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Kawaoka J, Lomvardas S. LiMCA: Hi-C gets an RNA twist. Nat Methods 2024:10.1038/s41592-024-02205-w. [PMID: 38622458 DOI: 10.1038/s41592-024-02205-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Affiliation(s)
- Jane Kawaoka
- Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA
| | - Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA.
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2
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Pourmorady AD, Bashkirova EV, Chiariello AM, Belagzhal H, Kodra A, Duffié R, Kahiapo J, Monahan K, Pulupa J, Schieren I, Osterhoudt A, Dekker J, Nicodemi M, Lomvardas S. RNA-mediated symmetry breaking enables singular olfactory receptor choice. Nature 2024; 625:181-188. [PMID: 38123679 PMCID: PMC10765522 DOI: 10.1038/s41586-023-06845-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 11/07/2023] [Indexed: 12/23/2023]
Abstract
Olfactory receptor (OR) choice provides an extreme example of allelic competition for transcriptional dominance, where every olfactory neuron stably transcribes one of approximately 2,000 or more OR alleles1,2. OR gene choice is mediated by a multichromosomal enhancer hub that activates transcription at a single OR3,4, followed by OR-translation-dependent feedback that stabilizes this choice5,6. Here, using single-cell genomics, we show formation of many competing hubs with variable enhancer composition, only one of which retains euchromatic features and transcriptional competence. Furthermore, we provide evidence that OR transcription recruits enhancers and reinforces enhancer hub activity locally, whereas OR RNA inhibits transcription of competing ORs over distance, promoting transition to transcriptional singularity. Whereas OR transcription is sufficient to break the symmetry between equipotent enhancer hubs, OR translation stabilizes transcription at the prevailing hub, indicating that there may be sequential non-coding and coding mechanisms that are implemented by OR alleles for transcriptional prevalence. We propose that coding OR mRNAs possess non-coding functions that influence nuclear architecture, enhance their own transcription and inhibit transcription from their competitors, with generalizable implications for probabilistic cell fate decisions.
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Affiliation(s)
- Ariel D Pourmorady
- Vagelos College of Physicians and Surgeons, Columbia University New York, New York, NY, USA
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
| | - Elizaveta V Bashkirova
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Andrea M Chiariello
- Department of Physics 'Ettore Pancini', University of Naples, and INFN, Napoli, Italy
| | - Houda Belagzhal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Albana Kodra
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Rachel Duffié
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
| | - Jerome Kahiapo
- Department of Molecular Biology & Biochemistry, Rutgers School of Arts and Sciences, Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Kevin Monahan
- Department of Molecular Biology & Biochemistry, Rutgers School of Arts and Sciences, Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Joan Pulupa
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
| | - Ira Schieren
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
| | - Alexa Osterhoudt
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Job Dekker
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mario Nicodemi
- Department of Physics 'Ettore Pancini', University of Naples, and INFN, Napoli, Italy
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, New York, NY, USA.
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3
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Bashkirova EV, Klimpert N, Monahan K, Campbell CE, Osinski J, Tan L, Schieren I, Pourmorady A, Stecky B, Barnea G, Xie XS, Abdus-Saboor I, Shykind BM, Marlin BJ, Gronostajski RM, Fleischmann A, Lomvardas S. Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice. eLife 2023; 12:RP87445. [PMID: 38108811 PMCID: PMC10727497 DOI: 10.7554/elife.87445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Olfactory receptor (OR) choice represents an example of genetically hardwired stochasticity, where every olfactory neuron expresses one out of ~2000 OR alleles in the mouse genome in a probabilistic, yet stereotypic fashion. Here, we propose that topographic restrictions in OR expression are established in neuronal progenitors by two opposing forces: polygenic transcription and genomic silencing, both of which are influenced by dorsoventral gradients of transcription factors NFIA, B, and X. Polygenic transcription of OR genes may define spatially constrained OR repertoires, among which one OR allele is selected for singular expression later in development. Heterochromatin assembly and genomic compartmentalization of OR alleles also vary across the axes of the olfactory epithelium and may preferentially eliminate ectopically expressed ORs with more dorsal expression destinations from this 'privileged' repertoire. Our experiments identify early transcription as a potential 'epigenetic' contributor to future developmental patterning and reveal how two spatially responsive probabilistic processes may act in concert to establish deterministic, precise, and reproducible territories of stochastic gene expression.
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Affiliation(s)
- Elizaveta V Bashkirova
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia UniversityNew YorkUnited States
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Nell Klimpert
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Kevin Monahan
- Department of Biochemistry and Molecular Biology, Rutgers UniversityNewarkUnited States
| | - Christine E Campbell
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
| | - Jason Osinski
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
| | - Longzhi Tan
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Ira Schieren
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Ariel Pourmorady
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia UniversityNew YorkUnited States
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Beka Stecky
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Gilad Barnea
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Xiaoliang Sunney Xie
- Beijing Innovation Center for Genomics, Peking UniversityBeijingChina
- Biomedical Pioneering Innovation Center, Peking UniversityBeijingChina
| | - Ishmail Abdus-Saboor
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Benjamin M Shykind
- Prevail Therapeutics- a wholly-owned subsidiary of Eli Lilly and CompanyNew YorkUnited States
| | - Bianca J Marlin
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Richard M Gronostajski
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
| | - Alexander Fleischmann
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Stavros Lomvardas
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
- Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia UniversityNew YorkUnited States
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4
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Bashkirova EV, Klimpert N, Monahan K, Campbell CE, Osinski JM, Tan L, Schieren I, Pourmorady A, Stecky B, Barnea G, Xie XS, Abdus-Saboor I, Shykind B, Jones-Marlin B, Gronostajski RM, Fleischmann A, Lomvardas S. Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice. bioRxiv 2023:2023.03.15.532726. [PMID: 36993168 PMCID: PMC10055043 DOI: 10.1101/2023.03.15.532726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Olfactory receptor (OR) choice represents an example of genetically hardwired stochasticity, where every olfactory neuron expresses one out of ~2000 OR alleles in a probabilistic, yet stereotypic fashion. Here, we propose that topographic restrictions in OR expression are established in neuronal progenitors by two opposing forces: polygenic transcription and genomic silencing, both of which are influenced by dorsoventral gradients of transcription factors NFIA, B, and X. Polygenic transcription of OR genes may define spatially constrained OR repertoires, among which one OR allele is selected for singular expression later in development. Heterochromatin assembly and genomic compartmentalization of OR alleles also vary across the axes of the olfactory epithelium and may preferentially eliminate ectopically expressed ORs with more dorsal expression destinations from this "privileged" repertoire. Our experiments identify early transcription as a potential "epigenetic" contributor to future developmental patterning and reveal how two spatially responsive probabilistic processes may act in concert to establish deterministic, precise, and reproducible territories of stochastic gene expression.
