1
|
Kanata E, Duffié R, Schulz EG. Establishment and maintenance of random monoallelic expression. Development 2024; 151:dev201741. [PMID: 38813842 PMCID: PMC11166465 DOI: 10.1242/dev.201741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
This Review elucidates the regulatory principles of random monoallelic expression by focusing on two well-studied examples: the X-chromosome inactivation regulator Xist and the olfactory receptor gene family. Although the choice of a single X chromosome or olfactory receptor occurs in different developmental contexts, common gene regulatory principles guide monoallelic expression in both systems. In both cases, an event breaks the symmetry between genetically and epigenetically identical copies of the gene, leading to the expression of one single random allele, stabilized through negative feedback control. Although many regulatory steps that govern the establishment and maintenance of monoallelic expression have been identified, key pieces of the puzzle are still missing. We provide an overview of the current knowledge and models for the monoallelic expression of Xist and olfactory receptors. We discuss their similarities and differences, and highlight open questions and approaches that could guide the study of other monoallelically expressed genes.
Collapse
Affiliation(s)
- Eleni Kanata
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Rachel Duffié
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Edda G. Schulz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| |
Collapse
|
2
|
Gruhn WH, Tang WW, Dietmann S, Alves-Lopes JP, Penfold CA, Wong FC, Ramakrishna NB, Surani MA. Epigenetic resetting in the human germ line entails histone modification remodeling. SCIENCE ADVANCES 2023; 9:eade1257. [PMID: 36652508 PMCID: PMC9848478 DOI: 10.1126/sciadv.ade1257] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Epigenetic resetting in the mammalian germ line entails acute DNA demethylation, which lays the foundation for gametogenesis, totipotency, and embryonic development. We characterize the epigenome of hypomethylated human primordial germ cells (hPGCs) to reveal mechanisms preventing the widespread derepression of genes and transposable elements (TEs). Along with the loss of DNA methylation, we show that hPGCs exhibit a profound reduction of repressive histone modifications resulting in diminished heterochromatic signatures at most genes and TEs and the acquisition of a neutral or paused epigenetic state without transcriptional activation. Efficient maintenance of a heterochromatic state is limited to a subset of genomic loci, such as evolutionarily young TEs and some developmental genes, which require H3K9me3 and H3K27me3, respectively, for efficient transcriptional repression. Accordingly, transcriptional repression in hPGCs presents an exemplary balanced system relying on local maintenance of heterochromatic features and a lack of inductive cues.
Collapse
Affiliation(s)
- Wolfram H. Gruhn
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
| | - Walfred W.C. Tang
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
| | - Sabine Dietmann
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
- Institute for Informatics, Washington University School of Medicine, St. Louis, MO, USA
| | - João P. Alves-Lopes
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- NORDFERTIL Research Lab Stockholm, Childhood Cancer Research Unit, J9:30, Department of Women’s and Children’s Health, Karolinska Institutet and Karolinska University Hospital, Visionsgatan 4, 17164, Solna, Stockholm, Sweden
| | - Christopher A. Penfold
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Frederick C. K. Wong
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
| | - Navin B. Ramakrishna
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Genome Institute of Singapore, A*STAR, Biopolis, Singapore 138672, Singapore
| | - M. Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| |
Collapse
|
3
|
Florini F, Visone JE, Deitsch KW. Shared Mechanisms for Mutually Exclusive Expression and Antigenic Variation by Protozoan Parasites. Front Cell Dev Biol 2022; 10:852239. [PMID: 35350381 PMCID: PMC8957917 DOI: 10.3389/fcell.2022.852239] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/17/2022] [Indexed: 01/05/2023] Open
Abstract
Cellular decision-making at the level of gene expression is a key process in the development and evolution of every organism. Variations in gene expression can lead to phenotypic diversity and the development of subpopulations with adaptive advantages. A prime example is the mutually exclusive activation of a single gene from within a multicopy gene family. In mammals, this ranges from the activation of one of the two immunoglobulin (Ig) alleles to the choice in olfactory sensory neurons of a single odorant receptor (OR) gene from a family of more than 1,000. Similarly, in parasites like Trypanosoma brucei, Giardia lamblia or Plasmodium falciparum, the process of antigenic variation required to escape recognition by the host immune system involves the monoallelic expression of vsg, vsp or var genes, respectively. Despite the importance of this process, understanding how this choice is made remains an enigma. The development of powerful techniques such as single cell RNA-seq and Hi-C has provided new insights into the mechanisms these different systems employ to achieve monoallelic gene expression. Studies utilizing these techniques have shown how the complex interplay between nuclear architecture, physical interactions between chromosomes and different chromatin states lead to single allele expression. Additionally, in several instances it has been observed that high-level expression of a single gene is preceded by a transient state where multiple genes are expressed at a low level. In this review, we will describe and compare the different strategies that organisms have evolved to choose one gene from within a large family and how parasites employ this strategy to ensure survival within their hosts.
