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Kuldell JC, Kaplan CD. RNA Polymerase II Activity Control of Gene Expression and Involvement in Disease. J Mol Biol 2024:168770. [PMID: 39214283 DOI: 10.1016/j.jmb.2024.168770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/26/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Gene expression is dependent on RNA Polymerase II (Pol II) activity in eukaryotes. In addition to determining the rate of RNA synthesis for all protein coding genes, Pol II serves as a platform for the recruitment of factors and regulation of co-transcriptional events, from RNA processing to chromatin modification and remodeling. The transcriptome can be shaped by changes in Pol II kinetics affecting RNA synthesis itself or because of alterations to co-transcriptional events that are responsive to or coupled with transcription. Genetic, biochemical, and structural approaches to Pol II in model organisms have revealed critical insights into how Pol II works and the types of factors that regulate it. The complexity of Pol II regulation generally increases with organismal complexity. In this review, we describe fundamental aspects of how Pol II activity can shape gene expression, discuss recent advances in how Pol II elongation is regulated on genes, and how altered Pol II function is linked to human disease and aging.
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Affiliation(s)
- James C Kuldell
- Department of Biological Sciences, 202A LSA, Fifth and Ruskin Avenues, University of Pittsburgh, Pittsburgh PA 15260, United States
| | - Craig D Kaplan
- Department of Biological Sciences, 202A LSA, Fifth and Ruskin Avenues, University of Pittsburgh, Pittsburgh PA 15260, United States.
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2
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Herrera ML, Paraíso-Luna J, Bustos-Martínez I, Barco Á. Targeting epigenetic dysregulation in autism spectrum disorders. Trends Mol Med 2024:S1471-4914(24)00162-X. [PMID: 38971705 DOI: 10.1016/j.molmed.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 07/08/2024]
Abstract
Autism spectrum disorders (ASD) comprise a range of neurodevelopmental pathologies characterized by deficits in social interaction and repetitive behaviors, collectively affecting almost 1% of the worldwide population. Deciphering the etiology of ASD has proven challenging due to the intricate interplay of genetic and environmental factors and the variety of molecular pathways affected. Epigenomic alterations have emerged as key players in ASD etiology. Their research has led to the identification of biomarkers for diagnosis and pinpointed specific gene targets for therapeutic interventions. This review examines the role of epigenetic alterations, resulting from both genetic and environmental influences, as a central causative factor in ASD, delving into its contribution to pathogenesis and treatment strategies.
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Affiliation(s)
- Macarena L Herrera
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas), Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Juan Paraíso-Luna
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas), Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Isabel Bustos-Martínez
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas), Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Ángel Barco
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas), Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain.
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3
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Feierman ER, Louzon S, Prescott NA, Biaco T, Gao Q, Qiu Q, Choi K, Palozola KC, Voss AJ, Mehta SD, Quaye CN, Lynch KT, Fuccillo MV, Wu H, David Y, Korb E. Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.575103. [PMID: 38352334 PMCID: PMC10862743 DOI: 10.1101/2024.01.29.575103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Regulation of histone proteins affects gene expression through multiple mechanisms including exchange with histone variants. However, widely expressed variants of H2B remain elusive. Recent findings link histone variants to neurological disorders, yet few are well studied in the brain. We applied new tools including novel antibodies, biochemical assays, and sequencing approaches to reveal broad expression of the H2B variant H2BE, and defined its role in regulating chromatin structure, neuronal transcription, and mouse behavior. We find that H2BE is enriched at promoters and a single unique amino acid allows it to dramatically enhance chromatin accessibility. Lastly, we show that H2BE is critical for synaptic gene expression and long-term memory. Together, these data reveal a novel mechanism linking histone variants to chromatin regulation, neuronal function, and memory. This work further identifies the first widely expressed H2B variant and uncovers a single histone amino acid with profound effects on genomic structure.
