1
|
Szelenyi ER, Navarrete JS, Murry AD, Zhang Y, Girven KS, Kuo L, Cline MM, Bernstein MX, Burdyniuk M, Bowler B, Goodwin NL, Juarez B, Zweifel LS, Golden SA. An arginine-rich nuclear localization signal (ArgiNLS) strategy for streamlined image segmentation of single cells. Proc Natl Acad Sci U S A 2024; 121:e2320250121. [PMID: 39074275 PMCID: PMC11317604 DOI: 10.1073/pnas.2320250121] [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: 11/29/2023] [Accepted: 06/25/2024] [Indexed: 07/31/2024] Open
Abstract
High-throughput volumetric fluorescent microscopy pipelines can spatially integrate whole-brain structure and function at the foundational level of single cells. However, conventional fluorescent protein (FP) modifications used to discriminate single cells possess limited efficacy or are detrimental to cellular health. Here, we introduce a synthetic and nondeleterious nuclear localization signal (NLS) tag strategy, called "Arginine-rich NLS" (ArgiNLS), that optimizes genetic labeling and downstream image segmentation of single cells by restricting FP localization near-exclusively in the nucleus through a poly-arginine mechanism. A single N-terminal ArgiNLS tag provides modular nuclear restriction consistently across spectrally separate FP variants. ArgiNLS performance in vivo displays functional conservation across major cortical cell classes and in response to both local and systemic brain-wide AAV administration. Crucially, the high signal-to-noise ratio afforded by ArgiNLS enhances machine learning-automated segmentation of single cells due to rapid classifier training and enrichment of labeled cell detection within 2D brain sections or 3D volumetric whole-brain image datasets, derived from both staining-amplified and native signal. This genetic strategy provides a simple and flexible basis for precise image segmentation of genetically labeled single cells at scale and paired with behavioral procedures.
Collapse
Affiliation(s)
- Eric R. Szelenyi
- Center of Excellence in Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA98195
- Department of Biological Structure, University of Washington, Seattle, WA98195
| | - Jovana S. Navarrete
- Center of Excellence in Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA98195
- Department of Biological Structure, University of Washington, Seattle, WA98195
- Graduate Program in Neuroscience, University of Washington, Seattle, WA98195
| | - Alexandria D. Murry
- Center of Excellence in Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA98195
- Department of Biological Structure, University of Washington, Seattle, WA98195
| | - Yizhe Zhang
- Center of Excellence in Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA98195
- Department of Biological Structure, University of Washington, Seattle, WA98195
| | - Kasey S. Girven
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195
| | - Lauren Kuo
- Center of Excellence in Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA98195
- Undergraduate Program in Biochemistry, University of Washington, Seattle, WA98195
| | - Marcella M. Cline
- Center of Excellence in Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA98195
- Department of Pharmacology, University of Washington, Seattle, WA98195
| | - Mollie X. Bernstein
- Center of Excellence in Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA98195
- Department of Pharmacology, University of Washington, Seattle, WA98195
| | | | - Bryce Bowler
- Department of Biological Structure, University of Washington, Seattle, WA98195
| | - Nastacia L. Goodwin
- Center of Excellence in Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA98195
- Department of Biological Structure, University of Washington, Seattle, WA98195
- Graduate Program in Neuroscience, University of Washington, Seattle, WA98195
| | - Barbara Juarez
- Center of Excellence in Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA98195
- Department of Pharmacology, University of Washington, Seattle, WA98195
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA98195
| | - Larry S. Zweifel
- Center of Excellence in Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA98195
- Department of Pharmacology, University of Washington, Seattle, WA98195
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA98195
| | - Sam A. Golden
- Center of Excellence in Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA98195
- Department of Biological Structure, University of Washington, Seattle, WA98195
| |
Collapse
|
2
|
Del Blanco B, Niñerola S, Martín-González AM, Paraíso-Luna J, Kim M, Muñoz-Viana R, Racovac C, Sanchez-Mut JV, Ruan Y, Barco Á. Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons. Nat Commun 2024; 15:1781. [PMID: 38453932 PMCID: PMC10920760 DOI: 10.1038/s41467-024-45773-3] [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: 07/27/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Kdm1a is a histone demethylase linked to intellectual disability with essential roles during gastrulation and the terminal differentiation of specialized cell types, including neurons, that remains highly expressed in the adult brain. To explore Kdm1a's function in adult neurons, we develop inducible and forebrain-restricted Kdm1a knockouts. By applying multi-omic transcriptome, epigenome and chromatin conformation data, combined with super-resolution microscopy, we find that Kdm1a elimination causes the neuronal activation of nonneuronal genes that are silenced by the polycomb repressor complex and interspersed with active genes. Functional assays demonstrate that the N-terminus of Kdm1a contains an intrinsically disordered region that is essential to segregate Kdm1a-repressed genes from the neighboring active chromatin environment. Finally, we show that the segregation of Kdm1a-target genes is weakened in neurons during natural aging, underscoring the role of Kdm1a safeguarding neuronal genome organization and gene silencing throughout life.
Collapse
Affiliation(s)
- Beatriz Del Blanco
- 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.
| | - Sergio Niñerola
- 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
| | - Ana M Martín-González
- 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
- Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Minji Kim
- The Jackson laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Rafael Muñoz-Viana
- 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
- Bioinformatics Unit, Hospital universitario Puerta de Hierro Majadahonda, 28220, Majadahonda, Spain
| | - Carina Racovac
- 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
| | - Jose V Sanchez-Mut
- 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
| | - Yijun Ruan
- The Jackson laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P.R. China
| | - 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.
| |
Collapse
|
3
|
Szelenyi ER, Navarrete JS, Murry AD, Zhang Y, Girven KS, Kuo L, Cline MM, Bernstein MX, Burdyniuk M, Bowler B, Goodwin NL, Juarez B, Zweifel LS, Golden SA. An arginine-rich nuclear localization signal (ArgiNLS) strategy for streamlined image segmentation of single-cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568319. [PMID: 38045271 PMCID: PMC10690249 DOI: 10.1101/2023.11.22.568319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
High-throughput volumetric fluorescent microscopy pipelines can spatially integrate whole-brain structure and function at the foundational level of single-cells. However, conventional fluorescent protein (FP) modifications used to discriminate single-cells possess limited efficacy or are detrimental to cellular health. Here, we introduce a synthetic and non-deleterious nuclear localization signal (NLS) tag strategy, called 'Arginine-rich NLS' (ArgiNLS), that optimizes genetic labeling and downstream image segmentation of single-cells by restricting FP localization near-exclusively in the nucleus through a poly-arginine mechanism. A single N-terminal ArgiNLS tag provides modular nuclear restriction consistently across spectrally separate FP variants. ArgiNLS performance in vivo displays functional conservation across major cortical cell classes, and in response to both local and systemic brain wide AAV administration. Crucially, the high signal-to-noise ratio afforded by ArgiNLS enhances ML-automated segmentation of single-cells due to rapid classifier training and enrichment of labeled cell detection within 2D brain sections or 3D volumetric whole-brain image datasets, derived from both staining-amplified and native signal. This genetic strategy provides a simple and flexible basis for precise image segmentation of genetically labeled single-cells at scale and paired with behavioral procedures.