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Affiliation(s)
- Elizaveta V Bashkirova
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
- Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Nell Klimpert
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Kevin Monahan
- Department of Biochemistry and Molecular Biology, Rutgers University, NJ, USA
| | - Christine E Campbell
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA
| | - Jason M Osinski
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA
| | - Longzhi Tan
- Department of Bioengineering, Stanford University, CA, USA
| | - Ira Schieren
- Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Ariel Pourmorady
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
- Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Beka Stecky
- Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Gilad Barnea
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - X Sunnie Xie
- Beijing Innovation Center for Genomics, Peking University, Beijing, China
- Biomedical Pioneering Innovation Center, Peking University, Beijing, China
| | - Ishmail Abdus-Saboor
- Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Benjamin Shykind
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Bianca Jones-Marlin
- Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Richard M Gronostajski
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA
| | - Alexander Fleischmann
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Stavros Lomvardas
- Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
- Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
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5
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Shayya HJ, Kahiapo JK, Duffié R, Lehmann KS, Bashkirova L, Monahan K, Dalton RP, Gao J, Jiao S, Schieren I, Belluscio L, Lomvardas S. ER stress transforms random olfactory receptor choice into axon targeting precision. Cell 2022; 185:3896-3912.e22. [PMID: 36167070 PMCID: PMC9588687 DOI: 10.1016/j.cell.2022.08.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 01/26/2023]
Abstract
Olfactory sensory neurons (OSNs) convert the stochastic choice of one of >1,000 olfactory receptor (OR) genes into precise and stereotyped axon targeting of OR-specific glomeruli in the olfactory bulb. Here, we show that the PERK arm of the unfolded protein response (UPR) regulates both the glomerular coalescence of like axons and the specificity of their projections. Subtle differences in OR protein sequences lead to distinct patterns of endoplasmic reticulum (ER) stress during OSN development, converting OR identity into distinct gene expression signatures. We identify the transcription factor Ddit3 as a key effector of PERK signaling that maps OR-dependent ER stress patterns to the transcriptional regulation of axon guidance and cell-adhesion genes, instructing targeting precision. Our results extend the known functions of the UPR from a quality-control pathway that protects cells from misfolded proteins to a sensor of cellular identity that interprets physiological states to direct axon wiring.
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Affiliation(s)
- Hani J Shayya
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Medical Scientist Training Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Jerome K Kahiapo
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Rachel Duffié
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Katherine S Lehmann
- Developmental Neural Plasticity Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lisa Bashkirova
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Kevin Monahan
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Ryan P Dalton
- The Miller Institute for Basic Research in Science, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joanna Gao
- Barnard College, New York, NY 10025, USA
| | - Song Jiao
- Developmental Neural Plasticity Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ira Schieren
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Leonardo Belluscio
- Developmental Neural Plasticity Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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6
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Frere JJ, Serafini RA, Pryce KD, Zazhytska M, Oishi K, Golynker I, Panis M, Zimering J, Horiuchi S, Hoagland DA, Møller R, Ruiz A, Kodra A, Overdevest JB, Canoll PD, Borczuk AC, Chandar V, Bram Y, Schwartz R, Lomvardas S, Zachariou V, tenOever BR. SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery. Sci Transl Med 2022; 14:eabq3059. [PMID: 35857629 PMCID: PMC9210449 DOI: 10.1126/scitranslmed.abq3059] [Citation(s) in RCA: 100] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/27/2022] [Indexed: 12/14/2022]
Abstract
The host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can result in prolonged pathologies collectively referred to as post-acute sequalae of COVID-19 (PASC) or long COVID. To better understand the mechanism underlying long COVID biology, we compared the short- and long-term systemic responses in the golden hamster after either SARS-CoV-2 or influenza A virus (IAV) infection. Results demonstrated that SARS-CoV-2 exceeded IAV in its capacity to cause permanent injury to the lung and kidney and uniquely affected the olfactory bulb (OB) and olfactory epithelium (OE). Despite a lack of detectable infectious virus, the OB and OE demonstrated myeloid and T cell activation, proinflammatory cytokine production, and an interferon response that correlated with behavioral changes extending a month after viral clearance. These sustained transcriptional changes could also be corroborated from tissue isolated from individuals who recovered from COVID-19. These data highlight a molecular mechanism for persistent COVID-19 symptomology and provide a small animal model to explore future therapeutics.
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Affiliation(s)
- Justin J. Frere
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016
| | - Randal A. Serafini
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kerri D. Pryce
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Marianna Zazhytska
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027
| | - Kohei Oishi
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016
| | - Ilona Golynker
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016
| | - Maryline Panis
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016
| | - Jeffrey Zimering
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Shu Horiuchi
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016
| | | | - Rasmus Møller
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016
| | - Anne Ruiz
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Albana Kodra
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027
| | - Jonathan B. Overdevest
- Department of Otolaryngology- Head and Neck Surgery, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Peter D. Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Alain C. Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021
| | - Vasuretha Chandar
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY 10021
| | - Yaron Bram
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY 10021
| | - Robert Schwartz
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY 10021
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027
| | - Venetia Zachariou
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Benjamin R. tenOever
- Department of Microbiology, New York University, Grossman School of Medicine, New York, NY 10016
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7
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Zazhytska M, Kodra A, Hoagland DA, Frere J, Fullard JF, Shayya H, McArthur NG, Moeller R, Uhl S, Omer AD, Gottesman ME, Firestein S, Gong Q, Canoll PD, Goldman JE, Roussos P, tenOever BR, Jonathan B Overdevest, Lomvardas S. Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia. Cell 2022; 185:1052-1064.e12. [PMID: 35180380 PMCID: PMC8808699 DOI: 10.1016/j.cell.2022.01.024] [Citation(s) in RCA: 127] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/06/2021] [Accepted: 01/26/2022] [Indexed: 12/22/2022]
Abstract
SARS-CoV-2 infects less than 1% of cells in the human body, yet it can cause severe damage in a variety of organs. Thus, deciphering the non-cell-autonomous effects of SARS-CoV-2 infection is imperative for understanding the cellular and molecular disruption it elicits. Neurological and cognitive defects are among the least understood symptoms of COVID-19 patients, with olfactory dysfunction being their most common sensory deficit. Here, we show that both in humans and hamsters, SARS-CoV-2 infection causes widespread downregulation of olfactory receptors (ORs) and of their signaling components. This non-cell-autonomous effect is preceded by a dramatic reorganization of the neuronal nuclear architecture, which results in dissipation of genomic compartments harboring OR genes. Our data provide a potential mechanism by which SARS-CoV-2 infection alters the cellular morphology and the transcriptome of cells it cannot infect, offering insight to its systemic effects in olfaction and beyond.
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Affiliation(s)
- Marianna Zazhytska
- Mortimer B. Zuckerman Mind, and Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Albana Kodra
- Mortimer B. Zuckerman Mind, and Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Genetics and Development, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Daisy A Hoagland
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Justin Frere
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Hani Shayya
- Mortimer B. Zuckerman Mind, and Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Genetics and Development, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Natalie G McArthur
- Department of Biological Sciences, Columbia University New York, NY 10027, USA
| | - Rasmus Moeller
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Skyler Uhl
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Arina D Omer
- Baylor Genetics, 2450 Holcombe Blvd, Houston, TX 77021, USA
| | - Max E Gottesman
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Stuart Firestein
- Department of Biological Sciences, Columbia University New York, NY 10027, USA
| | - Qizhi Gong
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Peter D Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - James E Goldman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA.
| | - Jonathan B Overdevest
- Department of Otolaryngology, Head and Neck Surgery, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind, and Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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8
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Zazhytska M, Kodra A, Hoagland DA, Fullard JF, Shayya H, Omer A, Firestein S, Gong Q, Canoll PD, Goldman JE, Roussos P, tenOever BR, Overdevest JB, Lomvardas S. Disruption of nuclear architecture as a cause of COVID-19 induced anosmia. bioRxiv 2021:2021.02.09.430314. [PMID: 33594368 PMCID: PMC7885920 DOI: 10.1101/2021.02.09.430314] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Olfaction relies on a coordinated partnership between odorant flow and neuronal communication. Disruption in our ability to detect odors, or anosmia, has emerged as a hallmark symptom of infection with SARS-CoV-2, yet the mechanism behind this abrupt sensory deficit remains elusive. Here, using molecular evaluation of human olfactory epithelium (OE) from subjects succumbing to COVID-19 and a hamster model of SARS-CoV-2 infection, we discovered widespread downregulation of olfactory receptors (ORs) as well as key components of their signaling pathway. OR downregulation likely represents a non-cell autonomous effect, since SARS-CoV-2 detection in OSNs is extremely rare both in human and hamster OEs. A likely explanation for the reduction of OR transcription is the striking reorganization of nuclear architecture observed in the OSN lineage, which disrupts multi-chromosomal compartments regulating OR expression in humans and hamsters. Our experiments uncover a novel molecular mechanism by which a virus with a very selective tropism can elicit persistent transcriptional changes in cells that evade it, contributing to the severity of COVID-19.
