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Gutierrez Fugón OJ, Sharifi O, Heath N, Soto DC, Gomez JA, Yasui DH, Mendiola AJP, O'Geen H, Beitnere U, Tomkova M, Haghani V, Dillon G, Segal DJ, LaSalle JM. Integration of CTCF loops, methylome, and transcriptome in differentiating LUHMES as a model for imprinting dynamics of the 15q11-q13 locus in human neurons. Hum Mol Genet 2024; 33:1711-1725. [PMID: 39045627 DOI: 10.1093/hmg/ddae111] [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: 03/20/2024] [Revised: 06/30/2024] [Accepted: 07/17/2024] [Indexed: 07/25/2024] Open
Abstract
Human cell line models, including the neuronal precursor line LUHMES, are important for investigating developmental transcriptional dynamics within imprinted regions, particularly the 15q11-q13 Angelman (AS) and Prader-Willi (PWS) syndrome locus. AS results from loss of maternal UBE3A in neurons, where the paternal allele is silenced by a convergent antisense transcript UBE3A-ATS, a lncRNA that terminates at PWAR1 in non-neurons. qRT-PCR analysis confirmed the exclusive and progressive increase in UBE3A-ATS in differentiating LUHMES neurons, validating their use for studying UBE3A silencing. Genome-wide transcriptome analyses revealed changes to 11 834 genes during neuronal differentiation, including the upregulation of most genes within the 15q11-q13 locus. To identify dynamic changes in chromatin loops linked to transcriptional activity, we performed a HiChIP validated by 4C, which identified two neuron-specific CTCF loops between MAGEL2-SNRPN and PWAR1-UBE3A. To determine if allele-specific differentially methylated regions (DMR) may be associated with CTCF loop anchors, whole genome long-read nanopore sequencing was performed. We identified a paternally hypomethylated DMR near the SNRPN upstream loop anchor exclusive to neurons and a paternally hypermethylated DMR near the PWAR1 CTCF anchor exclusive to undifferentiated cells, consistent with increases in neuronal transcription. Additionally, DMRs near CTCF loop anchors were observed in both cell types, indicative of allele-specific differences in chromatin loops regulating imprinted transcription. These results provide an integrated view of the 15q11-q13 epigenetic landscape during LUHMES neuronal differentiation, underscoring the complex interplay of transcription, chromatin looping, and DNA methylation. They also provide insights for future therapeutic approaches for AS and PWS.
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Affiliation(s)
- Orangel J Gutierrez Fugón
- Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, 451 Health Sciences Dr., Davis, CA 95616, United States
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, 1275 Med Science Dr, Davis, CA 95616, United States
| | - Osman Sharifi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, 1275 Med Science Dr, Davis, CA 95616, United States
| | - Nicholas Heath
- Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, 451 Health Sciences Dr., Davis, CA 95616, United States
| | - Daniela C Soto
- Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, 451 Health Sciences Dr., Davis, CA 95616, United States
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, 757 Westwood Plaza #4, Los Angeles, CA 90095, United States
| | - J Antonio Gomez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, 1275 Med Science Dr, Davis, CA 95616, United States
- Department of Natural Science, Seaver College, Pepperdine University, 24255 Pacific Coast Hwy, Malibu, CA 90263, United States
| | - Dag H Yasui
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, 1275 Med Science Dr, Davis, CA 95616, United States
| | - Aron Judd P Mendiola
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, 1275 Med Science Dr, Davis, CA 95616, United States
| | - Henriette O'Geen
- Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, 451 Health Sciences Dr., Davis, CA 95616, United States
| | - Ulrika Beitnere
- Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, 451 Health Sciences Dr., Davis, CA 95616, United States
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Marketa Tomkova
- Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, 451 Health Sciences Dr., Davis, CA 95616, United States
- Ludwig Cancer Research Center, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Viktoria Haghani
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, 1275 Med Science Dr, Davis, CA 95616, United States
| | - Greg Dillon
- Genetics and Neurodevelopmental Disorders Unit, Biogen, 225 Binney Street Cambridge, MA 02142 United States
| | - David J Segal
- Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, 451 Health Sciences Dr., Davis, CA 95616, United States