Collapse
Affiliation(s)
- Eric R. Szelenyi
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
| | - Jovana S. Navarrete
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
- University of Washington, Graduate Program in Neuroscience, Seattle, WA, USA
| | - Alexandria D. Murry
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
| | - Yizhe Zhang
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
| | - Kasey S. Girven
- University of Washington, Department of Anesthesiology and Pain Medicine
| | - Lauren Kuo
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington Undergraduate Program in Biochemistry
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Marcella M. Cline
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Pharmacology, Seattle, WA, USA
- Cajal Neuroscience, Seattle, WA, USA
| | - Mollie X. Bernstein
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Pharmacology, Seattle, WA, USA
| | | | - Bryce Bowler
- University of Washington, Department of Biological Structure, Seattle, WA, USA
| | - Nastacia L. Goodwin
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
- University of Washington, Graduate Program in Neuroscience, Seattle, WA, USA
| | - Barbara Juarez
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Psychiatry and Behavioral Sciences, Seattle, WA, USA
- University of Washington, Department of Pharmacology, Seattle, WA, USA
- University of Maryland School of Medicine, Department of Neurobiology, Baltimore, MD, USA
| | - Larry S. Zweifel
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Psychiatry and Behavioral Sciences, Seattle, WA, USA
- University of Washington, Department of Pharmacology, Seattle, WA, USA
| | - Sam A. Golden
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
| |
Collapse
|
4
|
Mir FA, Amanullah A, Jain BP, Hyderi Z, Gautam A. Neuroepigenetics of ageing and neurodegeneration-associated dementia: An updated review. Ageing Res Rev 2023; 91:102067. [PMID: 37689143 DOI: 10.1016/j.arr.2023.102067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]
Abstract
Gene expression is tremendously altered in the brain during memory acquisition, recall, and forgetfulness. However, non-genetic factors, including environmental elements, epigenetic changes, and lifestyle, have grabbed significant attention in recent years regarding the etiology of neurodegenerative diseases (NDD) and age-associated dementia. Epigenetic modifications are essential in regulating gene expression in all living organisms in a DNA sequence-independent manner. The genes implicated in ageing and NDD-related memory disorders are epigenetically regulated by processes such as DNA methylation, histone acetylation as well as messenger RNA editing machinery. The physiological and optimal state of the epigenome, especially within the CNS of humans, plays an intricate role in helping us adjust to the changing environment, and alterations in it cause many brain disorders, but the mechanisms behind it still need to be well understood. When fully understood, these epigenetic landscapes could act as vital targets for pharmacogenetic rescue strategies for treating several diseases, including neurodegeneration- and age-induced dementia. Keeping this objective in mind, this updated review summarises the epigenetic changes associated with age and neurodegeneration-associated dementia.
Collapse
Affiliation(s)
- Fayaz Ahmad Mir
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Zeeshan Hyderi
- Department of Biotechnology, Alagappa University, Karaikudi, India
| | - Akash Gautam
- Centre for Neural and Cognitive Sciences, University of Hyderabad, Hyderabad, India.
| |
Collapse
|
5
|
Musolino E, Pagiatakis C, Pierin F, Sabatino D, Finzi G, Gornati R, Bernardini G, Papait R. A chromEM-staining protocol optimized for cardiac tissue. Front Cell Dev Biol 2023; 11:1123114. [PMID: 37476155 PMCID: PMC10354428 DOI: 10.3389/fcell.2023.1123114] [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: 12/13/2022] [Accepted: 06/23/2023] [Indexed: 07/22/2023] Open
Abstract
Three-dimensional (3D) chromatin organization has a key role in defining the transcription program of cells during development. Its alteration is the cause of gene expression changes responsible for several diseases. Thus, we need new tools to study this aspect of gene expression regulation. To this end, ChromEM was recently developed: this is an electron-microscopy staining technique that selectively marks nuclear DNA without altering its structure and, thus, allows better visualization of 3D chromatin conformation. However, despite increasingly frequent application of this staining technique on cells, it has not yet been applied to visualize chromatin ultrastructure in tissues. Here, we provide a protocol to carry out ChromEM on myocardial tissue harvested from the left ventricles of C57BL/6J mice and use this in combination with transmission electron microscopy (TEM) to measure some morphological parameters of peripheral heterochromatin in cardiomyocytes. This protocol could also be used, in combination with electron tomography, to study 3D chromatin organization in cardiomyocytes in different aspects of heart pathobiology (e.g., heart development, cardiac aging, and heart failure) as well as help to set-up ChromEM in other tissues.
Collapse
Affiliation(s)
- Elettra Musolino
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Christina Pagiatakis
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Department of Cardiovascular Medicine, Humanitas Research Hospital–IRCCS, Rozzano (MI), Italy
| | - Federica Pierin
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | | | - Giovanna Finzi
- Department of Pathology, ASST Sette Laghi, Varese, Italy
| | - Rosalba Gornati
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Giovanni Bernardini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Roberto Papait
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Department of Cardiovascular Medicine, Humanitas Research Hospital–IRCCS, Rozzano (MI), Italy
| |
Collapse
|
6
|
Marion-Poll L, Roussarie JP, Taing L, Dard-Dascot C, Servant N, Jaszczyszyn Y, Jordi E, Mulugeta E, Hervé D, Bourc’his D, Greengard P, Thermes C, Girault JA. DNA methylation and hydroxymethylation characterize the identity of D1 and D2 striatal projection neurons. Commun Biol 2022; 5:1321. [PMID: 36456703 PMCID: PMC9715678 DOI: 10.1038/s42003-022-04269-w] [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: 01/10/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Neuronal DNA modifications differ from those in other cells, including methylation outside CpG context and abundant 5-hydroxymethylation whose relevance for neuronal identities are unclear. Striatal projection neurons expressing D1 or D2 dopamine receptors allow addressing this question, as they share many characteristics but differ in their gene expression profiles, connections, and functional roles. We compare translating mRNAs and DNA modifications in these two populations. DNA methylation differences occur predominantly in large genomic clusters including differentially expressed genes, potentially important for D1 and D2 neurons. Decreased gene body methylation is associated with higher gene expression. Hydroxymethylation differences are more scattered and affect transcription factor binding sites, which can influence gene expression. We also find a strong genome-wide hydroxymethylation asymmetry between the two DNA strands, particularly pronounced at expressed genes and retrotransposons. These results identify novel properties of neuronal DNA modifications and unveil epigenetic characteristics of striatal projection neurons heterogeneity.