Collapse
Affiliation(s)
| | | | - Kirk W. Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, United States
| |
Collapse
|
4
|
Olfactory receptor choice: a case study for gene regulation in a multi-enhancer system. Curr Opin Genet Dev 2021; 72:101-109. [PMID: 34896807 DOI: 10.1016/j.gde.2021.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/25/2021] [Accepted: 11/11/2021] [Indexed: 12/14/2022]
Abstract
The mammalian genome possesses >2000 olfactory receptor (OR) alleles regulated by 63 known OR-Enhancer elements, yet each olfactory sensory neuron (OSN) expresses only a single OR allele. Choreographed changes to OSN nuclear architecture are evidently necessary for OR expression. Additionally, the insulated organization of OR-enhancers around an OR allele is a hallmark of the chosen OR. However, the biology guiding OR choice itself is unclear. Innovations in single-cell and biophysics-based analysis of nuclear architecture are revising previous models of the nucleus to include its dynamic and probabilistic nature. In this review, we ground current knowledge of OR gene regulation in these emerging theories to speculate on mechanisms that may give rise to diverse and singular OR expression.
Collapse
|
5
|
Abbas G, Tang S, Noble J, Lane RP. Olfactory receptor coding sequences cause silencing of episomal constructs in multiple cell lines. Mol Cell Neurosci 2021; 117:103681. [PMID: 34742908 PMCID: PMC8669572 DOI: 10.1016/j.mcn.2021.103681] [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: 12/29/2020] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022] Open
Abstract
The mammalian olfactory system consists of sensory neurons with specialized odorant-binding capability accomplished by mutually exclusive odorant receptor (OR) expression. Mutually exclusive OR expression is a complex multi-step process regulated by a number of cis and trans factors, including pan-silencing of all OR genes preceding the robust and stable expression of the one OR selected in each sensory neuron. We transfected two olfactory-placode-derived cell lines modeling immature odorant sensory neurons, as well as the GD25 fibroblast cell line, with episomes containing CMV-driven GFP and TK-driven hygromycin reporter genes. We inserted various coding sequences, along with an IRES, immediately upstream of the GFP gene to produce bicistronic mRNAs driven from the local CMV promoter. We found that the presence of several OR coding sequences resulted in significantly diminished episomal expression of GFP in all three cell lines. These findings suggest that OR coding sequences have intrinsic self-silencing capability that might facilitate mutually exclusive OR expression in olfactory sensory neurons by making it less likely that multiple ORs acquire an above-threshold level of expression at once.
Collapse
Affiliation(s)
- Ghazia Abbas
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06457, USA
| | - Spencer Tang
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06457, USA
| | - Joyce Noble
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06457, USA
| | - Robert P Lane
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06457, USA.
| |
Collapse
|
6
|
Jafari S, Henriksson J, Yan H, Alenius M. Stress and odorant receptor feedback during a critical period after hatching regulates olfactory sensory neuron differentiation in Drosophila. PLoS Biol 2021; 19:e3001101. [PMID: 33793547 PMCID: PMC8043390 DOI: 10.1371/journal.pbio.3001101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/13/2021] [Accepted: 03/02/2021] [Indexed: 11/19/2022] Open
Abstract
Here, we reveal that the regulation of Drosophila odorant receptor (OR) expression during the pupal stage is permissive and imprecise. We found that directly after hatching an OR feedback mechanism both directs and refines OR expression. We demonstrate that, as in mice, dLsd1 and Su(var)3-9 balance heterochromatin formation to direct OR expression. We show that the expressed OR induces dLsd1 and Su(var)3-9 expression, linking OR level and possibly function to OR expression. OR expression refinement shows a restricted duration, suggesting that a gene regulatory critical period brings olfactory sensory neuron differentiation to an end. Consistent with a change in differentiation, stress during the critical period represses dLsd1 and Su(var)3-9 expression and makes the early permissive OR expression permanent. This induced permissive gene regulatory state makes OR expression resilient to stress later in life. Hence, during a critical period OR feedback, similar to in mouse OR selection, defines adult OR expression in Drosophila.