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Affiliation(s)
- Marianna Zazhytska
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Albana Kodra
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Daisy A Hoagland
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA
| | - John F Fullard
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA
| | - Hani Shayya
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Arina Omer
- Baylor Genetics, 2450 Holcombe Blvd, Houston, TX, 77021, USA
| | - Stuart Firestein
- Department of Biological Sciences, Columbia University New York, NY, 10027, USA
| | - Qizhi Gong
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Peter D Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - James E Goldman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Panos Roussos
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA
| | - Jonathan B Overdevest
- Department of Otolaryngology- Head and Neck Surgery, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
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9
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Greenberg ME, Lomvardas S. Editorial: Neural epigenetics. Curr Opin Neurobiol 2019; 59:iii-v. [PMID: 31787169 DOI: 10.1016/j.conb.2019.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Mukai J, Cannavò E, Crabtree GW, Sun Z, Diamantopoulou A, Thakur P, Chang CY, Cai Y, Lomvardas S, Takata A, Xu B, Gogos JA. Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mice. Neuron 2019; 104:471-487.e12. [PMID: 31606247 DOI: 10.1016/j.neuron.2019.09.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 07/28/2019] [Accepted: 09/10/2019] [Indexed: 12/15/2022]
Abstract
SETD1A, a lysine-methyltransferase, is a key schizophrenia susceptibility gene. Mice carrying a heterozygous loss-of-function mutation of the orthologous gene exhibit alterations in axonal branching and cortical synaptic dynamics accompanied by working memory deficits. We show that Setd1a binds both promoters and enhancers with a striking overlap between Setd1a and Mef2 on enhancers. Setd1a targets are highly expressed in pyramidal neurons and display a complex pattern of transcriptional up- and downregulations shaped by presumed opposing functions of Setd1a on promoters and Mef2-bound enhancers. Notably, evolutionarily conserved Setd1a targets are associated with neuropsychiatric genetic risk burden. Reinstating Setd1a expression in adulthood rescues cognitive deficits. Finally, we identify LSD1 as a major counteracting demethylase for Setd1a and show that its pharmacological antagonism results in a full rescue of the behavioral and morphological deficits in Setd1a-deficient mice. Our findings advance understanding of how SETD1A mutations predispose to schizophrenia (SCZ) and point to novel therapeutic interventions.
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Affiliation(s)
- Jun Mukai
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA
| | - Enrico Cannavò
- Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA
| | - Gregg W Crabtree
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA
| | - Ziyi Sun
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Anastasia Diamantopoulou
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Pratibha Thakur
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA
| | - Chia-Yuan Chang
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Yifei Cai
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University, New York, NY 10032, USA
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Bin Xu
- Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA
| | - Joseph A Gogos
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA; Department of Neuroscience, Columbia University, New York, NY 10032, USA.
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11
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Bashkirova E, Lomvardas S. Olfactory receptor genes make the case for inter-chromosomal interactions. Curr Opin Genet Dev 2019; 55:106-113. [PMID: 31491591 DOI: 10.1016/j.gde.2019.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 12/11/2022]
Abstract
The partitioning of the interphase nucleus into chromosome territories generally precludes DNA from making specific and reproducible inter-chromosomal contacts. However, with the development of powerful genomic and imaging tools for the analysis of the 3D genome, and with their application on an increasing number of cell types, it becomes apparent that regulated, specific, and functionally important inter-chromosomal contacts exist. Widespread and stereotypic inter-chromosomal interactions are at the center of chemosensation, where they regulate the singular and stochastic expression of olfactory receptor genes. In olfactory sensory neurons (OSNs) coalescence of multiple intergenic enhancers to a multi-chromosomal hub orchestrates the expression of a single OR allele, whereas convergence of the remaining OR genes from 18 chromosomes into a few heterochromatic compartments mediates their effective transcriptional silencing. In this review we describe the role of interchromosomal interactions in OR gene choice, and we describe other biological systems where such genomic interactions may contribute to regulatory robustness and transcriptional diversification.
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Affiliation(s)
- Elizaveta Bashkirova
- Department of Biochemistry and Molecular Biophysics, Roy Vangelos Columbia University Medical Center, New York, NY 10032, United States
| | - Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Roy Vangelos Columbia University Medical Center, New York, NY 10032, United States; Department of Neuroscience, Roy Vangelos Columbia University Medical Center, Columbia University, New York, NY 10032, United States; Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, United States; Kavli Institute for Neurosciences at Columbia University, New York, NY 10027, United States.
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12
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Alexander JM, Guan J, Li B, Maliskova L, Song M, Shen Y, Huang B, Lomvardas S, Weiner OD. Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. eLife 2019; 8:e41769. [PMID: 31124784 PMCID: PMC6534382 DOI: 10.7554/elife.41769] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 05/08/2019] [Indexed: 12/13/2022] Open
Abstract
Enhancers are important regulatory elements that can control gene activity across vast genetic distances. However, the underlying nature of this regulation remains obscured because it has been difficult to observe in living cells. Here, we visualize the spatial organization and transcriptional output of the key pluripotency regulator Sox2 and its essential enhancer Sox2 Control Region (SCR) in living embryonic stem cells (ESCs). We find that Sox2 and SCR show no evidence of enhanced spatial proximity and that spatial dynamics of this pair is limited over tens of minutes. Sox2 transcription occurs in short, intermittent bursts in ESCs and, intriguingly, we find this activity demonstrates no association with enhancer proximity, suggesting that direct enhancer-promoter contacts do not drive contemporaneous Sox2 transcription. Our study establishes a framework for interrogation of enhancer function in living cells and supports an unexpected mechanism for enhancer control of Sox2 expression that uncouples transcription from enhancer proximity.
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Affiliation(s)
- Jeffrey M Alexander
- Cardiovascular Research InstituteUniversity of California, San FranciscoSan FranciscoUnited States
| | - Juan Guan
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
| | - Bingkun Li
- Institute for Human GeneticsUniversity of California, San FranciscoSan FranciscoUnited States
| | - Lenka Maliskova
- Institute for Human GeneticsUniversity of California, San FranciscoSan FranciscoUnited States
| | - Michael Song
- Institute for Human GeneticsUniversity of California, San FranciscoSan FranciscoUnited States
- Pharmaceutical Sciences and Pharmacogenomics Graduate ProgramUniversity of California, San FranciscoSan FranciscoUnited States
| | - Yin Shen
- Institute for Human GeneticsUniversity of California, San FranciscoSan FranciscoUnited States
- Pharmaceutical Sciences and Pharmacogenomics Graduate ProgramUniversity of California, San FranciscoSan FranciscoUnited States
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Bo Huang
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and BiophysicsUniversity of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Stavros Lomvardas
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
- Mortimer B Zuckerman Mind Brain and Behavior InstituteColumbia UniversityNew York CityUnited States
| | - Orion D Weiner
- Cardiovascular Research InstituteUniversity of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and BiophysicsUniversity of California, San FranciscoSan FranciscoUnited States
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13
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Canzio D, Nwakeze CL, Horta A, Rajkumar SM, Coffey EL, Duffy EE, Duffié R, Monahan K, O'Keeffe S, Simon MD, Lomvardas S, Maniatis T. Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice. Cell 2019; 177:639-653.e15. [PMID: 30955885 DOI: 10.1016/j.cell.2019.03.008] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 11/08/2018] [Accepted: 03/04/2019] [Indexed: 11/15/2022]
Abstract
Stochastic activation of clustered Protocadherin (Pcdh) α, β, and γ genes generates a cell-surface identity code in individual neurons that functions in neural circuit assembly. Here, we show that Pcdhα gene choice involves the activation of an antisense promoter located in the first exon of each Pcdhα alternate gene. Transcription of an antisense long noncoding RNA (lncRNA) from this antisense promoter extends through the sense promoter, leading to DNA demethylation of the CTCF binding sites proximal to each promoter. Demethylation-dependent CTCF binding to both promoters facilitates cohesin-mediated DNA looping with a distal enhancer (HS5-1), locking in the transcriptional state of the chosen Pcdhα gene. Uncoupling DNA demethylation from antisense transcription by Tet3 overexpression in mouse olfactory neurons promotes CTCF binding to all Pcdhα promoters, resulting in proximity-biased DNA looping of the HS5-1 enhancer. Thus, antisense transcription-mediated promoter demethylation functions as a mechanism for distance-independent enhancer/promoter DNA looping to ensure stochastic Pcdhα promoter choice.