Collapse
Affiliation(s)
- Lucile Marion-Poll
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France ,Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005 France ,grid.8591.50000 0001 2322 4988Present Address: Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, Geneva, 1211 Switzerland
| | - Jean-Pierre Roussarie
- grid.134907.80000 0001 2166 1519Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065 USA ,grid.189504.10000 0004 1936 7558Present Address: Department of Anatomy & Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118 USA
| | - Lieng Taing
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Present Address: UMR1166 Inserm and Sorbonne Université, Faculty of Medicine, Paris, 75013 France
| | - Cloelia Dard-Dascot
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198 France
| | - Nicolas Servant
- grid.440907.e0000 0004 1784 3645Institut Curie, INSERM U900, CBIO-Centre for Computational Biology, Mines Paris Tech, PSL-Research University, Paris, 75005 France
| | - Yan Jaszczyszyn
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198 France
| | - Emmanuelle Jordi
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France ,Present Address: Coave Therapeutics, Paris, 75014 France
| | - Eskeatnaf Mulugeta
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005 France ,grid.5645.2000000040459992XPresent Address: Erasmus University Medical Center (Erasmus MC), Department of Cell Biology, Rotterdam, 3000 CA The Netherlands
| | - Denis Hervé
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France
| | - Déborah Bourc’his
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005 France
| | - Paul Greengard
- grid.134907.80000 0001 2166 1519Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065 USA
| | - Claude Thermes
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198 France
| | - Jean-Antoine Girault
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France
| |
Collapse
|
7
|
Lipinski M, Niñerola S, Fuentes-Ramos M, Valor LM, Del Blanco B, López-Atalaya JP, Barco A. CBP Is Required for Establishing Adaptive Gene Programs in the Adult Mouse Brain. J Neurosci 2022; 42:7984-8001. [PMID: 36109165 PMCID: PMC9617619 DOI: 10.1523/jneurosci.0970-22.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/03/2022] [Accepted: 08/26/2022] [Indexed: 11/21/2022] Open
Abstract
Environmental factors and life experiences impinge on brain circuits triggering adaptive changes. Epigenetic regulators contribute to this neuroadaptation by enhancing or suppressing specific gene programs. The paralogous transcriptional coactivators and lysine acetyltransferases CREB binding protein (CBP) and p300 are involved in brain plasticity and stimulus-dependent transcription, but their specific roles in neuroadaptation are not fully understood. Here we investigated the impact of eliminating either CBP or p300 in excitatory neurons of the adult forebrain of mice from both sexes using inducible and cell type-restricted knock-out strains. The elimination of CBP, but not p300, reduced the expression and chromatin acetylation of plasticity genes, dampened activity-driven transcription, and caused memory deficits. The defects became more prominent in elderly mice and in paradigms that involved enduring changes in transcription, such as kindling and environmental enrichment, in which CBP loss interfered with the establishment of activity-induced transcriptional and epigenetic changes in response to stimulus or experience. These findings further strengthen the link between CBP deficiency in excitatory neurons and etiopathology in the nervous system.SIGNIFICANCE STATEMENT How environmental conditions and life experiences impinge on mature brain circuits to elicit adaptive responses that favor the survival of the organism remains an outstanding question in neurosciences. Epigenetic regulators are thought to contribute to neuroadaptation by initiating or enhancing adaptive gene programs. In this article, we examined the role of CREB binding protein (CBP) and p300, two paralogous transcriptional coactivators and histone acetyltransferases involved in cognitive processes and intellectual disability, in neuroadaptation in adult hippocampal circuits. Our experiments demonstrate that CBP, but not its paralog p300, plays a highly specific role in the epigenetic regulation of neuronal plasticity gene programs in response to stimulus and provide unprecedented insight into the molecular mechanisms underlying neuroadaptation.
Collapse
Affiliation(s)
- Michal Lipinski
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Campus de Sant Joan, 03550 Alicante, Spain
| | - Sergio Niñerola
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Campus de Sant Joan, 03550 Alicante, Spain
| | - Miguel Fuentes-Ramos
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Campus de Sant Joan, 03550 Alicante, Spain
| | - Luis M Valor
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Campus de Sant Joan, 03550 Alicante, Spain
| | - Beatriz Del Blanco
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Campus de Sant Joan, 03550 Alicante, Spain
| | - Jose P López-Atalaya
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Campus de Sant Joan, 03550 Alicante, Spain
| | - Angel Barco
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas, Universidad Miguel Hernández, Campus de Sant Joan, 03550 Alicante, Spain
| |
Collapse
|
8
|
Arias A, Manubens-Gil L, Dierssen M. Fluorescent transgenic mouse models for whole-brain imaging in health and disease. Front Mol Neurosci 2022; 15:958222. [PMID: 36211979 PMCID: PMC9538927 DOI: 10.3389/fnmol.2022.958222] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
A paradigm shift is occurring in neuroscience and in general in life sciences converting biomedical research from a descriptive discipline into a quantitative, predictive, actionable science. Living systems are becoming amenable to quantitative description, with profound consequences for our ability to predict biological phenomena. New experimental tools such as tissue clearing, whole-brain imaging, and genetic engineering technologies have opened the opportunity to embrace this new paradigm, allowing to extract anatomical features such as cell number, their full morphology, and even their structural connectivity. These tools will also allow the exploration of new features such as their geometrical arrangement, within and across brain regions. This would be especially important to better characterize brain function and pathological alterations in neurological, neurodevelopmental, and neurodegenerative disorders. New animal models for mapping fluorescent protein-expressing neurons and axon pathways in adult mice are key to this aim. As a result of both developments, relevant cell populations with endogenous fluorescence signals can be comprehensively and quantitatively mapped to whole-brain images acquired at submicron resolution. However, they present intrinsic limitations: weak fluorescent signals, unequal signal strength across the same cell type, lack of specificity of fluorescent labels, overlapping signals in cell types with dense labeling, or undetectable signal at distal parts of the neurons, among others. In this review, we discuss the recent advances in the development of fluorescent transgenic mouse models that overcome to some extent the technical and conceptual limitations and tradeoffs between different strategies. We also discuss the potential use of these strains for understanding disease.
Collapse
Affiliation(s)
- Adrian Arias
- Department of System Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Linus Manubens-Gil
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Mara Dierssen
- Department of System Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| |
Collapse
|
9
|
Grabowska A, Sas-Nowosielska H, Wojtas B, Holm-Kaczmarek D, Januszewicz E, Yushkevich Y, Czaban I, Trzaskoma P, Krawczyk K, Gielniewski B, Martin-Gonzalez A, Filipkowski RK, Olszynski KH, Bernas T, Szczepankiewicz AA, Sliwinska MA, Kanhema T, Bramham CR, Bokota G, Plewczynski D, Wilczynski GM, Magalska A. Activation-induced chromatin reorganization in neurons depends on HDAC1 activity. Cell Rep 2022; 38:110352. [PMID: 35172152 DOI: 10.1016/j.celrep.2022.110352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 11/09/2021] [Accepted: 01/19/2022] [Indexed: 11/23/2022] Open
Abstract
Spatial chromatin organization is crucial for transcriptional regulation and might be particularly important in neurons since they dramatically change their transcriptome in response to external stimuli. We show that stimulation of neurons causes condensation of large chromatin domains. This phenomenon can be observed in vitro in cultured rat hippocampal neurons as well as in vivo in the amygdala and hippocampal neurons. Activity-induced chromatin condensation is an active, rapid, energy-dependent, and reversible process. It involves calcium-dependent pathways but is independent of active transcription. It is accompanied by the redistribution of posttranslational histone modifications and rearrangements in the spatial organization of chromosome territories. Moreover, it leads to the reorganization of nuclear speckles and active domains located in their proximity. Finally, we find that the histone deacetylase HDAC1 is the key regulator of this process. Our results suggest that HDAC1-dependent chromatin reorganization constitutes an important level of transcriptional regulation in neurons.