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, 1275 Med Science Dr, Davis, CA 95616, United States
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Michieletto P, Pensiero S, Diplotti L, Ronfani L, Giangreco M, Danieli A, Bonanni P. Strabismus surgery in Angelman syndrome: More than ocular alignment. PLoS One 2020; 15:e0242366. [PMID: 33186391 PMCID: PMC7665582 DOI: 10.1371/journal.pone.0242366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/01/2020] [Indexed: 11/18/2022] Open
Abstract
PURPOSE To report and evaluate strabismus surgery in children with Angelman syndrome, in order to optimize and standardize surgical approach. Other purposes are to understand the possible relation between ocular findings and motor ability, and between improvement in ocular alignment and changes in motor skills in this population. DESIGN Observational cross-sectional study. METHODS Medical records of pediatric patients with Angelman syndrome, who underwent strabismus surgery, were investigated. Collected data included: genotype, gender, age at the time of surgery, refractive error, pre-operative strabismus, surgical procedure, surgical outcome, gross and fine motor development assessment pre- and post-operatively. RESULTS Seventeen subjects, aged 3-15 years, were investigated. Fourteen patients were exotropic, three esotropic. Most patients presented astigmatism. Considering the exaggerated response to standard amounts of surgery and the risk of consecutive strabismus on long term follow-up reported by previous studies in children with developmental delay, a reduction of the amount of strabismus surgery was applied. Post-operatively, all patients presented with a significative reduction of the baseline deviation angle, with all esotropic patients and 7 exotropic patients (59%) achieving orthotropia. The surgical outcomes were variable according to the type and the amount of baseline strabismus, but no case presented with exaggerated surgical response. At baseline, patients showed important delays in all motor abilities, and, post-operatively, presented a significant improvement in walking and fine motor tasks. Pre- and post-operative motor abilities were negatively correlated to astigmatism, anisometropia, and amount of deviation. CONCLUSIONS According to our data, the standard nomograms for strabismus surgery may be successfully applied in subjects with Angelman syndrome and exotropia. Our data suggest that the reduction of the deviation angle improves motor skills in strabismic pediatric patients with Angelman syndrome.
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Affiliation(s)
- Paola Michieletto
- Ophthalmology Service, Scientific Institute IRCCS Eugenio Medea, Conegliano-Pieve di Soligo (TV), Italy
| | - Stefano Pensiero
- Department of Ophthalmology, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Trieste, Italy
| | - Laura Diplotti
- Department of Ophthalmology, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Trieste, Italy
- * E-mail:
| | - Luca Ronfani
- Clinical Epidemiology and Public Health Research Unit, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Trieste, Italy
| | - Manuela Giangreco
- Clinical Epidemiology and Public Health Research Unit, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, Trieste, Italy
| | - Alberto Danieli
- Epilepsy and Clinical Neurophysiology Unit, Scientific Institute IRCCS Eugenio Medea, Conegliano-Pieve di Soligo (TV), Italy
| | - Paolo Bonanni
- Epilepsy and Clinical Neurophysiology Unit, Scientific Institute IRCCS Eugenio Medea, Conegliano-Pieve di Soligo (TV), Italy
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Vogel Ciernia A, LaSalle J. The landscape of DNA methylation amid a perfect storm of autism aetiologies. Nat Rev Neurosci 2016; 17:411-23. [PMID: 27150399 PMCID: PMC4966286 DOI: 10.1038/nrn.2016.41] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Increasing evidence points to a complex interplay between genes and the environment in autism spectrum disorder (ASD), including rare de novo mutations in chromatin genes such as methyl-CpG binding protein 2 (MECP2) in Rett syndrome. Epigenetic mechanisms such as DNA methylation act at this interface, reflecting the plasticity in metabolic and neurodevelopmentally regulated gene pathways. Genome-wide studies of gene sequences, gene pathways and DNA methylation are providing valuable mechanistic insights into ASD. The dynamic developmental landscape of DNA methylation is vulnerable to numerous genetic and environmental insults: therefore, understanding pathways that are central to this 'perfect storm' will be crucial to improving the diagnosis and treatment of ASD.