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Affiliation(s)
- Daniele Canzio
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Chiamaka L Nwakeze
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Adan Horta
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Sandy M Rajkumar
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Eliot L Coffey
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Erin E Duffy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06516, USA
| | - Rachel Duffié
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Kevin Monahan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Sean O'Keeffe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06516, USA
| | - Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; New York Genome Center, New York, NY 10013, USA.
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14
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Weyn-Vanhentenryck SM, Feng H, Ustianenko D, Duffié R, Yan Q, Jacko M, Martinez JC, Goodwin M, Zhang X, Hengst U, Lomvardas S, Swanson MS, Zhang C. Precise temporal regulation of alternative splicing during neural development. Nat Commun 2018; 9:2189. [PMID: 29875359 PMCID: PMC5989265 DOI: 10.1038/s41467-018-04559-0] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/09/2018] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing (AS) is one crucial step of gene expression that must be tightly regulated during neurodevelopment. However, the precise timing of developmental splicing switches and the underlying regulatory mechanisms are poorly understood. Here we systematically analyze the temporal regulation of AS in a large number of transcriptome profiles of developing mouse cortices, in vivo purified neuronal subtypes, and neurons differentiated in vitro. Our analysis reveals early-switch and late-switch exons in genes with distinct functions, and these switches accurately define neuronal maturation stages. Integrative modeling suggests that these switches are under direct and combinatorial regulation by distinct sets of neuronal RNA-binding proteins including Nova, Rbfox, Mbnl, and Ptbp. Surprisingly, various neuronal subtypes in the sensory systems lack Nova and/or Rbfox expression. These neurons retain the "immature" splicing program in early-switch exons, affecting numerous synaptic genes. These results provide new insights into the organization and regulation of the neurodevelopmental transcriptome.
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Affiliation(s)
- Sebastien M Weyn-Vanhentenryck
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Huijuan Feng
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
- Department of Automation, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST, Tsinghua University, Beijing, 100084, China
| | - Dmytro Ustianenko
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Rachel Duffié
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Qinghong Yan
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
- Department of Comparative Biology and Safety Sciences, Amgen Inc., Cambridge, MA, 02141, USA
| | - Martin Jacko
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Jose C Martinez
- Department of Pathology and Cell Biology, The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, 10032, USA
| | - Marianne Goodwin
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - Xuegong Zhang
- Department of Automation, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST, Tsinghua University, Beijing, 100084, China
| | - Ulrich Hengst
- Department of Pathology and Cell Biology, The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, 10032, USA
| | - Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - Chaolin Zhang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA.
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15
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Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S. The 4D nucleome project. Nature 2018; 549:219-226. [PMID: 28905911 DOI: 10.1038/nature23884] [Citation(s) in RCA: 415] [Impact Index Per Article: 69.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/27/2017] [Indexed: 12/19/2022]
Abstract
The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights into how the nucleus is organized and functions. The project will develop and benchmark experimental and computational approaches for measuring genome conformation and nuclear organization, and investigate how these contribute to gene regulation and other genome functions. Validated experimental technologies will be combined with biophysical approaches to generate quantitative models of spatial genome organization in different biological states, both in cell populations and in single cells.
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Affiliation(s)
- Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Howard Hughes Medical Institute, Worcester, Massachusetts 01605, USA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Victor O Leshyk
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, New York 10027, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Clodagh C O'Shea
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, University of California San Diego, La Jolla California 92093, USA
| | - Joan C Ritland Politz
- Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Howard Hughes Medical Institute, Seattle, Washington 98109, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
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16
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Le Gros MA, Clowney EJ, Magklara A, Yen A, Markenscoff-Papadimitriou E, Colquitt B, Myllys M, Kellis M, Lomvardas S, Larabell CA. Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo. Cell Rep 2017; 17:2125-2136. [PMID: 27851973 DOI: 10.1016/j.celrep.2016.10.060] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 08/28/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
The realization that nuclear distribution of DNA, RNA, and proteins differs between cell types and developmental stages suggests that nuclear organization serves regulatory functions. Understanding the logic of nuclear architecture and how it contributes to differentiation and cell fate commitment remains challenging. Here, we use soft X-ray tomography (SXT) to image chromatin organization, distribution, and biophysical properties during neurogenesis in vivo. Our analyses reveal that chromatin with similar biophysical properties forms an elaborate connected network throughout the entire nucleus. Although this interconnectivity is present in every developmental stage, differentiation proceeds with concomitant increase in chromatin compaction and re-distribution of condensed chromatin toward the nuclear core. HP1β, but not nucleosome spacing or phasing, regulates chromatin rearrangements because it governs both the compaction of chromatin and its interactions with the nuclear envelope. Our experiments introduce SXT as a powerful imaging technology for nuclear architecture.
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Affiliation(s)
- Mark A Le Gros
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94158, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; National Center for X-Ray Tomography, University of California San Francisco, San Francisco, CA 94158, USA; Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - E Josephine Clowney
- Program in Biomedical Sciences, 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, Ioannina, Greece
| | - Angela Yen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | | | - Bradley Colquitt
- Program in Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Markko Myllys
- Department of Physics, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - Stavros Lomvardas
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94158, USA; Program in Biomedical Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Program in Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Carolyn A Larabell
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94158, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; National Center for X-Ray Tomography, University of California San Francisco, San Francisco, CA 94158, USA.
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17
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Monahan K, Schieren I, Cheung J, Mumbey-Wafula A, Monuki ES, Lomvardas S. Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons. eLife 2017; 6. [PMID: 28933695 PMCID: PMC5608512 DOI: 10.7554/elife.28620] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 08/28/2017] [Indexed: 12/16/2022] Open
Abstract
The monogenic and monoallelic expression of only one out of >1000 mouse olfactory receptor (ORs) genes requires the formation of large heterochromatic chromatin domains that sequester the OR gene clusters. Within these domains, intergenic transcriptional enhancers evade heterochromatic silencing and converge into interchromosomal hubs that assemble over the transcriptionally active OR. The significance of this nuclear organization in OR choice remains elusive. Here, we show that transcription factors Lhx2 and Ebf specify OR enhancers by binding in a functionally cooperative fashion to stereotypically spaced motifs that defy heterochromatin. Specific displacement of Lhx2 and Ebf from OR enhancers resulted in pervasive, long-range, and trans downregulation of OR transcription, whereas pre-assembly of a multi-enhancer hub increased the frequency of OR choice in cis. Our data provide genetic support for the requirement and sufficiency of interchromosomal interactions in singular OR choice and generate general regulatory principles for stochastic, mutually exclusive gene expression programs.
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Affiliation(s)
- Kevin Monahan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - Ira Schieren
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - Jonah Cheung
- New York Structural Biology Center, New York, United States
| | - Alice Mumbey-Wafula
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - Edwin S Monuki
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, United States
| | - Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Department of Neuroscience, Columbia University, New York, United States.,Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, United States
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18
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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.
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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
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19
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Abstract
Genetic material is not randomly organized within the nucleus of a cell. How this organization occurs and why it matters are questions that Cell editor Marta Koch posed to Mitchell Guttman, Job Dekker, and Stavros Lomvardas. Excerpts from this Conversation are presented below, and an audio file of the full discussion is available with the article online.
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20
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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.
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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; ,
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21
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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.