Collapse
Affiliation(s)
- Shadi Jafari
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Johan Henriksson
- Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Hua Yan
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Mattias Alenius
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| |
Collapse
|
7
|
Maes T, Mascaró C, Rotllant D, Lufino MMP, Estiarte A, Guibourt N, Cavalcanti F, Griñan-Ferré C, Pallàs M, Nadal R, Armario A, Ferrer I, Ortega A, Valls N, Fyfe M, Martinell M, Castro Palomino JC, Buesa Arjol C. Modulation of KDM1A with vafidemstat rescues memory deficit and behavioral alterations. PLoS One 2020; 15:e0233468. [PMID: 32469975 PMCID: PMC7259601 DOI: 10.1371/journal.pone.0233468] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
Transcription disequilibria are characteristic of many neurodegenerative diseases. The activity-evoked transcription of immediate early genes (IEGs), important for neuronal plasticity, memory and behavior, is altered in CNS diseases and governed by epigenetic modulation. KDM1A, a histone 3 lysine 4 demethylase that forms part of transcription regulation complexes, has been implicated in the control of IEG transcription. Here we report the development of vafidemstat (ORY-2001), a brain penetrant inhibitor of KDM1A and MAOB. ORY-2001 efficiently inhibits brain KDM1A at doses suitable for long term treatment, and corrects memory deficit as assessed in the novel object recognition testing in the Senescence Accelerated Mouse Prone 8 (SAMP8) model for accelerated aging and Alzheimer's disease. Comparison with a selective KDM1A or MAOB inhibitor reveals that KDM1A inhibition is key for efficacy. ORY-2001 further corrects behavior alterations including aggression and social interaction deficits in SAMP8 mice and social avoidance in the rat rearing isolation model. ORY-2001 increases the responsiveness of IEGs, induces genes required for cognitive function and reduces a neuroinflammatory signature in SAMP8 mice. Multiple genes modulated by ORY-2001 are differentially expressed in Late Onset Alzheimer's Disease. Most strikingly, the amplifier of inflammation S100A9 is highly expressed in LOAD and in the hippocampus of SAMP8 mice, and down-regulated by ORY-2001. ORY-2001 is currently in multiple Phase IIa studies.
Collapse
Affiliation(s)
- Tamara Maes
- Oryzon Genomics, S.A., Cornellà de Llobregat, Spain
| | | | | | | | | | | | | | - Christian Griñan-Ferré
- Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, University of Barcelona, Barcelona, Spain
| | - Mercè Pallàs
- Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, University of Barcelona, Barcelona, Spain
| | - Roser Nadal
- Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Antonio Armario
- Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Isidro Ferrer
- Institut de Neuropatologia, Servei Anatomia Patologica, IDIBELL-Hospital Universitari de Bellvitge, L’Hospitalet de Llobregat, Spain
| | | | - Nuria Valls
- Oryzon Genomics, S.A., Cornellà de Llobregat, Spain
| | - Matthew Fyfe
- Oryzon Genomics, S.A., Cornellà de Llobregat, Spain
| | | | | | | |
Collapse
|
8
|
Affiliation(s)
- Longzhi Tan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
9
|
Lysine-specific demethylase-1 (LSD1) depletion disrupts monogenic and monoallelic odorant receptor (OR) expression in an olfactory neuronal cell line. Mol Cell Neurosci 2017; 82:1-11. [PMID: 28414096 DOI: 10.1016/j.mcn.2017.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 04/05/2017] [Accepted: 04/13/2017] [Indexed: 11/22/2022] Open
Abstract
Function of the mammalian olfactory system depends on specialized olfactory sensory neurons (OSNs) that each express only one allele ("monoallelic") of one odorant receptor (OR) gene ("monogenic"). The lysine-specific demethylase-1 (LSD1) protein removes activating H3K4 or silencing H3K9 methylation marks in a variety of developmental contexts, and is thought to be important for proper OR regulation. Most of the focus in the field has been on a potential "activating" function for LSD1; e.g., in the demethylation of H3K9 associated with the expressed OR allele. Here we show that depletion of LSD1 in an immortalized olfactory-placode-derived cell line (OP6) results in multigenic and multiallelic OR transcription per cell, while not seemingly disrupting the ability of these cells to activate new OR genes during clonal expansion. These results are consistent with LSD1 having a role in silencing additional OR alleles, as opposed to being required for the activation of OR alleles, within the OP6 cellular context.