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Affiliation(s)
- Annie Vogel Ciernia
- Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, California 95616, USA
| | - Janine LaSalle
- Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, California 95616, USA
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Joyce EF, Erceg J, Wu CT. Pairing and anti-pairing: a balancing act in the diploid genome. Curr Opin Genet Dev 2016; 37:119-128. [PMID: 27065367 DOI: 10.1016/j.gde.2016.03.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/02/2016] [Accepted: 03/05/2016] [Indexed: 12/22/2022]
Abstract
The presence of maternal and paternal homologs appears to be much more than just a doubling of genetic material. We know this because genomes have evolved elaborate mechanisms that permit homologous regions to sense and then respond to each other. One way in which homologs communicate is to come into contact and, in fact, Dipteran insects such as Drosophila excel at this task, aligning all pairs of maternal and paternal chromosomes, end-to-end, in essentially all somatic tissues throughout development. Here, we reexamine the widely held tenet that extensive somatic pairing of homologous sequences cannot occur in mammals and suggest, instead, that pairing may be a widespread and significant potential that has gone unnoticed in mammals because they expend considerable effort to prevent it. We then extend this discussion to interchromosomal interactions, in general, and speculate about the potential of nuclear organization and pairing to impact inheritance.
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Affiliation(s)
- Eric F Joyce
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States.
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - C-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States.
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Judson MC, Sosa-Pagan JO, Del Cid WA, Han JE, Philpot BD. Allelic specificity of Ube3a expression in the mouse brain during postnatal development. J Comp Neurol 2014; 522:1874-96. [PMID: 24254964 DOI: 10.1002/cne.23507] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 10/30/2013] [Accepted: 11/15/2013] [Indexed: 12/23/2022]
Abstract
Genetic alterations of the maternal UBE3A allele result in Angelman syndrome (AS), a neurodevelopmental disorder characterized by severe developmental delay, lack of speech, and difficulty with movement and balance. The combined effects of maternal UBE3A mutation and cell type-specific epigenetic silencing of paternal UBE3A are hypothesized to result in a complete loss of functional UBE3A protein in neurons. However, the allelic specificity of UBE3A expression in neurons and other cell types in the brain has yet to be characterized throughout development, including the early postnatal period when AS phenotypes emerge. Here we define maternal and paternal allele-specific Ube3a protein expression throughout postnatal brain development in the mouse, a species that exhibits orthologous epigenetic silencing of paternal Ube3a in neurons and AS-like behavioral phenotypes subsequent to maternal Ube3a deletion. We find that neurons downregulate paternal Ube3a protein expression as they mature and, with the exception of neurons born from postnatal stem cell niches, do not express detectable paternal Ube3a beyond the first postnatal week. By contrast, neurons express maternal Ube3a throughout postnatal development, during which time localization of the protein becomes increasingly nuclear. Unlike neurons, astrocytes and oligodendrotyes biallelically express Ube3a. Notably, mature oligodendrocytes emerge as the predominant Ube3a-expressing glial cell type in the cortex and white matter tracts during postnatal development. These findings demonstrate the spatiotemporal characteristics of allele-specific Ube3a expression in key brain cell types, thereby improving our understanding of the developmental parameters of paternal Ube3a silencing and the cellular basis of AS.
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Affiliation(s)
- Matthew C Judson
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, 27599
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Mitchell A, Roussos P, Peter C, Tsankova N, Akbarian S. The future of neuroepigenetics in the human brain. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 128:199-228. [PMID: 25410546 DOI: 10.1016/b978-0-12-800977-2.00008-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Complex mechanisms shape the genome of brain cells into transcriptional units, clusters of condensed chromatin, and many other features that distinguish between various cell types and developmental stages sharing the same genetic material. Only a few years ago, the field's focus was almost entirely on a single mark, CpG methylation; the emerging complexity of neuronal and glial epigenomes now includes multiple types of DNA cytosine methylation, more than 100 residue-specific posttranslational histone modifications and histone variants, all of which superimposed by a dynamic and highly regulated three-dimensional organization of the chromosomal material inside the cell nucleus. Here, we provide an update on the most innovative approaches in neuroepigenetics and their potential contributions to approach cognitive functions and disorders unique to human. We propose that comprehensive, cell type-specific mappings of DNA and histone modifications, chromatin-associated RNAs, and chromosomal "loopings" and other determinants of three-dimensional genome organization will critically advance insight into the pathophysiology of the disease. For example, superimposing the epigenetic landscapes of neuronal and glial genomes onto genetic maps for complex disorders, ranging from Alzheimer's disease to schizophrenia, could provide important clues about neurological function for some of the risk-associated noncoding sequences in the human genome.