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22
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Chadwick LH, Sawa A, Yang IV, Baccarelli A, Breakefield XO, Deng HW, Dolinoy DC, Fallin MD, Holland NT, Houseman EA, Lomvardas S, Rao M, Satterlee JS, Tyson FL, Vijayanand P, Greally JM. New insights and updated guidelines for epigenome-wide association studies. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.nepig.2014.10.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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24
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Markenscoff-Papadimitriou E, Allen WE, Colquitt BM, Goh T, Murphy KK, Monahan K, Mosley CP, Ahituv N, Lomvardas S. Enhancer interaction networks as a means for singular olfactory receptor expression. Cell 2014; 159:543-57. [PMID: 25417106 PMCID: PMC4243057 DOI: 10.1016/j.cell.2014.09.033] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 07/07/2014] [Accepted: 09/10/2014] [Indexed: 12/20/2022]
Abstract
The transcriptional activation of one out of ?2800 olfactory receptor (OR) alleles is a poorly understood process. Here, we identify a plethora of putative OR enhancers and study their in vivo activity in olfactory neurons. Distinguished by an unusual epigenetic signature, candidate OR enhancers are characterized by extensive interchromosomal interactions associated with OR transcription and share a similar pattern of transcription factor footprints. In particular, we establish the role of the transcription factor Bptf as a facilitator of both enhancer interactions and OR transcription. Our observations agree with the model whereby OR transcription occurs in the context of multiple interacting enhancers. Disruption of these interchromosomal interactions results in weak and multigenic OR expression, suggesting that the rare coincidence of numerous enhancers over a stochastically chosen OR may account for the singularity and robustness in OR transcription.
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Affiliation(s)
| | - William E Allen
- Neuroscience Graduate Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bradley M Colquitt
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tracie Goh
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Karl K Murphy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevin Monahan
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Colleen P Mosley
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stavros Lomvardas
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA.
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Lyons DB, Lomvardas S. Repressive histone methylation: a case study in deterministic versus stochastic gene regulation. Biochim Biophys Acta 2014; 1839:1373-84. [PMID: 24859457 DOI: 10.1016/j.bbagrm.2014.05.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/09/2014] [Accepted: 05/13/2014] [Indexed: 01/21/2023]
Abstract
Transcriptionally repressive histone lysine methylation is used by eukaryotes to tightly control cell fate. Here we explore the importance of this form of regulation in the control of clustered genes in the genome. Two distinctly regulated gene families with important roles in vertebrates are discussed, namely the Hox genes and olfactory receptor genes. Major recent advances in these two fields are compared and contrasted, with an emphasis on the roles of the two different forms of histone trimethylation. We discuss how this repression may impact both the transcriptional output of these loci and the way higher-order chromatin organization is related to their unique control.
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Affiliation(s)
- David B Lyons
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stavros Lomvardas
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Anatomy, University of California San Francisco, CA 94920, USA.
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26
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Alexander JM, Lomvardas S. Nuclear architecture as an epigenetic regulator of neural development and function. Neuroscience 2014; 264:39-50. [PMID: 24486963 PMCID: PMC4006947 DOI: 10.1016/j.neuroscience.2014.01.044] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/11/2014] [Accepted: 01/22/2014] [Indexed: 12/23/2022]
Abstract
The nervous system of higher organisms is characterized by an enormous diversity of cell types that function in concert to carry out a myriad of neuronal functions. Differences in connectivity, and subsequent physiology of the connected neurons, are a result of differences in transcriptional programs. The extraordinary complexity of the nervous system requires an equally complex regulatory system. It is well established that transcription factor combinations and the organization of cis-regulatory sequences control commitment to differentiation programs and preserve a nuclear plasticity required for neuronal functions. However, an additional level of regulation is provided by epigenetic controls. Among various epigenetic processes, nuclear organization and the control of genome architecture emerge as an efficient and powerful form of gene regulation that meets the unique needs of the post-mitotic neuron. Here, we present an outline of how nuclear architecture affects transcription and provide examples from the recent literature where these principles are used by the nervous system.
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Affiliation(s)
- J M Alexander
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - S Lomvardas
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA.
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27
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Fancy SPJ, Harrington EP, Baranzini SE, Silbereis JC, Shiow LR, Yuen TJ, Huang EJ, Lomvardas S, Rowitch DH. Parallel states of pathological Wnt signaling in neonatal brain injury and colon cancer. Nat Neurosci 2014; 17:506-12. [PMID: 24609463 PMCID: PMC3975168 DOI: 10.1038/nn.3676] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 02/13/2014] [Indexed: 02/07/2023]
Abstract
In colon cancer, mutation of the Wnt repressor Adenomatous polyposis coli (APC) leads to a state of aberrant and unrestricted “high-activity” signaling. However, relevance of high Wnt tone in non-genetic human disease is unknown. Here we demonstrate that distinct Wnt activity functional states determine oligodendrocyte precursor (OPC) differentiation and myelination. Murine OPCs with genetic Wnt dysregulation (high tone) express multiple genes in common with colon cancer including Lef1, SP5, Ets2, Rnf43 and Dusp4. Surprisingly, we find that OPCs in lesions of hypoxic human neonatal white matter injury upregulate markers of high Wnt activity and lack expression of APC. Finally, we show lack of Wnt repressor tone promotes permanent white matter injury after mild hypoxic insult. These findings suggest a state of pathological high-activity Wnt signaling in human disease tissues that lack pre-disposing genetic mutation.
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Affiliation(s)
- Stephen P J Fancy
- 1] Department of Pediatrics, University of California, San Francisco (UCSF), San Francisco, California, USA. [2] Department of Neurology, UCSF, San Francisco, California, USA. [3] Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine and Howard Hughes Medical Institute, UCSF, San Francisco, California, USA. [4]
| | - Emily P Harrington
- 1] Department of Pediatrics, University of California, San Francisco (UCSF), San Francisco, California, USA. [2] Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine and Howard Hughes Medical Institute, UCSF, San Francisco, California, USA. [3] Medical Scientist Training Program, UCSF, San Francisco, California, USA. [4]
| | | | - John C Silbereis
- 1] Department of Pediatrics, University of California, San Francisco (UCSF), San Francisco, California, USA. [2] Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine and Howard Hughes Medical Institute, UCSF, San Francisco, California, USA
| | - Lawrence R Shiow
- 1] Department of Pediatrics, University of California, San Francisco (UCSF), San Francisco, California, USA. [2] Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine and Howard Hughes Medical Institute, UCSF, San Francisco, California, USA
| | - Tracy J Yuen
- 1] Department of Pediatrics, University of California, San Francisco (UCSF), San Francisco, California, USA. [2] Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine and Howard Hughes Medical Institute, UCSF, San Francisco, California, USA
| | - Eric J Huang
- Department of Pathology, UCSF, San Francisco, California, USA
| | | | - David H Rowitch
- 1] Department of Pediatrics, University of California, San Francisco (UCSF), San Francisco, California, USA. [2] Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine and Howard Hughes Medical Institute, UCSF, San Francisco, California, USA
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28
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Dalton RP, Lyons DB, Lomvardas S. Co-opting the unfolded protein response to elicit olfactory receptor feedback. Cell 2013; 155:321-32. [PMID: 24120133 DOI: 10.1016/j.cell.2013.09.033] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 09/10/2013] [Accepted: 09/19/2013] [Indexed: 11/19/2022]
Abstract
Olfactory receptor (OR) expression requires the transcriptional activation of 1 out of 1,000s of OR alleles and a feedback signal that preserves this transcriptional choice. The mechanism by which olfactory sensory neurons (OSNs) detect ORs to signal to the nucleus remains elusive. Here, we show that OR proteins generate this feedback by activating the unfolded protein response (UPR). OR expression induces Perk-mediated phosphorylation of the translation initiation factor eif2α causing selective translation of activating transcription factor 5 (ATF5). ATF5 induces the transcription of adenylyl cyclase 3 (Adcy3), which relieves the UPR. Our data provide a role for the UPR in defining neuronal identity and cell fate commitment and support a two-step model for the feedback signal: (1) OR protein, as a stress stimulus, alters the translational landscape of the OSN and induces Adcy3 expression; (2), Adcy3 relieves that stress, restores global translation, and makes OR choice permanent.