Collapse
Affiliation(s)
- Agnieszka Grabowska
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Hanna Sas-Nowosielska
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Bartosz Wojtas
- Laboratory of Sequencing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Dagmara Holm-Kaczmarek
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Elzbieta Januszewicz
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Yana Yushkevich
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Iwona Czaban
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Pawel Trzaskoma
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Katarzyna Krawczyk
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Bartlomiej Gielniewski
- Laboratory of Sequencing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Ana Martin-Gonzalez
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland; Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, San Juan de Alicante, 03550 Alicante, Spain
| | - Robert Kuba Filipkowski
- Behavior and Metabolism Research Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Krzysztof Hubert Olszynski
- Behavior and Metabolism Research Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Tytus Bernas
- Laboratory of Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland; Department of Anatomy and Neurology, VCU School of Medicine, Richmond, VA 23284, USA
| | - Andrzej Antoni Szczepankiewicz
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Malgorzata Alicja Sliwinska
- Laboratory of Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Tambudzai Kanhema
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, 5020 Bergen, Norway
| | - Clive R Bramham
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, 5020 Bergen, Norway
| | - Grzegorz Bokota
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; Institute of Informatics, University of Warsaw, 02-097 Warsaw, Poland
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Grzegorz Marek Wilczynski
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Adriana Magalska
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland.
| |
Collapse
|
10
|
Brändle F, Frühbauer B, Jagannathan M. Principles and functions of pericentromeric satellite DNA clustering into chromocenters. Semin Cell Dev Biol 2022; 128:26-39. [PMID: 35144860 DOI: 10.1016/j.semcdb.2022.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/29/2022]
Abstract
Simple non-coding tandem repeats known as satellite DNA are observed widely across eukaryotes. These repeats occupy vast regions at the centromere and pericentromere of chromosomes but their contribution to cellular function has remained incompletely understood. Here, we review the literature on pericentromeric satellite DNA and discuss its organization and functions across eukaryotic species. We specifically focus on chromocenters, DNA-dense nuclear foci that contain clustered pericentromeric satellite DNA repeats from multiple chromosomes. We first discuss chromocenter formation and the roles that epigenetic modifications, satellite DNA transcripts and sequence-specific satellite DNA-binding play in this process. We then review the newly emerging functions of chromocenters in genome encapsulation, the maintenance of cell fate and speciation. We specifically highlight how the rapid divergence of satellite DNA repeats impacts reproductive isolation between closely related species. Together, we underline the importance of this so-called 'junk DNA' in fundamental biological processes.
Collapse
Affiliation(s)
- Franziska Brändle
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Benjamin Frühbauer
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Madhav Jagannathan
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland.
| |
Collapse
|
11
|
Denoth-Lippuner A, Jaeger BN, Liang T, Royall LN, Chie SE, Buthey K, Machado D, Korobeynyk VI, Kruse M, Munz CM, Gerbaulet A, Simons BD, Jessberger S. Visualization of individual cell division history in complex tissues using iCOUNT. Cell Stem Cell 2021; 28:2020-2034.e12. [PMID: 34525348 PMCID: PMC8577829 DOI: 10.1016/j.stem.2021.08.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/29/2021] [Accepted: 08/12/2021] [Indexed: 12/26/2022]
Abstract
The division potential of individual stem cells and the molecular consequences of successive rounds of proliferation remain largely unknown. Here, we developed an inducible cell division counter (iCOUNT) that reports cell division events in human and mouse tissues in vitro and in vivo. Analyzing cell division histories of neural stem/progenitor cells (NSPCs) in the developing and adult brain, we show that iCOUNT can provide novel insights into stem cell behavior. Further, we use single-cell RNA sequencing (scRNA-seq) of iCOUNT-labeled NSPCs and their progenies from the developing mouse cortex and forebrain-regionalized human organoids to identify functionally relevant molecular pathways that are commonly regulated between mouse and human cells, depending on individual cell division histories. Thus, we developed a tool to characterize the molecular consequences of repeated cell divisions of stem cells that allows an analysis of the cellular principles underlying tissue formation, homeostasis, and repair.
Collapse
Affiliation(s)
- Annina Denoth-Lippuner
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Baptiste N Jaeger
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Tong Liang
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Lars N Royall
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Stefanie E Chie
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Kilian Buthey
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Diana Machado
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Vladislav I Korobeynyk
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Merit Kruse
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Clara M Munz
- Institute for Immunology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Alexander Gerbaulet
- Institute for Immunology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Benjamin D Simons
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK; The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
| | - Sebastian Jessberger
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland.
| |
Collapse
|
12
|
Medvedeva AV, Tokmatcheva EV, Kaminskaya AN, Vasileva SA, Nikitina EA, Zhuravlev SA, Zakharov GA, Zatsepina OG, Savvateeva-Popova EV. Parent-of-origin effects on nuclear chromatin organization and behavior in a Drosophila model for Williams-Beuren Syndrome. Vavilovskii Zhurnal Genet Selektsii 2021; 25:472-485. [PMID: 34595370 PMCID: PMC8460428 DOI: 10.18699/vj21.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 11/19/2022] Open
Abstract
Prognosis of neuropsychiatric disorders in progeny requires consideration of individual (1) parent-of-origin effects (POEs) relying on (2) the nerve cell nuclear 3D chromatin architecture and (3) impact of parent-specific miRNAs. Additionally, the shaping of cognitive phenotypes in parents depends on both learning acquisition and forgetting, or memory erasure. These processes are independent and controlled by different signal cascades: the first is cAMPdependent, the second relies on actin remodeling by small GTPase Rac1 - LIMK1 (LIM-kinase 1). Simple experimental model systems such as Drosophila help probe the causes and consequences leading to human neurocognitive pathologies. Recently, we have developed a Drosophila model for Williams-Beuren Syndrome (WBS): a mutant agnts3 of the agnostic locus (X:11AB) harboring the dlimk1 gene. The agnts3 mutation drastically increases the frequency of ectopic contacts (FEC) in specific regions of intercalary heterochromatin, suppresses learning/memory and affects locomotion. As is shown in this study, the polytene X chromosome bands in reciprocal hybrids between agnts3 and the wild type strain Berlin are heterogeneous in modes of FEC regulation depending either on maternal or paternal gene origin. Bioinformatic analysis reveals that FEC between X:11AB and the other X chromosome bands correlates with the occurrence of short (~30 bp) identical DNA fragments partly homologous to Drosophila 372-bp satellite DNA repeat. Although learning acquisition in a conditioned courtship suppression paradigm is similar in hybrids, the middle-term memory formation shows patroclinic inheritance. Seemingly, this depends on changes in miR-974 expression. Several parameters of locomotion demonstrate heterosis. Our data indicate that the agnts3 locus is capable of trans-regulating gene activity via POEs on the chromatin nuclear organization, thereby affecting behavior.
Collapse
Affiliation(s)
- A V Medvedeva
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - E V Tokmatcheva
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - A N Kaminskaya
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - S A Vasileva
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - E A Nikitina
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia Herzen State Pedagogical University of Russia, St. Petersburg, Russia
| | - S A Zhuravlev
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - G A Zakharov
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - O G Zatsepina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - E V Savvateeva-Popova
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| |
Collapse
|
13
|
Dileep V, Tsai LH. Three-dimensional chromatin organization in brain function and dysfunction. Curr Opin Neurobiol 2021; 69:214-221. [PMID: 34111830 DOI: 10.1016/j.conb.2021.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/20/2021] [Accepted: 04/29/2021] [Indexed: 01/24/2023]
Abstract
The three-dimensional (3D) organization of chromatin within the nucleus is now recognized as a bona fide epigenetic property influencing genome function, replication, and maintenance. In the recent years, several studies have revealed how 3D chromatin organization is associated with brain function and its emerging role in disorders of the brain. 3D chromatin organization plays a crucial role in the development of different cell types of the nervous system and some neuronal cell types have adapted unique modifications to this organization that deviates from all other cell types. In post-mitotic neurons, dynamic changes in chromatin interactions in response to neuronal activity underlie learning and memory formation. Finally, new evidence directly links 3D chromatin organization to several disorders of the brain. These recent findings position 3D chromatin organization as a fundamental regulatory mechanism poised to reveal the etiology of brain function and dysfunctions.