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Affiliation(s)
- Amanda Mitchell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Cyril Peter
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Nadejda Tsankova
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
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Tushir JS, Akbarian S. Chromatin-bound RNA and the neurobiology of psychiatric disease. Neuroscience 2013; 264:131-41. [PMID: 23831425 DOI: 10.1016/j.neuroscience.2013.06.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 11/18/2022]
Abstract
A large, and still rapidly expanding literature on epigenetic regulation in the nervous system has provided fundamental insights into the dynamic regulation of DNA methylation and post-translational histone modifications in the context of neuronal plasticity in health and disease. Remarkably, however, very little is known about the potential role of chromatin-bound RNAs, including many long non-coding transcripts and various types of small RNAs. Here, we provide an overview on RNA-mediated regulation of chromatin structure and function, with focus on histone lysine methylation and psychiatric disease. Examples of recently discovered chromatin-bound long non-coding RNAs important for neuronal health and function include the brain-derived neurotrophic factor antisense transcript (Bdnf-AS) which regulates expression of the corresponding sense transcript, and LOC389023 which is associated with human-specific histone methylation signatures at the chromosome 2q14.1 neurodevelopmental risk locus by regulating expression of DPP10, an auxillary subunit for voltage-gated K(+) channels. We predict that the exploration of chromatin-bound RNA will significantly advance our current knowledge base in neuroepigenetics and biological psychiatry.
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Affiliation(s)
- J S Tushir
- Friedman Brain Institute, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - S Akbarian
- Friedman Brain Institute, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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Powell WT, Coulson RL, Crary FK, Wong SS, Ach RA, Tsang P, Alice Yamada N, Yasui DH, Lasalle JM. A Prader-Willi locus lncRNA cloud modulates diurnal genes and energy expenditure. Hum Mol Genet 2013; 22:4318-28. [PMID: 23771028 PMCID: PMC3792690 DOI: 10.1093/hmg/ddt281] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Prader–Willi syndrome (PWS), a genetic disorder of obesity, intellectual disability and sleep abnormalities, is caused by loss of non-coding RNAs on paternal chromosome 15q11-q13. The imprinted minimal PWS locus encompasses a long non-coding RNA (lncRNA) transcript processed into multiple SNORD116 small nucleolar RNAs and the spliced exons of the host gene, 116HG. However, both the molecular function and the disease relevance of the spliced lncRNA 116HG are unknown. Here, we show that 116HG forms a subnuclear RNA cloud that co-purifies with the transcriptional activator RBBP5 and active metabolic genes, remains tethered to the site of its transcription and increases in size in post-natal neurons and during sleep. Snord116del mice lacking 116HG exhibited increased energy expenditure corresponding to the dysregulation of diurnally expressed Mtor and circadian genes Clock, Cry1 and Per2. These combined genomic and metabolic analyses demonstrate that 116HG regulates the diurnal energy expenditure of the brain. These novel molecular insights into the energy imbalance in PWS should lead to improved therapies and understanding of lncRNA roles in complex neurodevelopmental and metabolic disorders.
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Affiliation(s)
- Weston T Powell
- Medical Microbiology and Immunology, Genome Center, MIND Institute, University of California, Davis, CA 95616, USA
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Gapp K, Woldemichael BT, Bohacek J, Mansuy IM. Epigenetic regulation in neurodevelopment and neurodegenerative diseases. Neuroscience 2012; 264:99-111. [PMID: 23256926 DOI: 10.1016/j.neuroscience.2012.11.040] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 11/08/2012] [Accepted: 11/21/2012] [Indexed: 01/25/2023]
Abstract
From fertilization throughout development and until death, cellular programs in individual cells are dynamically regulated to fulfill multiple functions ranging from cell lineage specification to adaptation to internal and external stimuli. Such regulation is of major importance in brain cells, because the brain continues to develop long after birth and incorporates information from the environment across life. When compromised, these regulatory mechanisms can have detrimental consequences on neurodevelopment and lead to severe brain pathologies and neurodegenerative diseases in the adult individual. Elucidating these processes is essential to better understand their implication in disease etiology. Because they are strongly influenced by environmental factors, they have been postulated to depend on epigenetic mechanisms. This review describes recent studies that have identified epigenetic dysfunctions in the pathophysiology of several neurodevelopmental and neurodegenerative diseases. It discusses currently known pathways and molecular targets implicated in pathologies including imprinting disorders, Rett syndrome, and Alzheimer's, Parkinson's and Hungtinton's disease, and their relevance to these diseases.
