HDACs) are essential catalytic components of the transcription silencing machinery and they play important roles in the programming of multicellular development. HDACs are present within multisubunit protein complexes, other components of which govern HDAC target gene specificity by controlling interactions with sequence-specific DNA-binding proteins. Here, I review the different developmental roles of the Sin3, NuRD, CoREST and NCoR/SMRT Class I HDAC complexes. With their distinct subunit composition, these versatile molecular devices function in many different settings, to promote axis specification and tissue patterning, to maintain stem cell pluripotency, facilitate self-renewal, guide lineage commitment and drive cell differentiation.
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Affiliation(s)
- Vincent T Cunliffe
- MRC Centre for Developmental and Biomedical Genetics and Department of Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom.
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22
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Bender AM, Kirienko NV, Olson SK, Esko JD, Fay DS. lin-35/Rb and the CoREST ortholog spr-1 coordinately regulate vulval morphogenesis and gonad development in C. elegans. Dev Biol 2007; 302:448-62. [PMID: 17070797 PMCID: PMC1933485 DOI: 10.1016/j.ydbio.2006.09.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Revised: 08/28/2006] [Accepted: 09/30/2006] [Indexed: 11/21/2022]
Abstract
Using a genetic screen to identify genes that carry out redundant functions during development with lin-35/Rb, the C. elegans Retinoblastoma family ortholog, we have identified a mutation in spr-1. spr-1 encodes the C. elegans ortholog of human CoREST, a protein containing Myb-like SANT and ELM2 domains, which functions as part of a transcriptional regulatory complex. CoREST recruits mediators of transcriptional repression, including histone deacetylase, and demethylase, and interacts with the tumor suppression protein REST. spr-1/CoREST was previously shown in C. elegans to suppress defects associated with loss of the presenilin sel-12, which functions in the proteolytic processing of LIN-12/Notch. Here we show that lin-35 and spr-1 coordinately regulate several developmental processes in C. elegans including the ingression of vulval cells as well as germline proliferation. We also show that loss of lin-35 and spr-1 hypersensitizes animals to a reduction in LIN-12/Notch activity, leading to the generation of proximal germline tumors. This defect, which is observed in lin-35; spr-1; lin-12(RNAi) and lin-35; spr-1; hop-1(RNAi) triple mutants is likely due to a delay in the entry of germ cells into meiosis.
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Affiliation(s)
- Aaron M. Bender
- University of Wyoming, College of Agriculture, Department of Molecular Biology Dept 3944, 1000 E. University Avenue, Laramie, WY 82071
| | - Natalia V. Kirienko
- University of Wyoming, College of Agriculture, Department of Molecular Biology Dept 3944, 1000 E. University Avenue, Laramie, WY 82071
| | - Sara K. Olson
- Department of Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla CA 92093
| | - Jeffery D. Esko
- Department of Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla CA 92093
| | - David S Fay
- University of Wyoming, College of Agriculture, Department of Molecular Biology Dept 3944, 1000 E. University Avenue, Laramie, WY 82071
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Lakowski B, Roelens I, Jacob S. CoREST-like complexes regulate chromatin modification and neuronal gene expression. J Mol Neurosci 2007; 29:227-39. [PMID: 17085781 DOI: 10.1385/jmn:29:3:227] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Revised: 11/30/1999] [Accepted: 02/03/2006] [Indexed: 12/29/2022]
Abstract
The mammalian CoREST ([co]repressor for element-1-silencing transcription factor) complex was first identified associated with the repressor for element-1 silencing transcription factor (REST)/neuronal restrictive silencing factor. The CoREST complex is a chromatin-modifying corepressor complex that acts with REST to regulate neuronal gene expression and neuronal stem cell fate. Components of a CoREST-like complex have been identified recently in Xenopus laevis, Caenorhabditis elegans, and Drosophila melanogaster. Like the mammalian complex, the Drosophila complex is required to regulate neuronal gene expression, whereas the C. elegans homologs regulate the expression of the hop-1 presenilin gene, suggesting an ancient conserved function of CoREST complexes in regulating neuronal gene expression.
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Affiliation(s)
- Bernard Lakowski
- Nematode Genetics Group, Department of Neuroscience, Pasteur Institute, 75724 Paris Cedex 15, France.