Collapse
|
10
|
Lomvardas S, Maniatis T. Histone and DNA Modifications as Regulators of Neuronal Development and Function. Cold Spring Harb Perspect Biol 2016; 8:8/7/a024208. [PMID: 27371659 DOI: 10.1101/cshperspect.a024208] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA and histone modifications, together with constraints imposed by nuclear architecture, contribute to the transcriptional regulatory landscape of the nervous system. Here, we provide select examples showing how these regulatory layers, often referred to as epigenetic, contribute to neuronal differentiation and function. We describe the interplay between DNA methylation and Polycomb-mediated repression during neuronal differentiation, the role of DNA methylation and long-range enhancer-promoter interactions in Protocadherin promoter choice, and the contribution of heterochromatic silencing and nuclear organization in singular olfactory receptor expression. Finally, we explain how the activity-dependent expression of a histone variant determines the longevity of olfactory sensory neurons.
Collapse
Affiliation(s)
- Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032
| |
Collapse
|
11
|
Regeneration and rewiring of rodent olfactory sensory neurons. Exp Neurol 2016; 287:395-408. [PMID: 27264358 DOI: 10.1016/j.expneurol.2016.06.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/27/2016] [Accepted: 06/01/2016] [Indexed: 12/24/2022]
Abstract
The olfactory sensory neurons are the only neurons in the mammalian nervous system that not only regenerate naturally and in response to injury, but also project to specific targets in the brain. The stem cells in the olfactory epithelium commit to both neuronal and non-neuronal lineages depending on the environmental conditions. They provide a continuous supply of new neurons. A newly generated neuron must express a specific odorant receptor gene and project to a central target consist of axons expressing the same receptor type. Recent studies have provided insights into this highly regulated, complex process. However, the molecular mechanisms that determine the regenerative capacity of stem cells, and the ability of newly generated neurons in directing their axons toward specific targets, remain elusive. Here we review progresses and controversies in the field and offer testable models.
Collapse
|
12
|
Achieving diverse and monoallelic olfactory receptor selection through dual-objective optimization design. Proc Natl Acad Sci U S A 2016; 113:E2889-98. [PMID: 27162367 DOI: 10.1073/pnas.1601722113] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multiple-objective optimization is common in biological systems. In the mammalian olfactory system, each sensory neuron stochastically expresses only one out of up to thousands of olfactory receptor (OR) gene alleles; at the organism level, the types of expressed ORs need to be maximized. Existing models focus only on monoallele activation, and cannot explain recent observations in mutants, especially the reduced global diversity of expressed ORs in G9a/GLP knockouts. In this work we integrated existing information on OR expression, and constructed a comprehensive model that has all its components based on physical interactions. Analyzing the model reveals an evolutionarily optimized three-layer regulation mechanism, which includes zonal segregation, epigenetic barrier crossing coupled to a negative feedback loop that mechanistically differs from previous theoretical proposals, and a previously unidentified enhancer competition step. This model not only recapitulates monoallelic OR expression, but also elucidates how the olfactory system maximizes and maintains the diversity of OR expression, and has multiple predictions validated by existing experimental results. Through making an analogy to a physical system with thermally activated barrier crossing and comparative reverse engineering analyses, the study reveals that the olfactory receptor selection system is optimally designed, and particularly underscores cooperativity and synergy as a general design principle for multiobjective optimization in biology.
Collapse
|
13
|
Abdus-Saboor I, Al Nufal MJ, Agha MV, Ruinart de Brimont M, Fleischmann A, Shykind BM. An Expression Refinement Process Ensures Singular Odorant Receptor Gene Choice. Curr Biol 2016; 26:1083-90. [PMID: 27040780 DOI: 10.1016/j.cub.2016.02.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/25/2015] [Accepted: 02/12/2016] [Indexed: 12/11/2022]
Abstract
Odorant receptor (OR) gene choice in mammals is a paradigmatic example of monogenic and monoallelic transcriptional selection, in which each olfactory sensory neuron (OSN) chooses to express one OR allele from over 1,000 encoded in the genome [1-3]. This process, critical for generation of the circuit from nose to brain [4-6], is thought to occur in two steps: a slow initial phase that randomly activates a single OR allele, followed by a rapid feedback that halts subsequent expression [7-14]. Inherent in this model is a finite failure rate wherein multiple OR alleles may be activated prior to feedback suppression [15, 16]. Confronted with more than one receptor, the neuron would need to activate a refinement mechanism to eliminate multigenic OR expression and resolve unique neuronal identity [16], critical to the generation of the circuit from nose to olfactory bulb. Here we used a genetic approach in mice to reveal a new facet of OR regulation that corrects adventitious activation of multiple OR alleles, restoring monogenic OR expression and unique neuronal identity. Using the tetM71tg model system, in which the M71 OR is expressed in >95% of mature OSNs and potently suppresses the expression of the endogenous OR repertoire [10], we provide clear evidence of a post-selection refinement (PSR) process that winnows down the number of ORs. We further demonstrate that PSR efficiency is linked to OR expression level, suggesting an underlying competitive process and shedding light on OR gene switching and the fundamental mechanism of singular OR choice.