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Affiliation(s)
- Emily R. Feierman
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Sean Louzon
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Nicholas A. Prescott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Tracy Biaco
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Qingzeng Gao
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Kyuhyun Choi
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katherine C. Palozola
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Anna J. Voss
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Shreya D. Mehta
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Camille N. Quaye
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katherine T. Lynch
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Marc V. Fuccillo
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Erica Korb
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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Iglesias-Ortega L, Megías-Fernández C, Domínguez-Giménez P, Jimeno-González S, Rivero S. Cell consequences of loss of function of the epigenetic factor EHMT1. Cell Signal 2023:110734. [PMID: 37257768 DOI: 10.1016/j.cellsig.2023.110734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 05/20/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
EHMT1 is an epigenetic factor with histone methyltransferase activity that appears mutated in Kleefstra syndrome, a neurodevelopmental genetic disorder characterized by developmental delay, intellectual disability, and autistic-like features. Despite recent progress in the study of the function of this gene and the molecular etiology of the disease, our knowledge of how EHMT1 haploinsufficiency causes Kleefstra syndrome is still very limited. Here, we show that EHMT1 depletion in RPE1 cells leads to alterations in the morphology and distribution of different subcellular structures, such as the Golgi apparatus, the lysosomes and different cell adhesion components. EHMT1 downregulation also increases centriolar satellites detection, which may indicate a role for EHMT1 in centrosome functioning. Furthermore, the migration process is also altered in EHMT1 depleted cells, which show reduced migration capacity. We consider that the described phenotypes could open new possibilities for understanding the functional impact of EHMT1 haploinsufficiency in Kleefstra syndrome, helping to elucidate the link between epigenetic regulation and the underlying cellular mechanisms that result in this neurodevelopmental disorder. This knowledge could be relevant not only for the treatment of this syndrome, but also for other neurodevelopmental conditions that could share similar deregulated cellular pathways.
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Affiliation(s)
- Lucía Iglesias-Ortega
- Departamento de Citología e Histología Normal y Patológica, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Clara Megías-Fernández
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Paloma Domínguez-Giménez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Silvia Jimeno-González
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Sabrina Rivero
- Departamento de Citología e Histología Normal y Patológica, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain; Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain.
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Porter RS, Iwase S. Modulation of chromatin architecture influences the neuronal nucleus through activity-regulated gene expression. Biochem Soc Trans 2023; 51:703-713. [PMID: 36929379 PMCID: PMC10959270 DOI: 10.1042/bst20220889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/02/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023]
Abstract
The disruption of chromatin-regulating genes is associated with many neurocognitive syndromes. While most of these genes are ubiquitously expressed across various cell-types, many chromatin regulators act upon activity regulated genes (ARGs) that play central roles in synaptic development and plasticity. Recent literature suggests a link between ARG expression disruption in neurons with the human phenotypes observed in various neurocognitive syndromes. Advances in chromatin biology have demonstrated how chromatin structure, from nucleosome occupancy to higher-order structures such as topologically associated domains, impacts the kinetics of transcription. This review discusses the dynamics of these various levels of chromatin structure and their influence on the expression of ARGs.
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Affiliation(s)
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
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Lee SY, Kweon H, Kang H, Kim E. Age-differential sexual dimorphisms in CHD8-S62X-mutant mouse synapses and transcriptomes. Front Mol Neurosci 2023; 16:1111388. [PMID: 36873104 PMCID: PMC9978779 DOI: 10.3389/fnmol.2023.1111388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/18/2023] [Indexed: 02/18/2023] Open
Abstract
Chd8+/N2373K mice with a human C-terminal-truncating mutation (N2373K) display autistic-like behaviors in juvenile and adult males but not in females. In contrast, Chd8+/S62X mice with a human N-terminal-truncating mutation (S62X) display behavioral deficits in juvenile males (not females) and adult males and females, indicative of age-differential sexually dimorphic behaviors. Excitatory synaptic transmission is suppressed and enhanced in male and female Chd8+/S62X juveniles, respectively, but similarly enhanced in adult male and female mutants. ASD-like transcriptomic changes are stronger in newborn and juvenile (but not adult) Chd8+/S62X males but in newborn and adult (not juvenile) Chd8+/S62X females. These results point to age-differential sexual dimorphisms in Chd8+/S62X mice at synaptic and transcriptomic levels, in addition to the behavioral level.
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Affiliation(s)
- Soo Yeon Lee
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Hanseul Kweon
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Hyojin Kang
- Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, Republic of Korea
| | - Eunjoon Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
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