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Affiliation(s)
- Ryan P Dalton
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94158, USA; Neuroscience Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
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29
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Abstract
One of the remarkable characteristics of higher organisms is the enormous assortment of cell types that emerge from a common genome. The immune system, with the daunting duty of detecting an astounding number of pathogens, and the nervous system with the equally bewildering task of perceiving and interpreting the external world, are the quintessence of cellular diversity. As we began to appreciate decades ago, achieving distinct expression programs among similar cell types cannot be accomplished solely by deterministic regulatory systems, but by the involvement of some type of stochasticity. In the last few years our understanding of these non-deterministic mechanisms is advancing, and this review will provide a brief summary of the current view of stochastic gene expression with focus on olfactory receptor (OR) gene choice, the epigenetic underpinnings of which recently began to emerge.
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Affiliation(s)
- Angeliki Magklara
- Department of Anatomy, University of California San Francisco, CA 94920, USA.
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30
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Lyons DB, Allen WE, Goh T, Tsai L, Barnea G, Lomvardas S. An epigenetic trap stabilizes singular olfactory receptor expression. Cell 2013; 154:325-36. [PMID: 23870122 PMCID: PMC3929589 DOI: 10.1016/j.cell.2013.06.039] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 05/06/2013] [Accepted: 06/20/2013] [Indexed: 11/27/2022]
Abstract
The molecular mechanisms regulating olfactory receptor (OR) expression in the mammalian nose are not yet understood. Here, we identify the transient expression of histone demethylase LSD1 and the OR-dependent expression of adenylyl cyclase 3 (Adcy3) as requirements for initiation and stabilization of OR expression. As a transcriptional coactivator, LSD1 is necessary for desilencing and initiating OR transcription, but as a transcriptional corepressor, it is incompatible with maintenance of OR expression, and its downregulation is imperative for stable OR choice. Adcy3, a sensor of OR expression and a transmitter of an OR-elicited feedback, mediates the downregulation of LSD1 and promotes the differentiation of olfactory sensory neurons (OSNs). This novel, three-node signaling cascade locks the epigenetic state of the chosen OR, stabilizes its singular expression, and prevents the transcriptional activation of additional OR alleles for the life of the neuron.
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Affiliation(s)
- David B Lyons
- Tetrad Program, University of California, San Francisco, San Francisco, CA 94158, USA
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31
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Abstract
A protein that is found in the main olfactory epithelium of mice ensures that odour-sensing neurons that are active to have longer lifespans than those that are inactive.
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Affiliation(s)
- Kevin Monahan
- is in the Department of Anatomy , University of California , San Francisco , USA
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32
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Clowney EJ, LeGros MA, Mosley CP, Clowney FG, Markenskoff-Papadimitriou EC, Myllys M, Barnea G, Larabell CA, Lomvardas S. Nuclear aggregation of olfactory receptor genes governs their monogenic expression. Cell 2012; 151:724-737. [PMID: 23141535 PMCID: PMC3659163 DOI: 10.1016/j.cell.2012.09.043] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 05/18/2012] [Accepted: 09/26/2012] [Indexed: 12/13/2022]
Abstract
Gene positioning and regulation of nuclear architecture are thought to influence gene expression. Here, we show that, in mouse olfactory neurons, silent olfactory receptor (OR) genes from different chromosomes converge in a small number of heterochromatic foci. These foci are OR exclusive and form in a cell-type-specific and differentiation-dependent manner. The aggregation of OR genes is developmentally synchronous with the downregulation of lamin b receptor (LBR) and can be reversed by ectopic expression of LBR in mature olfactory neurons. LBR-induced reorganization of nuclear architecture and disruption of OR aggregates perturbs the singularity of OR transcription and disrupts the targeting specificity of the olfactory neurons. Our observations propose spatial sequestering of heterochromatinized OR family members as a basis of monogenic and monoallelic gene expression.
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Affiliation(s)
- E Josephine Clowney
- Program in Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mark A LeGros
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Colleen P Mosley
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Fiona G Clowney
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Markko Myllys
- Department of Physics, University of Jyväskylä, Jyväskylä FI-40014, Finland
| | - Gilad Barnea
- Department of Neuroscience, Brown University, Providence, RI 02912, USA
| | - Carolyn A Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stavros Lomvardas
- Program in Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Program in Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
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33
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Birnbaum RY, Clowney EJ, Agamy O, Kim MJ, Zhao J, Yamanaka T, Pappalardo Z, Clarke SL, Wenger AM, Nguyen L, Gurrieri F, Everman DB, Schwartz CE, Birk OS, Bejerano G, Lomvardas S, Ahituv N. Coding exons function as tissue-specific enhancers of nearby genes. Genome Res 2012; 22:1059-68. [PMID: 22442009 PMCID: PMC3371700 DOI: 10.1101/gr.133546.111] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 03/19/2012] [Indexed: 01/17/2023]
Abstract
Enhancers are essential gene regulatory elements whose alteration can lead to morphological differences between species, developmental abnormalities, and human disease. Current strategies to identify enhancers focus primarily on noncoding sequences and tend to exclude protein coding sequences. Here, we analyzed 25 available ChIP-seq data sets that identify enhancers in an unbiased manner (H3K4me1, H3K27ac, and EP300) for peaks that overlap exons. We find that, on average, 7% of all ChIP-seq peaks overlap coding exons (after excluding for peaks that overlap with first exons). By using mouse and zebrafish enhancer assays, we demonstrate that several of these exonic enhancer (eExons) candidates can function as enhancers of their neighboring genes and that the exonic sequence is necessary for enhancer activity. Using ChIP, 3C, and DNA FISH, we further show that one of these exonic limb enhancers, Dync1i1 exon 15, has active enhancer marks and physically interacts with Dlx5/6 promoter regions 900 kb away. In addition, its removal by chromosomal abnormalities in humans could cause split hand and foot malformation 1 (SHFM1), a disorder associated with DLX5/6. These results demonstrate that DNA sequences can have a dual function, operating as coding exons in one tissue and enhancers of nearby gene(s) in another tissue, suggesting that phenotypes resulting from coding mutations could be caused not only by protein alteration but also by disrupting the regulation of another gene.