Collapse
Affiliation(s)
- Vishnu Dileep
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| |
Collapse
|
14
|
Skupien-Jaroszek A, Walczak A, Czaban I, Pels KK, Szczepankiewicz AA, Krawczyk K, Ruszczycki B, Wilczynski GM, Dzwonek J, Magalska A. The interplay of seizures-induced axonal sprouting and transcription-dependent Bdnf repositioning in the model of temporal lobe epilepsy. PLoS One 2021; 16:e0239111. [PMID: 34086671 PMCID: PMC8177504 DOI: 10.1371/journal.pone.0239111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 05/17/2021] [Indexed: 01/19/2023] Open
Abstract
The Brain-Derived Neurotrophic Factor is one of the most important trophic proteins in the brain. The role of this growth factor in neuronal plasticity, in health and disease, has been extensively studied. However, mechanisms of epigenetic regulation of Bdnf gene expression in epilepsy are still elusive. In our previous work, using a rat model of neuronal activation upon kainate-induced seizures, we observed a repositioning of Bdnf alleles from the nuclear periphery towards the nuclear center. This change of Bdnf intranuclear position was associated with transcriptional gene activity. In the present study, using the same neuronal activation model, we analyzed the relation between the percentage of the Bdnf allele at the nuclear periphery and clinical and morphological traits of epilepsy. We observed that the decrease of the percentage of the Bdnf allele at the nuclear periphery correlates with stronger mossy fiber sprouting-an aberrant form of excitatory circuits formation. Moreover, using in vitro hippocampal cultures we showed that Bdnf repositioning is a consequence of transcriptional activity. Inhibition of RNA polymerase II activity in primary cultured neurons with Actinomycin D completely blocked Bdnf gene transcription and repositioning occurring after neuronal excitation. Interestingly, we observed that histone deacetylases inhibition with Trichostatin A induced a slight increase of Bdnf gene transcription and its repositioning even in the absence of neuronal excitation. Presented results provide novel insight into the role of BDNF in epileptogenesis. Moreover, they strengthen the statement that this particular gene is a good candidate to search for a new generation of antiepileptic therapies.
Collapse
Affiliation(s)
- Anna Skupien-Jaroszek
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Walczak
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Iwona Czaban
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Karolina Pels
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Andrzej Antoni Szczepankiewicz
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Krawczyk
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Błażej Ruszczycki
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Grzegorz Marek Wilczynski
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Dzwonek
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- * E-mail: (AM); (JD)
| | - Adriana Magalska
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- * E-mail: (AM); (JD)
| |
Collapse
|
15
|
Harabula I, Pombo A. The dynamics of chromatin architecture in brain development and function. Curr Opin Genet Dev 2021; 67:84-93. [DOI: 10.1016/j.gde.2020.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/07/2020] [Accepted: 12/13/2020] [Indexed: 12/22/2022]
|
16
|
4D Genome Rewiring during Oncogene-Induced and Replicative Senescence. Mol Cell 2020; 78:522-538.e9. [PMID: 32220303 PMCID: PMC7208559 DOI: 10.1016/j.molcel.2020.03.007] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 12/20/2019] [Accepted: 03/04/2020] [Indexed: 12/26/2022]
Abstract
To understand the role of the extensive senescence-associated 3D genome reorganization, we generated genome-wide chromatin interaction maps, epigenome, replication-timing, whole-genome bisulfite sequencing, and gene expression profiles from cells entering replicative senescence (RS) or upon oncogene-induced senescence (OIS). We identify senescence-associated heterochromatin domains (SAHDs). Differential intra- versus inter-SAHD interactions lead to the formation of senescence-associated heterochromatin foci (SAHFs) in OIS but not in RS. This OIS-specific configuration brings active genes located in genomic regions adjacent to SAHDs in close spatial proximity and favors their expression. We also identify DNMT1 as a factor that induces SAHFs by promoting HMGA2 expression. Upon DNMT1 depletion, OIS cells transition to a 3D genome conformation akin to that of cells in replicative senescence. These data show how multi-omics and imaging can identify critical features of RS and OIS and discover determinants of acute senescence and SAHF formation. Deep multi-omics characterization of replicative and oncogene-induced senescence Senescence-associated heterochromatin domains (SAHDs) form SAHFs via 3D changes DNMT1 is required for SAHF formation via regulation of HMGA2 expression SAHF formation leads to expression of SAHF-adjacent genes via 3D chromatin contacts
Collapse
|
17
|
Chen SY, Lin MC, Tsai JS, He PL, Luo WT, Chiu IM, Herschman HR, Li HJ. Exosomal 2',3'-CNP from mesenchymal stem cells promotes hippocampus CA1 neurogenesis/neuritogenesis and contributes to rescue of cognition/learning deficiencies of damaged brain. Stem Cells Transl Med 2020; 9:499-517. [PMID: 31943851 PMCID: PMC7103625 DOI: 10.1002/sctm.19-0174] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/25/2019] [Indexed: 12/28/2022] Open
Abstract
Mesenchymal stem cells (MSCs) have been used in clinical studies to treat neurological diseases and damage. However, implanted MSCs do not achieve their regenerative effects by differentiating into and replacing neural cells. Instead, MSC secretome components mediate the regenerative effects of MSCs. MSC-derived extracellular vesicles (EVs)/exosomes carry cargo responsible for rescuing brain damage. We previously showed that EP4 antagonist-induced MSC EVs/exosomes have enhanced regenerative potential to rescue hippocampal damage, compared with EVs/exosomes from untreated MSCs. Here we show that EP4 antagonist-induced MSC EVs/exosomes promote neurosphere formation in vitro and increase neurogenesis and neuritogenesis in damaged hippocampi; basal MSC EVs/exosomes do not contribute to these regenerative effects. 2',3'-Cyclic nucleotide 3'-phosphodiesterase (CNP) levels in EP4 antagonist-induced MSC EVs/exosomes are 20-fold higher than CNP levels in basal MSC EVs/exosomes. Decreasing elevated exosomal CNP levels in EP4 antagonist-induced MSC EVs/exosomes reduced the efficacy of these EVs/exosomes in promoting β3-tubulin polymerization and in converting toxic 2',3'-cAMP into neuroprotective adenosine. CNP-depleted EP4 antagonist-induced MSC EVs/exosomes lost the ability to promote neurogenesis and neuritogenesis in damaged hippocampi. Systemic administration of EV/exosomes from EP4 -antagonist derived MSC EVs/exosomes repaired cognition, learning, and memory deficiencies in mice caused by hippocampal damage. In contrast, CNP-depleted EP4 antagonist-induced MSC EVs/exosomes failed to repair this damage. Exosomal CNP contributes to the ability of EP4 antagonist-elicited MSC EVs/exosomes to promote neurogenesis and neuritogenesis in damaged hippocampi and recovery of cognition, memory, and learning. This experimental approach should be generally applicable to identifying the role of EV/exosomal components in eliciting a variety of biological responses.
Collapse
Affiliation(s)
- Shih-Yin Chen
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Meng-Chieh Lin
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Jia-Shiuan Tsai
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Pei-Lin He
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Wen-Ting Luo
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Ing-Ming Chiu
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Harvey R Herschman
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, California.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California
| | - Hua-Jung Li
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, Taiwan
| |
Collapse
|
18
|
Ruszczycki B, Pels KK, Walczak A, Zamłyńska K, Such M, Szczepankiewicz AA, Hall MH, Magalska A, Magnowska M, Wolny A, Bokota G, Basu S, Pal A, Plewczynski D, Wilczyński GM. Three-Dimensional Segmentation and Reconstruction of Neuronal Nuclei in Confocal Microscopic Images. Front Neuroanat 2019; 13:81. [PMID: 31481881 PMCID: PMC6710455 DOI: 10.3389/fnana.2019.00081] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/31/2019] [Indexed: 12/31/2022] Open
Abstract
The detailed architectural examination of the neuronal nuclei in any brain region, using confocal microscopy, requires quantification of fluorescent signals in three-dimensional stacks of confocal images. An essential prerequisite to any quantification is the segmentation of the nuclei which are typically tightly packed in the tissue, the extreme being the hippocampal dentate gyrus (DG), in which nuclei frequently appear to overlap due to limitations in microscope resolution. Segmentation in DG is a challenging task due to the presence of a significant amount of image artifacts and densely packed nuclei. Accordingly, we established an algorithm based on continuous boundary tracing criterion aiming to reconstruct the nucleus surface and to separate the adjacent nuclei. The presented algorithm neither uses a pre-built nucleus model, nor performs image thresholding, which makes it robust against variations in image intensity and poor contrast. Further, the reconstructed surface is used to study morphology and spatial arrangement of the nuclear interior. The presented method is generally dedicated to segmentation of crowded, overlapping objects in 3D space. In particular, it allows us to study quantitatively the architecture of the neuronal nucleus using confocal-microscopic approach.