Collapse
Affiliation(s)
- Ishmail Abdus-Saboor
- Weill Cornell Medical College in Qatar, Qatar Foundation - Education City, Doha 24144, Qatar
| | - Mohammed J Al Nufal
- Weill Cornell Medical College in Qatar, Qatar Foundation - Education City, Doha 24144, Qatar
| | - Maha V Agha
- Weill Cornell Medical College in Qatar, Qatar Foundation - Education City, Doha 24144, Qatar
| | - Marion Ruinart de Brimont
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, and INSERM U1050, Paris 75005, France
| | - Alexander Fleischmann
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, and INSERM U1050, Paris 75005, France
| | - Benjamin M Shykind
- Weill Cornell Medical College in Qatar, Qatar Foundation - Education City, Doha 24144, Qatar.
| |
Collapse
|
14
|
Kilinc S, Savarino A, Coleman JH, Schwob JE, Lane RP. Lysine-specific demethylase-1 (LSD1) is compartmentalized at nuclear chromocenters in early post-mitotic cells of the olfactory sensory neuronal lineage. Mol Cell Neurosci 2016; 74:58-70. [PMID: 26947098 DOI: 10.1016/j.mcn.2016.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 01/29/2016] [Accepted: 03/02/2016] [Indexed: 12/12/2022] Open
Abstract
Mammalian olfaction depends on the development of specialized olfactory sensory neurons (OSNs) that each express one odorant receptor (OR) protein from a large family of OR genes encoded in the genome. The lysine-specific demethylase-1 (LSD1) protein removes activating H3K4 or silencing H3K9 methylation marks at gene promoters and is required for proper OR regulation. We show that LSD1 protein exhibits variable organization within nuclei of developing OSNs, and tends to consolidate into a single dominant compartment at the edges of chromocenters within nuclei of early post-mitotic cells of the mouse olfactory epithelium (MOE). Using an immortalized cell line derived from developing olfactory placode, we show that consolidation of LSD1 appears to be cell-cycle regulated, with a peak occurrence in early G1. LSD1 co-compartmentalizes with CoREST, a protein known to collaborate with LSD1 to carry out a variety of chromatin-modifying functions. We show that LSD1 compartments co-localize with 1-3 OR loci at the exclusion of most OR genes, and commonly associate with Lhx2, a transcription factor involved in OR regulation. Together, our data suggests that LSD1 is sequestered into a distinct nuclear space that might restrict a histone-modifying function to a narrow developmental time window and/or range of OR gene targets.
Collapse
Affiliation(s)
- Seda Kilinc
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06457, USA.
| | - Alyssa Savarino
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06457, USA
| | - Julie H Coleman
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - James E Schwob
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Robert P Lane
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06457, USA.
| |
Collapse
|
15
|
Tan L, Li Q, Xie XS. Olfactory sensory neurons transiently express multiple olfactory receptors during development. Mol Syst Biol 2015; 11:844. [PMID: 26646940 PMCID: PMC4704490 DOI: 10.15252/msb.20156639] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In mammals, each olfactory sensory neuron randomly expresses one, and only one, olfactory receptor (OR)--a phenomenon called the "one-neuron-one-receptor" rule. Although extensively studied, this rule was never proven for all ~1,000 OR genes in one cell at once, and little is known about its dynamics. Here, we directly tested this rule by single-cell transcriptomic sequencing of 178 cells from the main olfactory epithelium of adult and newborn mice. To our surprise, a subset of cells expressed multiple ORs. Most of these cells were developmentally immature. Our results illustrated how the "one-neuron-one-receptor" rule may have been established: At first, a single neuron temporarily expressed multiple ORs--seemingly violating the rule--and then all but one OR were eliminated. This work provided experimental evidence that epigenetic regulation in the olfactory system selects a single OR by suppressing a few transiently expressed ORs in a single cell during development.