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Affiliation(s)
- Ramon Y. Birnbaum
- Department of Bioengineering and Therapeutic Sciences
- Institute for Human Genetics
| | - E. Josephine Clowney
- Department of Anatomy
- Program in Biomedical Sciences, University of California, San Francisco, California 94143, USA
| | - Orly Agamy
- The Morris Kahn Laboratory of Human Genetics, NIBN, Ben-Gurion University, Beer-Sheva 84105, Israel
| | - Mee J. Kim
- Department of Bioengineering and Therapeutic Sciences
- Institute for Human Genetics
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences
- Institute for Human Genetics
- Key Laboratory of Advanced Control and Optimization for Chemical Processes of the Ministry of Education, East China University of Science and Technology, Shanghai 200237, China
| | - Takayuki Yamanaka
- Department of Bioengineering and Therapeutic Sciences
- Institute for Human Genetics
| | - Zachary Pappalardo
- Department of Bioengineering and Therapeutic Sciences
- Institute for Human Genetics
| | | | - Aaron M. Wenger
- Department of Computer Science, Stanford University, Stanford, California 94305-5329, USA
| | - Loan Nguyen
- Department of Bioengineering and Therapeutic Sciences
- Institute for Human Genetics
| | - Fiorella Gurrieri
- Istituto di Genetica Medica, Università Cattolica S. Cuore, Rome 00168, Italy
| | - David B. Everman
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, South Carolina 29646, USA
| | - Charles E. Schwartz
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, South Carolina 29646, USA
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Ohad S. Birk
- The Morris Kahn Laboratory of Human Genetics, NIBN, Ben-Gurion University, Beer-Sheva 84105, Israel
| | - Gill Bejerano
- Department of Computer Science, Stanford University, Stanford, California 94305-5329, USA
- Department of Developmental Biology, Stanford University, Stanford, California 94305-5329, USA
| | | | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences
- Institute for Human Genetics
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Clowney EJ, Magklara A, Colquitt BM, Pathak N, Lane RP, Lomvardas S. High-throughput mapping of the promoters of the mouse olfactory receptor genes reveals a new type of mammalian promoter and provides insight into olfactory receptor gene regulation. Genome Res 2011; 21:1249-59. [PMID: 21705439 PMCID: PMC3149492 DOI: 10.1101/gr.120162.110] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 05/16/2011] [Indexed: 11/25/2022]
Abstract
The olfactory receptor (OR) genes are the largest mammalian gene family and are expressed in a monogenic and monoallelic fashion in olfactory neurons. Using a high-throughput approach, we mapped the transcription start sites of 1085 of the 1400 murine OR genes and performed computational analysis that revealed potential transcription factor binding sites shared by the majority of these promoters. Our analysis produced a hierarchical model for OR promoter recognition in which unusually high AT content, a unique epigenetic signature, and a stereotypically positioned O/E site distinguish OR promoters from the rest of the murine promoters. Our computations revealed an intriguing correlation between promoter AT content and evolutionary plasticity, as the most AT-rich promoters regulate rapidly evolving gene families. Within the AT-rich promoter category the position of the TATA-box does not correlate with the transcription start site. Instead, a spike in GC composition might define the exact location of the TSS, introducing the concept of "genomic contrast" in transcriptional regulation. Finally, our experiments show that genomic neighborhood rather than promoter sequence correlates with the probability of different OR genes to be expressed in the same olfactory cell.
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Affiliation(s)
- E. Josephine Clowney
- Program in Biomedical Sciences, University of California, San Francisco, San Francisco, California 94158, USA
| | - Angeliki Magklara
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94158, USA
| | - Bradley M. Colquitt
- Program in Neurosciences, University of California, San Francisco, San Francisco, California 94158, USA
| | - Nidhi Pathak
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06457, USA
| | - Robert P. Lane
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06457, USA
| | - Stavros Lomvardas
- Program in Biomedical Sciences, University of California, San Francisco, San Francisco, California 94158, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94158, USA
- Program in Neurosciences, University of California, San Francisco, San Francisco, California 94158, USA
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Magklara A, Yen A, Colquitt BM, Clowney EJ, Allen W, Markenscoff-Papadimitriou E, Evans ZA, Kheradpour P, Mountoufaris G, Carey C, Barnea G, Kellis M, Lomvardas S. An epigenetic signature for monoallelic olfactory receptor expression. Cell 2011; 145:555-70. [PMID: 21529909 PMCID: PMC3094500 DOI: 10.1016/j.cell.2011.03.040] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 03/10/2011] [Accepted: 03/17/2011] [Indexed: 12/29/2022]
Abstract
Constitutive heterochromatin is traditionally viewed as the static form of heterochromatin that silences pericentromeric and telomeric repeats in a cell cycle- and differentiation-independent manner. Here, we show that, in the mouse olfactory epithelium, olfactory receptor (OR) genes are marked in a highly dynamic fashion with the molecular hallmarks of constitutive heterochromatin, H3K9me3 and H4K20me3. The cell type and developmentally dependent deposition of these marks along the OR clusters are, most likely, reversed during the process of OR choice to allow for monogenic and monoallelic OR expression. In contrast to the current view of OR choice, our data suggest that OR silencing takes place before OR expression, indicating that it is not the product of an OR-elicited feedback signal. Our findings suggest that chromatin-mediated silencing lays a molecular foundation upon which singular and stochastic selection for gene expression can be applied.
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Affiliation(s)
- Angeliki Magklara
- Department of Anatomy, University of California, San Francisco, CA 94158, USA
| | - Angela Yen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - Bradley M. Colquitt
- Program in Neurosciences, University of California, San Francisco, CA 94158, USA
| | - E. Josephine Clowney
- Program in Biomedical Sciences, University of California, San Francisco, CA 94158, USA
| | - William Allen
- Department of Neuroscience, Brown University, Providence, RI 02912, USA
| | | | - Zoe A. Evans
- Department of Anatomy, University of California, San Francisco, CA 94158, USA
| | - Pouya Kheradpour
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - George Mountoufaris
- Department of Anatomy, University of California, San Francisco, CA 94158, USA
| | - Catriona Carey
- Department of Anatomy, University of California, San Francisco, CA 94158, USA
| | - Gilad Barnea
- Department of Neuroscience, Brown University, Providence, RI 02912, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - Stavros Lomvardas
- Department of Anatomy, University of California, San Francisco, CA 94158, USA
- Program in Neurosciences, University of California, San Francisco, CA 94158, USA
- Program in Biomedical Sciences, University of California, San Francisco, CA 94158, USA
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Lomvardas S, Barnea G, Pisapia DJ, Mendelsohn M, Kirkland J, Axel R. Interchromosomal interactions and olfactory receptor choice. Cell 2006; 126:403-13. [PMID: 16873069 DOI: 10.1016/j.cell.2006.06.035] [Citation(s) in RCA: 459] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2006] [Revised: 04/28/2006] [Accepted: 06/22/2006] [Indexed: 12/31/2022]
Abstract
The expression of a single odorant receptor (OR) gene from a large gene family in individual sensory neurons is an essential feature of the organization and function of the olfactory system. We have used chromosome conformation capture to demonstrate the specific association of an enhancer element, H, on chromosome 14 with multiple OR gene promoters on different chromosomes. DNA and RNA fluorescence in situ hybridization (FISH) experiments allow us to visualize the colocalization of the H enhancer with the single OR allele that is transcribed in a sensory neuron. In transgenic mice bearing additional H elements, sensory neurons that express OR pseudogenes also express a second functional receptor. These data suggest a model of receptor choice in which a single trans-acting enhancer element may allow the stochastic activation of only one OR allele in an olfactory sensory neuron.
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Affiliation(s)
- Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics and Howard Hughes Medical Institute, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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Guan Z, Kim JH, Lomvardas S, Holick K, Xu S, Kandel ER, Schwartz JH. p38 MAP kinase mediates both short-term and long-term synaptic depression in aplysia. J Neurosci 2003; 23:7317-25. [PMID: 12917365 PMCID: PMC6740437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2002] [Revised: 06/25/2003] [Accepted: 06/26/2003] [Indexed: 03/04/2023] Open
Abstract
At Aplysia sensory-to-motor neuron synapses, the inhibitory neuropeptide Phe-Met-Arg-Phe-NH2 (FMRFa) produces depression, and serotonin (5-HT) produces facilitation. Short-term depression has been found to result from the activation of a phospholipase A2. The released arachidonate is metabolized by 12-lipoxygenase to active second messengers. We find that FMRFa leads to the phosphorylation and activation of p38 mitogen-activated protein (MAP) kinase. Short-term depression and the release of arachidonate are blocked by the specific p38 kinase inhibitor SB 203580. Both the inhibitor and an affinity-purified antibody raised against recombinant Aplysia p38 kinase injected into sensory neurons prevented long-term depression, which depends on the phosphorylation of translation factors cAMP response element-binding protein 2 (CREB2) and activating transcription factor 2. Facilitation produced by 5-HT, on the other hand, inactivates p38 kinase. Chromatin immunoprecipitation assays indicate that p38 kinase activates CREB2. p38 kinase also is pivotal in the bidirectional regulation of synaptic plasticity: when the kinase is inhibited, brief treatment with 5-HT that normally produces only short-term facilitation now results in long-term facilitation. Conversely, in sensory neurons injected with the activated kinase, long-term facilitation is blocked, and brief exposure to FMRFa, which normally results in short-term depression, results in long-term depression. We conclude that p38 kinase, which itself is bidirectionally regulated by FMRFa and 5-HT, acts as a modulator of synaptic plasticity by positively regulating depression and serving as an inhibitory constraint for facilitation.