Collapse
Affiliation(s)
- Błażej Ruszczycki
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | | | - Agnieszka Walczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | | | - Michał Such
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.,Center of New Technologies, University of Warsaw, Warsaw, Poland
| | | | - Małgorzata Hanna Hall
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.,Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Adriana Magalska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Marta Magnowska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Artur Wolny
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Grzegorz Bokota
- Center of New Technologies, University of Warsaw, Warsaw, Poland
| | - Subhadip Basu
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, India
| | - Ayan Pal
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, India
| | - Dariusz Plewczynski
- Center of New Technologies, University of Warsaw, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | | |
Collapse
|
19
|
Kaczmarczyk L, Bansal V, Rajput A, Rahman RU, Krzyżak W, Degen J, Poll S, Fuhrmann M, Bonn S, Jackson WS. Tagger-A Swiss army knife for multiomics to dissect cell type-specific mechanisms of gene expression in mice. PLoS Biol 2019; 17:e3000374. [PMID: 31393866 PMCID: PMC6701817 DOI: 10.1371/journal.pbio.3000374] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/20/2019] [Accepted: 07/17/2019] [Indexed: 12/22/2022] Open
Abstract
A deep understanding of how regulation of the multiple levels of gene expression in mammalian tissues give rise to complex phenotypes has been impeded by cellular diversity. A handful of techniques were developed to tag-select nucleic acids of interest in specific cell types, thereby enabling their capture. We expanded this strategy by developing the Tagger knock-in mouse line bearing a quad-cistronic transgene combining enrichment tools for nuclei, nascent RNA, translating mRNA, and mature microRNA (miRNA). We demonstrate that Tagger can capture the desired nucleic acids, enabling multiple omics approaches to be applied to specific cell types in vivo using a single transgenic mouse line. This Methods and Resources paper describes Tagger, a knock-in mouse line bearing a quad-cistronic transgene that enables the capture of translating mRNAs, mature miRNAs, pulse-labeled total RNA, and the nucleus, all from specific cells of complex tissues.
Collapse
Affiliation(s)
- Lech Kaczmarczyk
- Wallenberg Center for Molecular Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Vikas Bansal
- Institute for Medical Systems Biology, Center for Molecular Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ashish Rajput
- Institute for Medical Systems Biology, Center for Molecular Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Raza-ur Rahman
- Institute for Medical Systems Biology, Center for Molecular Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Wiesław Krzyżak
- Life & Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Joachim Degen
- Life & Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Stefanie Poll
- German Center for Neurodegenerative Diseases, Bonn, Germany
| | | | - Stefan Bonn
- Institute for Medical Systems Biology, Center for Molecular Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Neurodegenerative Diseases, Tübingen, Germany
- * E-mail: (SB); (WSJ)
| | - Walker Scot Jackson
- Wallenberg Center for Molecular Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- German Center for Neurodegenerative Diseases, Bonn, Germany
- * E-mail: (SB); (WSJ)
| |
Collapse
|
20
|
Chitaman JM, Fraser P, Feng J. Three-dimensional chromosome architecture and drug addiction. Curr Opin Neurobiol 2019; 59:137-145. [PMID: 31276935 DOI: 10.1016/j.conb.2019.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 05/04/2019] [Accepted: 05/28/2019] [Indexed: 10/26/2022]
Abstract
Aberrant gene expression underlies drug addiction. Therefore, studying the regulation of gene expression in drug addiction may provide mechanistic insights into this disease, for which there are still only limited treatments. Recently, the three-dimensional (3D) organization of linear DNA in the nucleus has been recognized as having a major influence on gene transcription. Here, we review its roles in both basic brain function and neuropsychiatric disorders, while also highlighting its emerging implications in drug addiction. Unraveling the 3D architecture of chromosomes in drug addiction is adding to our understanding of this disease and has the potential to trigger novel approaches for better diagnosis and therapy.
Collapse
Affiliation(s)
- Javed M Chitaman
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA; Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Peter Fraser
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Jian Feng
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA; Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA.
| |
Collapse
|
21
|
Histone acetyltransferase CBP-related H3K23 acetylation contributes to courtship learning in Drosophila. BMC DEVELOPMENTAL BIOLOGY 2018; 18:20. [PMID: 30458702 PMCID: PMC6247617 DOI: 10.1186/s12861-018-0179-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022]
Abstract
Background Histone modifications are critical in regulating neuronal processes. However, the impacts of individual histone modifications on learning and memory are elusive. Here, we investigated the contributions of histone H3 lysine modifications to learning and memory in Drosophila by using histone lysine-to-alanine mutants. Results Behavioural analysis indicated that compared to the H3WT group, mutants overexpressing H3K23A displayed impaired courtship learning. Chromatin immunoprecipitation analysis of H3K23A mutants showed that H3K23 acetylation (H3K23ac) levels were decreased on learning-related genes. Knockdown of CREB-binding protein (CBP) decreased H3K23ac levels, attenuated the expression of learning-related genes, led to a courtship learning defect and altered development of the mushroom bodies. A decline in courtship learning ability was observed in both larvae and adult treatments with ICG-001. Furthermore, treatment of Drosophila overexpressing mutated H3K23A with a CBP inhibitor did not aggravate the learning defect. Conclusions H3K23ac, catalysed by the acetyltransferases dCBP, contributes to Drosophila learning, likely by controlling the expression of specific genes. This is a novel epigenetic regulatory mechanism underlying neuronal behaviours. Electronic supplementary material The online version of this article (10.1186/s12861-018-0179-z) contains supplementary material, which is available to authorized users.
Collapse
|
22
|
Chatterjee S, Cassel R, Schneider-Anthony A, Merienne K, Cosquer B, Tzeplaeff L, Halder Sinha S, Kumar M, Chaturbedy P, Eswaramoorthy M, Le Gras S, Keime C, Bousiges O, Dutar P, Petsophonsakul P, Rampon C, Cassel JC, Buée L, Blum D, Kundu TK, Boutillier AL. Reinstating plasticity and memory in a tauopathy mouse model with an acetyltransferase activator. EMBO Mol Med 2018; 10:e8587. [PMID: 30275019 PMCID: PMC6220301 DOI: 10.15252/emmm.201708587] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 08/31/2018] [Accepted: 09/05/2018] [Indexed: 12/17/2022] Open
Abstract
Chromatin acetylation, a critical regulator of synaptic plasticity and memory processes, is thought to be altered in neurodegenerative diseases. Here, we demonstrate that spatial memory and plasticity (LTD, dendritic spine formation) deficits can be restored in a mouse model of tauopathy following treatment with CSP-TTK21, a small-molecule activator of CBP/p300 histone acetyltransferases (HAT). At the transcriptional level, CSP-TTK21 re-established half of the hippocampal transcriptome in learning mice, likely through increased expression of neuronal activity genes and memory enhancers. At the epigenomic level, the hippocampus of tauopathic mice showed a significant decrease in H2B but not H3K27 acetylation levels, both marks co-localizing at TSS and CBP enhancers. Importantly, CSP-TTK21 treatment increased H2B acetylation levels at decreased peaks, CBP enhancers, and TSS, including genes associated with plasticity and neuronal functions, overall providing a 95% rescue of the H2B acetylome in tauopathic mice. This study is the first to provide in vivo proof-of-concept evidence that CBP/p300 HAT activation efficiently reverses epigenetic, transcriptional, synaptic plasticity, and behavioral deficits associated with Alzheimer's disease lesions in mice.