Collapse
Affiliation(s)
- Longzhi Tan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Qian Li
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - X Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| |
Collapse
|
16
|
Abdus-Saboor I, Fleischmann A, Shykind B. Setting limits: maintaining order in a large gene family. Transcription 2015; 5:e28978. [PMID: 25764336 PMCID: PMC4215173 DOI: 10.4161/trns.28978] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Odorant receptor (OR) gene choice is a paradigmatic example of stochastic regulation in which olfactory neurons choose one OR from > 1,000 possibilities. Recent biochemical, mathematical, and in vivo findings have revealed key players, introduced new axes of control, and brought the core mechanisms of the process into sharper focus.
Collapse
Affiliation(s)
- Ishmail Abdus-Saboor
- a Weill Cornell Medical College in Qatar; Qatar Foundation-Education City; Doha, Qatar
| | | | | |
Collapse
|
17
|
Shukla C, Koch LG, Britton SL, Cai M, Hruby VJ, Bednarek M, Novak CM. Contribution of regional brain melanocortin receptor subtypes to elevated activity energy expenditure in lean, active rats. Neuroscience 2015; 310:252-67. [PMID: 26404873 DOI: 10.1016/j.neuroscience.2015.09.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/10/2015] [Accepted: 09/11/2015] [Indexed: 12/13/2022]
Abstract
Physical activity and non-exercise activity thermogenesis (NEAT) are crucial factors accounting for individual differences in body weight, interacting with genetic predisposition. In the brain, a number of neuroendocrine intermediates regulate food intake and energy expenditure (EE); this includes the brain melanocortin (MC) system, consisting of MC peptides as well as their receptors (MCR). MC3R and MC4R have emerged as critical modulators of EE and food intake. To determine how variance in MC signaling may underlie individual differences in physical activity levels, we examined behavioral response to MC receptor agonists and antagonists in rats that show high and low levels of physical activity and NEAT, that is, high- and low-capacity runners (HCR, LCR), developed by artificial selection for differential intrinsic aerobic running capacity. Focusing on the hypothalamus, we identified brain region-specific elevations in expression of MCR 3, 4, and also MC5R, in the highly active, lean HCR relative to the less active and obesity-prone LCR. Further, the differences in activity and associated EE as a result of MCR activation or suppression using specific agonists and antagonists were similarly region-specific and directly corresponded to the differential MCR expression patterns. The agonists and antagonists investigated here did not significantly impact food intake at the doses used, suggesting that the differential pattern of receptor expression may by more meaningful to physical activity than to other aspects of energy balance regulation. Thus, MCR-mediated physical activity may be a key neural mechanism in distinguishing the lean phenotype and a target for enhancing physical activity and NEAT.
Collapse
Affiliation(s)
- C Shukla
- Department of Biological Sciences, Kent State University, Kent, OH, United States; Harvard Medical School - VA Boston Healthcare System, Boston, MA, United States.
| | - L G Koch
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - S L Britton
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - M Cai
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, United States
| | - V J Hruby
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, United States
| | - M Bednarek
- MedImmune Limited, Cambridge, United Kingdom
| | - C M Novak
- Department of Biological Sciences, Kent State University, Kent, OH, United States
| |
Collapse
|
18
|
Abstract
The sense of smell collects vital information about the environment by detecting a multitude of chemical odorants. Breadth and sensitivity are provided by a huge number of chemosensory receptor proteins, including more than 1,400 olfactory receptors (ORs). Organizing the sensory information generated by these receptors so that it can be processed and evaluated by the central nervous system is a major challenge. This challenge is overcome by monogenic and monoallelic expression of OR genes. The single OR expressed by each olfactory sensory neuron determines the neuron's odor sensitivity and the axonal connections it will make to downstream neurons in the olfactory bulb. The expression of a single OR per neuron is accomplished by coupling a slow chromatin-mediated activation process to a fast negative-feedback signal that prevents activation of additional ORs. Singular OR activation is likely orchestrated by a network of interchromosomal enhancer interactions and large-scale changes in nuclear architecture.