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Kraemer B, Schellenberg GD. Using Caenorhabditis elegans models of neurodegenerative disease to identify neuroprotective strategies. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2007; 77:219-46. [PMID: 17178476 DOI: 10.1016/s0074-7742(06)77007-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Brian Kraemer
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle Division, Seattle, Washington 98108, USA
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Abstract
The genome of the nematode Caenorhabditis elegans contains homologs of several genes associated with familial Alzheimer's disease in humans. apl-1 encodes a transmembrane protein belonging to the amyloid precursor protein family, sel-12 and hop-1 are the two somatically expressed presenilin genes that resemble PS1 and PS2 on both a structural and a functional level. Mutations in the sel-12-encoded presenilin gene cause defective Notch/lin-12 signaling and result in reduced egg-laying, caused by cell specification and cell attachment defects. spr-1, spr-3, spr-4 and spr-5 were identified as the suppressors of the egg-laying defect of presenilin/sel-12 loss of function mutants in genetic suppressor screens. The corresponding proteins are C. elegans homologs of human REST, CoREST and LSD1, respectively. REST/NSRF (Re1 silencing transcription factor/neural-restrictive silencing factor) is a transcriptional repressor that blocks the expression of neuronal genes in non-neuronal tissues in vertebrates. CoREST is a conserved histone deacetylase and demethylase-containing co-repressor complex possessing a potential chromatin-modifying activity. It is recruited to the promoter via REST-mediated DNA binding. LSD1 is a flavin-dependent demethylase of histone H3. Mutations in spr-1, spr-3, spr-4 and spr-5 genes suppress the egg-laying phenotype of sel-12 loss of function mutants by derepressing the expression of the second C. elegans presenilin gene, hop-1.
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Affiliation(s)
- Agata Smialowska
- Bio3/Bioinformatics and Molecular Genetics, University of Freiburg, Freiburg, Germany
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Mortazavi A, Thompson ECL, Garcia ST, Myers RM, Wold B. Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire. Genes Dev 2006; 16:1208-21. [PMID: 16963704 PMCID: PMC1581430 DOI: 10.1101/gr.4997306] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Accepted: 07/19/2006] [Indexed: 01/09/2023]
Abstract
We constructed and applied an open source informatic framework called Cistematic in an effort to predict the target gene repertoire for transcription factors with large binding sites. Cistematic uses two different evolutionary conservation-filtering algorithms in conjunction with several analysis modules. Beginning with a single conserved and biologically tested site for the neuronal repressor NRSF/REST, Cistematic generated a refined PSFM (position specific frequency matrix) based on conserved site occurrences in mouse, human, and dog genomes. Predictions from this model were validated by chromatin immunoprecipitation (ChIP) followed by quantitative PCR. The combination of transfection assays and ChIP enrichment data provided an objective basis for setting a threshold for membership and rank-ordering a final gene cohort model consisting of 842 high-confidence sites in the human genome associated with 733 genes. Statistically significant enrichment of NRSE-associated genes was found for neuron-specific Gene Ontology (GO) terms and neuronal mRNA expression profiles. A more extensive evolutionary survey showed that NRSE sites matching the PSFM model exist in roughly similar numbers in all fully sequenced vertebrate genomes but are notably absent from invertebrate and protochordate genomes, as is NRSF itself. Some NRSF/REST sites reside in repeats, which suggests a mechanism for both ancient and modern dispersal of NRSEs through vertebrate genomes. Multiple predicted sites are located near neuronal microRNA and splicing-factor genes, and these tested positive for NRSF/REST occupancy in vivo. The resulting network model integrates post-transcriptional and translational controllers, including candidate feedback loops on NRSF and its corepressor, CoREST.
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Affiliation(s)
- Ali Mortazavi
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Sarah T. Garcia
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Richard M. Myers
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Barbara Wold
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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Nishihara S, Tsuda L, Ogura T. The canonical Wnt pathway directly regulates NRSF/REST expression in chick spinal cord. Biochem Biophys Res Commun 2004; 311:55-63. [PMID: 14575694 DOI: 10.1016/j.bbrc.2003.09.158] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neural precursor cells actively proliferate in the ventricular zone to self-renew the stem cell population, and in parallel, maintain their undifferentiated state. This progenitor pool generates postmitotic cells that migrate to the mantle layer and differentiate into mature neurons. The growth of these stem cells is strictly controlled by the canonical Wnt signaling cascade, in part mediated by the direct regulation of Cyclin D1, a critical regulator of cell cycle progression. Here, we report that the canonical Wnt pathway directly controls the expression of NRSF/REST. The Wnt-activated beta-catenin/TCF complex up-regulates this gene through a conserved element found in its exon 1a, a critical result obtained by a novel in ovo transcriptional assay. Hence, our data show that the canonical Wnt signaling cascade directly regulates the NRSF/REST and Cyclin D1 genes, thereby controlling the progenitor cells. In addition, we show that our in ovo transcription assay is a powerful way to analyze gene regulation in a natural in vivo context.
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Affiliation(s)
- Shigeki Nishihara
- Institute of Development, Aging and Cancer, Tohoku University, Aoba, Sendai, Miyagi, Japan
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