Collapse
Affiliation(s)
- Snehajyoti Chatterjee
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| | - Raphaelle Cassel
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| | - Anne Schneider-Anthony
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| | - Karine Merienne
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| | - Brigitte Cosquer
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| | - Laura Tzeplaeff
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| | - Sarmistha Halder Sinha
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Manoj Kumar
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Piyush Chaturbedy
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Muthusamy Eswaramoorthy
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Stéphanie Le Gras
- CNRS, Inserm, UMR 7104, Microarray and Sequencing Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
| | - Céline Keime
- CNRS, Inserm, UMR 7104, Microarray and Sequencing Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
| | - Olivier Bousiges
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- Laboratory of Biochemistry and Molecular Biology, Hôpital de Hautepierre, University Hospital of Strasbourg, Strasbourg, France
| | - Patrick Dutar
- Centre de Psychiatrie et Neurosciences, INSERM UMRS894, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Petnoi Petsophonsakul
- Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Claire Rampon
- Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Jean-Christophe Cassel
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| | - Luc Buée
- Inserm, CHU-Lille, UMR-S 1172, Alzheimer & Tauopathies, Université de Lille, Lille, France
| | - David Blum
- Inserm, CHU-Lille, UMR-S 1172, Alzheimer & Tauopathies, Université de Lille, Lille, France
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Anne-Laurence Boutillier
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| |
Collapse
|
23
|
Early alteration of epigenetic-related transcription in Huntington's disease mouse models. Sci Rep 2018; 8:9925. [PMID: 29967375 PMCID: PMC6028428 DOI: 10.1038/s41598-018-28185-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/18/2018] [Indexed: 12/18/2022] Open
Abstract
Transcriptional dysregulation in Huntington’s disease (HD) affects the expression of genes involved in survival and neuronal functions throughout the progression of the pathology. In recent years, extensive research has focused on epigenetic and chromatin-modifying factors as a causative explanation for such dysregulation, offering attractive targets for pharmacological therapies. In this work, we extensively examined the gene expression profiles in the cortex, striatum, hippocampus and cerebellum of juvenile R6/1 and N171-82Q mice, models of rapidly progressive HD, to retrieve the early transcriptional signatures associated with this pathology. These profiles were largely consistent across HD datasets, contained tissular and neuronal-specific genes and showed significant correspondence with the transcriptional changes in mouse strains deficient for epigenetic regulatory genes. The most prominent cases were the conditional knockout of the lysine acetyltransferase CBP in post-mitotic forebrain neurons, the double knockout of the histone methyltransferases Ezh1 and Ezh2, components of the polycomb repressor complex 2 (PRC2), and the conditional mutants of the histone methyltransferases G9a (Ehmt2) and GLP (Ehmt1). Based on these observations, we propose that the neuronal epigenetic status is compromised in the prodromal stages of HD, leading to an altered transcriptional programme that is prominently involved in neuronal identity.
Collapse
|
24
|
Lima AF, May G, Díaz-Colunga J, Pedreiro S, Paiva A, Ferreira L, Enver T, Iborra FJ, Pires das Neves R. Osmotic modulation of chromatin impacts on efficiency and kinetics of cell fate modulation. Sci Rep 2018; 8:7210. [PMID: 29740078 PMCID: PMC5940679 DOI: 10.1038/s41598-018-25517-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 04/12/2018] [Indexed: 11/23/2022] Open
Abstract
Chromatin structure is a major regulator of transcription and gene expression. Herein we explore the use of osmotic modulation to modify the chromatin structure and reprogram gene expression. In this study we use the extracellular osmotic pressure as a chromatin structure and transcriptional modulator. Hyposmotic modulation promotes chromatin loosening and induces changes in RNA polymerase II (Pol II) activity. The chromatin decondensation opens space for higher amounts of DNA engaged RNA Pol II. Hyposmotic modulation constitutes an alternative route to manipulate cell fate decisions. This technology was tested in model protocols of induced pluripotency and transdifferentiation in cells growing in suspension and adherent to substrates, CD34+ umbilical-cord-blood (UCB), fibroblasts and B-cells. The efficiency and kinetics of these cell fate modulation processes were improved by transient hyposmotic modulation of the cell environment.
Collapse
Affiliation(s)
- A F Lima
- UC-Biotech, CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3060-197, Cantanhede, Portugal.,Faculty of Science and Technology, University Nova of Lisbon (MIT-Portugal PhD Program), 2829-516, Caparica, Portugal
| | - G May
- University College London, Gower Street, London, WC1E 6BT, UK
| | - J Díaz-Colunga
- Centro Nacional de Biotecnología, CSIC. Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - S Pedreiro
- Unidade de Gestão Operacional de Citometria, Centro Hospitalar e Universitário de Coimbra, 3000-075, Coimbra, Portugal
| | - A Paiva
- Unidade de Gestão Operacional de Citometria, Centro Hospitalar e Universitário de Coimbra, 3000-075, Coimbra, Portugal.,Coimbra Institute for Clinical and Biomedical Research, Faculty of Medicine,University of Coimbra, 3004-504, Coimbra, Portugal
| | - L Ferreira
- UC-Biotech, CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3060-197, Cantanhede, Portugal.,Faculty of Medicine, University of Coimbra, 3004-504, Coimbra, Portugal
| | - T Enver
- University College London, Gower Street, London, WC1E 6BT, UK
| | - F J Iborra
- Centro Nacional de Biotecnología, CSIC. Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - R Pires das Neves
- UC-Biotech, CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3060-197, Cantanhede, Portugal. .,Institute for Interdisciplinary Research, University of Coimbra, 3030-789, Coimbra, Portugal.
| |
Collapse
|
25
|
Scandaglia M, Lopez-Atalaya JP, Medrano-Fernandez A, Lopez-Cascales MT, Del Blanco B, Lipinski M, Benito E, Olivares R, Iwase S, Shi Y, Barco A. Loss of Kdm5c Causes Spurious Transcription and Prevents the Fine-Tuning of Activity-Regulated Enhancers in Neurons. Cell Rep 2017; 21:47-59. [PMID: 28978483 PMCID: PMC5679733 DOI: 10.1016/j.celrep.2017.09.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/29/2017] [Accepted: 09/04/2017] [Indexed: 12/17/2022] Open
Abstract
During development, chromatin-modifying enzymes regulate both the timely establishment of cell-type-specific gene programs and the coordinated repression of alternative cell fates. To dissect the role of one such enzyme, the intellectual-disability-linked lysine demethylase 5C (Kdm5c), in the developing and adult brain, we conducted parallel behavioral, transcriptomic, and epigenomic studies in Kdm5c-null and forebrain-restricted inducible knockout mice. Together, genomic analyses and functional assays demonstrate that Kdm5c plays a critical role as a repressor responsible for the developmental silencing of germline genes during cellular differentiation and in fine-tuning activity-regulated enhancers during neuronal maturation. Although the importance of these functions declines after birth, Kdm5c retains an important genome surveillance role preventing the incorrect activation of non-neuronal and cryptic promoters in adult neurons.