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Affiliation(s)
- K Gapp
- Brain Research Institute, Medical Faculty of the University of Zürich and Swiss Federal Institute of Technology, Neuroscience Center Zürich, Zürich, Switzerland
| | - B T Woldemichael
- Brain Research Institute, Medical Faculty of the University of Zürich and Swiss Federal Institute of Technology, Neuroscience Center Zürich, Zürich, Switzerland
| | - J Bohacek
- Brain Research Institute, Medical Faculty of the University of Zürich and Swiss Federal Institute of Technology, Neuroscience Center Zürich, Zürich, Switzerland
| | - I M Mansuy
- Brain Research Institute, Medical Faculty of the University of Zürich and Swiss Federal Institute of Technology, Neuroscience Center Zürich, Zürich, Switzerland.
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Hibaoui Y, Feki A. Human pluripotent stem cells: applications and challenges in neurological diseases. Front Physiol 2012; 3:267. [PMID: 22934023 PMCID: PMC3429043 DOI: 10.3389/fphys.2012.00267] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 06/25/2012] [Indexed: 12/16/2022] Open
Abstract
The ability to generate human pluripotent stem cells (hPSCs) holds great promise for the understanding and the treatment of human neurological diseases in modern medicine. The hPSCs are considered for their in vitro use as research tools to provide relevant cellular model for human diseases, drug discovery, and toxicity assays and for their in vivo use in regenerative medicine applications. In this review, we highlight recent progress, promises, and challenges of hPSC applications in human neurological disease modeling and therapies.
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Affiliation(s)
- Youssef Hibaoui
- Stem Cell Research Laboratory, Department of Obstetrics and Gynecology, Geneva University Hospitals Geneva, Switzerland
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Joyce EF, Williams BR, Xie T, Wu CT. Identification of genes that promote or antagonize somatic homolog pairing using a high-throughput FISH-based screen. PLoS Genet 2012; 8:e1002667. [PMID: 22589731 PMCID: PMC3349724 DOI: 10.1371/journal.pgen.1002667] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 03/07/2012] [Indexed: 12/22/2022] Open
Abstract
The pairing of homologous chromosomes is a fundamental feature of the meiotic cell. In addition, a number of species exhibit homolog pairing in nonmeiotic, somatic cells as well, with evidence for its impact on both gene regulation and double-strand break (DSB) repair. An extreme example of somatic pairing can be observed in Drosophila melanogaster, where homologous chromosomes remain aligned throughout most of development. However, our understanding of the mechanism of somatic homolog pairing remains unclear, as only a few genes have been implicated in this process. In this study, we introduce a novel high-throughput fluorescent in situ hybridization (FISH) technology that enabled us to conduct a genome-wide RNAi screen for factors involved in the robust somatic pairing observed in Drosophila. We identified both candidate "pairing promoting genes" and candidate "anti-pairing genes," providing evidence that pairing is a dynamic process that can be both enhanced and antagonized. Many of the genes found to be important for promoting pairing are highly enriched for functions associated with mitotic cell division, suggesting a genetic framework for a long-standing link between chromosome dynamics during mitosis and nuclear organization during interphase. In contrast, several of the candidate anti-pairing genes have known interphase functions associated with S-phase progression, DNA replication, and chromatin compaction, including several components of the condensin II complex. In combination with a variety of secondary assays, these results provide insights into the mechanism and dynamics of somatic pairing.
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Affiliation(s)
- Eric F. Joyce
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Benjamin R. Williams
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Tiao Xie
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Image and Data Analysis Core, Harvard Medical School, Boston, Massachusetts, United States of America
| | - C.-ting Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
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