Collapse
Affiliation(s)
- Kevin Monahan
- Department of Biochemistry and Molecular Biophysics, Department of Neuroscience, and Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY 10032; ,
| | - Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Department of Neuroscience, and Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY 10032; ,
| |
Collapse
|
19
|
Ito H, Hasegawa K, Hasegawa Y, Nishimaki T, Hosomichi K, Kimura S, Ohba M, Yao H, Onimaru M, Inoue I, Inoue H. Silver Nanoscale Hexagonal Column Chips for Detecting Cell-free DNA and Circulating Nucleosomes in Cancer Patients. Sci Rep 2015; 5:10455. [PMID: 25994878 PMCID: PMC4440038 DOI: 10.1038/srep10455] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/13/2015] [Indexed: 01/05/2023] Open
Abstract
Blood tests, which are commonly used for cancer screening, generally have low sensitivity. Here, we developed a novel rapid and simple method to generate silver nanoscale hexagonal columns (NHCs) for use in surface-enhanced Raman scattering (SERS). We reported that the intensity of SERS spectra of clinical serum samples obtained from gastrointestinal cancer patients is was significantly higher than that of SERS spectra of clinical serum samples obtained from non-cancer patients. We estimated the combined constituents on silver NHCs by using a field emission-type scanning electron microscope, Raman microscopes, and a 3D laser scanning confocal microscope. We obtained the Raman scattering spectra of samples of physically fractured cells and clinical serum. No spectra were obtained for chemically lysed cultured cells and DNA, RNA, and protein extracted from cultured cells. We believe that our method, which uses SERS with silver NHCs to detect circulating nucleosomes bound by methylated cell-free DNA, may be successfully implemented in blood tests for cancer screening.
Collapse
Affiliation(s)
- Hiroaki Ito
- Digestive Disease Center, Showa University Koto Toyosu Hospital, Tokyo, Japan
| | | | | | - Tadashi Nishimaki
- Unit of Organ Oriented Medicine, Division of Digestive and General Surgery, Department of Medicine, Ryukyu University, Okinawa, Japan
| | | | - Satoshi Kimura
- Department of Laboratory Medicine and Central Clinical Laboratory, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Motoi Ohba
- Institute of Molecular Oncology, Showa University, Tokyo, Japan
| | - Hiroshi Yao
- Graduate School of Material Science, University of Hyogo, Hyogo, Japan
| | - Manabu Onimaru
- Digestive Disease Center, Showa University Koto Toyosu Hospital, Tokyo, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Haruhiro Inoue
- Digestive Disease Center, Showa University Koto Toyosu Hospital, Tokyo, Japan
| |
Collapse
|
20
|
Abstract
The senses provide a means by which data on the physical and chemical properties of the environment may be collected and meaningfully interpreted. Sensation begins at the periphery, where a multitude of different sensory cell types are activated by environmental stimuli as different as photons and odorant molecules. Stimulus sensitivity is due to expression of different cell surface sensory receptors, and therefore the receptive field of each sense is defined by the aggregate of expressed receptors in each sensory tissue. Here, we review current understanding on patterns of expression and modes of regulation of sensory receptors.
Collapse
|
21
|
McClintock TS. Odorant Receptor Gene Choice. CHEMOSENSE 2015; 16:3-13. [PMID: 27942249 PMCID: PMC5142827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
|
22
|
Maes T, Mascaró C, Ortega A, Lunardi S, Ciceri F, Somervaille TCP, Buesa C. KDM1 histone lysine demethylases as targets for treatments of oncological and neurodegenerative disease. Epigenomics 2015; 7:609-26. [PMID: 26111032 DOI: 10.2217/epi.15.9] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Histone methylation and demethylation are important processes associated with the regulation of gene transcription, and alterations in histone methylation status have been linked to a large number of human diseases. Initially thought to be an irreversible process, histone methylation is now known to be reversed by two families of proteins containing over 30 members that act to remove methyl groups from specific lysine residues present in the tails of histone H3 and histone H4. A rapidly growing number of reports have implicated the FAD-dependent lysine specific demethylase (KDM1) family in cancer, and several small-molecule inhibitors are in development for the treatment of cancer. An additional role has emerged for KDM1 in brain function, offering additional opportunities for the development of novel therapeutic strategies in neurodegenerative disease. A decade after the identification of KDM1A as a histone demethylase, the first selective inhibitors have now reached the clinic.