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Affiliation(s)
- Zhonghui Guan
- Center for Neurobiology and Behavior, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
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38
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Guan Z, Giustetto M, Lomvardas S, Kim JH, Miniaci MC, Schwartz JH, Thanos D, Kandel ER. Integration of long-term-memory-related synaptic plasticity involves bidirectional regulation of gene expression and chromatin structure. Cell 2002; 111:483-93. [PMID: 12437922 DOI: 10.1016/s0092-8674(02)01074-7] [Citation(s) in RCA: 411] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Excitatory and inhibitory inputs converge on single neurons and are integrated into a coherent output. Although much is known about short-term integration, little is known about how neurons sum opposing signals for long-term synaptic plasticity and memory storage. In Aplysia, we find that when a sensory neuron simultaneously receives inputs from the facilitatory transmitter 5-HT at one set of synapses and the inhibitory transmitter FMRFamide at another, long-term facilitation is blocked and synapse-specific long-term depression dominates. Chromatin immunoprecipitation assays show that 5-HT induces the downstream gene C/EBP by activating CREB1, which recruits CBP for histone acetylation, whereas FMRFa leads to CREB1 displacement by CREB2 and recruitment of HDAC5 to deacetylate histones. When the two transmitters are applied together, facilitation is blocked because CREB2 and HDAC5 displace CREB1-CBP, thereby deacetylating histones.
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Affiliation(s)
- Zhonghui Guan
- Center for Neurobiology and Behavior, College of Physicians and Surgeons, Columbia University, New York State Psychiatric Institute, 1051 Riverside Drive, New York, NY 10032, USA
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Abstract
Transcriptional activation of the IFN-beta gene in response to virus infection requires the assembly of an enhanceosome, which instructs a recruitment program of chromatin modifiers/remodelers and general transcription factors to the promoter. This program culminates with sliding of a nucleosome blocking the core promoter to a downstream position, a prerequisite for transcriptional activation. We show that delivery of this nucleosome to the same downstream position to create an accessible IFN-beta core promoter prior to enhanceosome assembly results in major changes in the gene expression program with regard to the temporal pattern and the signal specificity of the transcriptional response. Thus, the identity of a gene expression program is achieved and maintained by the dynamic interplay between specific enhanceosomes and specific local chromatin structure.
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Affiliation(s)
- Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
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Abstract
How the transcriptional apparatus gains access to and subsequently opens compacted chromatin has remained a mystery. Now in this issue of Molecular Cell, Zaret and coworkers show that chromatin opening in vitro is not mediated by the classical chromatin remodeling machines but instead occurs through specific transcription factor-histone interactions.
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Affiliation(s)
- Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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41
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Abstract
Here, we show that a nucleosome obstructing transcription from the IFN-beta promoter slides in vivo in response to virus infection, thus exposing the previously masked TATA box and the initiation site, a requirement for transcriptional activation. Our experiments also revealed that this mode of chromatin remodeling is a two-step reaction. First, the enhanceosome recruits the SWI/SNF chromatin-remodeling complex that modifies the nucleosome to allow binding of TBP. Second, DNA bending is induced by TBP binding, and the nucleosome slides to a new position. Experiments with other DNA binding proteins demonstrated a strong correlation between the ability to bend DNA and nucleosome sliding, suggesting that the sliding is induced by the bend.
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Affiliation(s)
- S Lomvardas
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
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Abstract
Dynamic control of interferon-beta (IFN-beta) gene expression requires the regulated assembly and disassembly of the enhanceosome, a higher-order nucleoprotein complex formed in response to virus infection. The enhanceosome activates transcription by recruiting the histone acetyltransferase proteins CREB binding protein (CBP) and p300/CBP-associated factors (PCAF)/GCN5, which, in addition to modifying histones, acetylate HMGI(Y), the architectural component required for enhanceosome assembly. We show that the accurate execution of the IFN-beta transcriptional switch depends on the ordered acetylation of the high-mobility group I protein HMGI(Y) by PCAF/GCN5 and CBP, which acetylate HMGI(Y) at distinct lysine residues on endogenous promoters. Whereas acetylation of HMGI(Y) by CBP at lysine-65 destabilizes the enhanceosome, acetylation of HMGI(Y) by PCAF/GCN5 at lysine-71 potentiates transcription by stabilizing the enhanceosome and preventing acetylation by CBP.
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Affiliation(s)
- N Munshi
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
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Munshi N, Yie Y, Merika M, Senger K, Lomvardas S, Agalioti T, Thanos D. The IFN-beta enhancer: a paradigm for understanding activation and repression of inducible gene expression. Cold Spring Harb Symp Quant Biol 2001; 64:149-59. [PMID: 11232280 DOI: 10.1101/sqb.1999.64.149] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- N Munshi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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Agalioti T, Lomvardas S, Parekh B, Yie J, Maniatis T, Thanos D. Ordered recruitment of chromatin modifying and general transcription factors to the IFN-beta promoter. Cell 2000; 103:667-78. [PMID: 11106736 DOI: 10.1016/s0092-8674(00)00169-0] [Citation(s) in RCA: 575] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Here, we show that the IFN-beta enhanceosome activates transcription by directing the ordered recruitment of chromatin modifying and general transcription factors to the IFN-beta promoter. The enhanceosome is assembled in the nucleosome-free enhancer region of the IFN-beta gene, leading to the modification and remodeling of a strategically positioned nucleosome that masks the TATA box and the start site of transcription. Initially, the GCN5 complex is recruited, which acetylates the nucleosome, and this is followed by recruitment of the CBP-PolII holoenzyme complex. Nucleosome acetylation in turn facilitates SWI/SNF recruitment by CBP, resulting in chromatin remodeling. This program of recruitment culminates in the binding of TFIID to the promoter and the activation of transcription.
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Affiliation(s)
- T Agalioti
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
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45
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Jho EH, Lomvardas S, Costantini F. A GSK3beta phosphorylation site in axin modulates interaction with beta-catenin and Tcf-mediated gene expression. Biochem Biophys Res Commun 1999; 266:28-35. [PMID: 10581160 DOI: 10.1006/bbrc.1999.1760] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Upon binding of a Wnt to its receptor, GSK3beta is inhibited through an unknown mechanism involving Dishevelled (Dsh), resulting in the dephosphorylation and stabilization of beta-catenin, which translocates to the nucleus and interacts with Lef/Tcf transcription factors to activate target gene expression. Axin is a scaffold protein which binds beta-catenin and GSK3beta (as well as several other proteins) and thus promotes the phosphorylation of beta-catenin. Here we report that Axin is phosphorylated on Ser and Thr residues in several regions in vivo, while only one region (amino acids 600-672) is efficiently phosphorylated by GSK3beta in vitro. Site-directed mutagenesis, together with in vitro and in vivo phosphorylation assays, demonstrates that Axin residues T609 and S614 are physiological GSK3beta targets. Substitutions for one or more of these residues, which lie within a beta-catenin binding site, reduce the ability of Axin to modulate Wnt-induced signaling in a Lef/Tcf reporter assay. These amino acid substitutions also reduce the binding between Axin and beta-catenin. We propose a model in which inhibition of GSK3beta activity upon Wnt signaling leads to the dephosphorylation of GSK3beta sites in Axin, resulting in the release of beta-catenin from the phosphorylation complex.
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Affiliation(s)
- E h Jho
- Department of Genetics and Development, College of Physicians and Surgeons, Columbia University, 701 West 168th Street, New York, New York, 10032, USA
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