Collapse
Affiliation(s)
- Tamara Maes
- Oryzon Genomics S.A., Carrer Sant Ferran 74, 08940 Cornella de Llobregat, Barcelona, España
| | - Cristina Mascaró
- Oryzon Genomics S.A., Carrer Sant Ferran 74, 08940 Cornella de Llobregat, Barcelona, España
| | - Alberto Ortega
- Oryzon Genomics S.A., Carrer Sant Ferran 74, 08940 Cornella de Llobregat, Barcelona, España
| | - Serena Lunardi
- Oryzon Genomics S.A., Carrer Sant Ferran 74, 08940 Cornella de Llobregat, Barcelona, España
| | - Filippo Ciceri
- Oryzon Genomics S.A., Carrer Sant Ferran 74, 08940 Cornella de Llobregat, Barcelona, España
| | - Tim C P Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, Manchester, M20 4BX, UK
| | - Carlos Buesa
- Oryzon Genomics S.A., Carrer Sant Ferran 74, 08940 Cornella de Llobregat, Barcelona, España
| |
Collapse
|
23
|
Persuy MA, Sanz G, Tromelin A, Thomas-Danguin T, Gibrat JF, Pajot-Augy E. Mammalian olfactory receptors: molecular mechanisms of odorant detection, 3D-modeling, and structure-activity relationships. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 130:1-36. [PMID: 25623335 DOI: 10.1016/bs.pmbts.2014.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This chapter describes the main characteristics of olfactory receptor (OR) genes of vertebrates, including generation of this large multigenic family and pseudogenization. OR genes are compared in relation to evolution and among species. OR gene structure and selection of a given gene for expression in an olfactory sensory neuron (OSN) are tackled. The specificities of OR proteins, their expression, and their function are presented. The expression of OR proteins in locations other than the nasal cavity is regulated by different mechanisms, and ORs display various additional functions. A conventional olfactory signal transduction cascade is observed in OSNs, but individual ORs can also mediate different signaling pathways, through the involvement of other molecular partners and depending on the odorant ligand encountered. ORs are engaged in constitutive dimers. Ligand binding induces conformational changes in the ORs that regulate their level of activity depending on odorant dose. When present, odorant binding proteins induce an allosteric modulation of OR activity. Since no 3D structure of an OR has been yet resolved, modeling has to be performed using the closest G-protein-coupled receptor 3D structures available, to facilitate virtual ligand screening using the models. The study of odorant binding modes and affinities may infer best-bet OR ligands, to be subsequently checked experimentally. The relationship between spatial and steric features of odorants and their activity in terms of perceived odor quality are also fields of research that development of computing tools may enhance.
Collapse
Affiliation(s)
- Marie-Annick Persuy
- INRA UR 1197 NeuroBiologie de l'Olfaction, Domaine de Vilvert, Jouy-en-Josas, France
| | - Guenhaël Sanz
- INRA UR 1197 NeuroBiologie de l'Olfaction, Domaine de Vilvert, Jouy-en-Josas, France
| | - Anne Tromelin
- INRA UMR 1129 Flaveur, Vision et Comportement du Consommateur, Dijon, France
| | | | - Jean-François Gibrat
- INRA UR1077 Mathématique Informatique et Génome, Domaine de Vilvert, Jouy-en-Josas, France
| | - Edith Pajot-Augy
- INRA UR 1197 NeuroBiologie de l'Olfaction, Domaine de Vilvert, Jouy-en-Josas, France.
| |
Collapse
|
24
|
Lyons DB, Magklara A, Goh T, Sampath SC, Schaefer A, Schotta G, Lomvardas S. Heterochromatin-mediated gene silencing facilitates the diversification of olfactory neurons. Cell Rep 2014; 9:884-92. [PMID: 25437545 PMCID: PMC4251488 DOI: 10.1016/j.celrep.2014.10.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 08/29/2014] [Accepted: 09/27/2014] [Indexed: 01/26/2023] Open
Abstract
An astounding property of the nervous system is its cellular diversity. This diversity, which was initially realized by morphological and electrophysiological differences, is ultimately produced by variations in gene-expression programs. In most cases, these variations are determined by external cues. However, a growing number of neuronal types have been identified in which inductive signals cannot explain the few but decisive transcriptional differences that cause cell diversification. Here, we show that heterochromatic silencing, which we find is governed by histone methyltransferases G9a (KMT1C) and GLP (KMT1D), is essential for stochastic and singular olfactory receptor (OR) expression. Deletion of G9a and GLP dramatically reduces the complexity of the OR transcriptome, resulting in transcriptional domination by a few ORs and loss of singularity in OR expression. Thus, our data suggest that, in addition to its previously known functions, heterochromatin creates an epigenetic platform that affords stochastic, mutually exclusive gene choices and promotes cellular diversity.
Collapse
Affiliation(s)
- David B Lyons
- Tetrad Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Angeliki Magklara
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 45110 Ioannina, Greece
| | - Tracie Goh
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94920, USA
| | - Srihari C Sampath
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Anne Schaefer
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Gunnar Schotta
- Munich Center for Integrated Protein Science, Adolf-Butenandt-Institute, Ludwig Maximilian University, Schillerstrasse 44, 80336 Munich, Germany
| | - Stavros Lomvardas
- Tetrad Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94920, USA.
| |
Collapse
|