Collapse
Affiliation(s)
- Marilyn Scandaglia
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Jose P Lopez-Atalaya
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Alejandro Medrano-Fernandez
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Maria T Lopez-Cascales
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Beatriz Del Blanco
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Michal Lipinski
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Eva Benito
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Roman Olivares
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
| | - Yang Shi
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Angel Barco
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain.
| |
Collapse
|
26
|
Fujita Y, Yamashita T. Spatial organization of genome architecture in neuronal development and disease. Neurochem Int 2017; 119:49-56. [PMID: 28757389 DOI: 10.1016/j.neuint.2017.06.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/19/2017] [Accepted: 06/26/2017] [Indexed: 01/19/2023]
Abstract
Although mammalian genomes encode genetic information in their linear sequences, their fundamental function with regard to gene expression depends on the higher-order structure of chromosomes. Current techniques for the evaluation of chromosomal structure have revealed that genomes are arranged at several hierarchical levels in three-dimensional space. The spatial organization of genomes involves the formation of chromatin loops that bypass a wide range of genomic distances, providing a connection between enhancers and chromosomal domains. Furthermore, they form chromatin domains that are arranged into chromosome territories in the three-dimensional space of the cell nucleus. Recent studies have shown that the spatial organization of the genome is essential for normal brain development and function. Activity-dependent alterations in the spatial organization of the genome can regulate transcriptional activity related to neuronal plasticity. Disruptions in the higher-order chromatin architecture have been implicated in neuropsychiatric disorders, such as cognitive dysfunction and anxiety. Here, we discuss the growing interest in the role of genome organization in brain development and neurological disorders.
Collapse
Affiliation(s)
- Yuki Fujita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Frontier Biosciences, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
27
|
Cebrián-Silla A, Alfaro-Cervelló C, Herranz-Pérez V, Kaneko N, Park DH, Sawamoto K, Alvarez-Buylla A, Lim DA, García-Verdugo JM. Unique Organization of the Nuclear Envelope in the Post-natal Quiescent Neural Stem Cells. Stem Cell Reports 2017. [PMID: 28648897 PMCID: PMC5511107 DOI: 10.1016/j.stemcr.2017.05.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Neural stem cells (B1 astrocytes; NSCs) in the adult ventricular-subventricular-zone (V-SVZ) originate in the embryo. Surprisingly, recent work has shown that B1 cells remain largely quiescent. They are reactivated postnatally to function as primary progenitors for neurons destined for the olfactory bulb and some corpus callosum oligodendrocytes. The cellular and molecular properties of quiescent B1 cells remain unknown. Here we found that a subpopulation of B1 cells has a unique nuclear envelope invagination specialization similar to envelope-limited chromatin sheets (ELCS), reported in certain lymphocytes and some cancer cells. Using molecular markers, [3H]thymidine birth-dating, and Ara-C, we found that B1 cells with ELCS correspond to quiescent NSCs. ELCS begin forming in embryonic radial glia cells and represent a specific nuclear compartment containing particular epigenetic modifications and telomeres. These results reveal a unique nuclear compartment in quiescent NSCs, which is useful for identifying these primary progenitors and study their gene regulation. A subpopulation of V-SVZ B cells presents nuclear ELCS ELCS appear in RGCs at E14.5 and remain in a subpopulation of B cells postnatally Type B cells with ELCS exhibit characteristics of quiescent NSCs ELCS present characteristic chromatin modifications
Collapse
Affiliation(s)
- Arantxa Cebrián-Silla
- Laboratory of Comparative Neurobiology, Institute Cavanilles, University of Valencia, CIBERNED, 46980 Valencia, Spain
| | - Clara Alfaro-Cervelló
- Servicio de Anatomía Patológica, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
| | - Vicente Herranz-Pérez
- Laboratory of Comparative Neurobiology, Institute Cavanilles, University of Valencia, CIBERNED, 46980 Valencia, Spain; Predepartamental Unit of Medicine, Faculty of Health Sciences, Universitat Jaume I, 12071 Castelló de la Plana, Spain
| | - Naoko Kaneko
- Department of Developmental and Regenerative Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Dae Hwi Park
- Department of Neurological Surgery, The Eli and Edythe Broad Center of Regeneration Medicine, Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kazunobu Sawamoto
- Department of Developmental and Regenerative Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan; Division of Neural Development and Regeneration, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Arturo Alvarez-Buylla
- Department of Neurological Surgery, The Eli and Edythe Broad Center of Regeneration Medicine, Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel A Lim
- Department of Neurological Surgery, The Eli and Edythe Broad Center of Regeneration Medicine, Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Veterans Affairs Medical Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - José Manuel García-Verdugo
- Laboratory of Comparative Neurobiology, Institute Cavanilles, University of Valencia, CIBERNED, 46980 Valencia, Spain; Multiple Sclerosis and Neuroregeneration Mixed Unit, IIS Hospital La Fe, 46026 Valencia, Spain.
| |
Collapse
|
28
|
Longitudinal assessment of neuronal 3D genomes in mouse prefrontal cortex. Nat Commun 2016; 7:12743. [PMID: 27597321 PMCID: PMC5025847 DOI: 10.1038/ncomms12743] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 07/28/2016] [Indexed: 12/15/2022] Open
Abstract
Neuronal epigenomes, including chromosomal loopings moving distal cis-regulatory elements into proximity of target genes, could serve as molecular proxy linking present-day-behaviour to past exposures. However, longitudinal assessment of chromatin state is challenging, because conventional chromosome conformation capture assays essentially provide single snapshots at a given time point, thus reflecting genome organization at the time of brain harvest and therefore are non-informative about the past. Here we introduce 'NeuroDam' to assess epigenome status retrospectively. Short-term expression of the bacterial DNA adenine methyltransferase Dam, tethered to the Gad1 gene promoter in mouse prefrontal cortex neurons, results in stable G(methyl)ATC tags at Gad1-bound chromosomal contacts. We show by NeuroDam that mice with defective cognition 4 months after pharmacological NMDA receptor blockade already were affected by disrupted chromosomal conformations shortly after drug exposure. Retrospective profiling of neuronal epigenomes is likely to illuminate epigenetic determinants of normal and diseased brain development in longitudinal context.
Collapse
|
29
|
Medrano-Fernández A, Barco A. Nuclear organization and 3D chromatin architecture in cognition and neuropsychiatric disorders. Mol Brain 2016; 9:83. [PMID: 27595843 PMCID: PMC5011999 DOI: 10.1186/s13041-016-0263-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/06/2016] [Indexed: 01/08/2023] Open
Abstract
The current view of neuroplasticity depicts the changes in the strength and number of synaptic connections as the main physical substrate for behavioral adaptation to new experiences in a changing environment. Although transcriptional regulation is known to play a role in these synaptic changes, the specific contribution of activity-induced changes to both the structure of the nucleus and the organization of the genome remains insufficiently characterized. Increasing evidence indicates that plasticity-related genes may work in coordination and share architectural and transcriptional machinery within discrete genomic foci. Here we review the molecular and cellular mechanisms through which neuronal nuclei structurally adapt to stimuli and discuss how the perturbation of these mechanisms can trigger behavioral malfunction.
Collapse
Affiliation(s)
- Alejandro Medrano-Fernández
- 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
| | - Angel 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.
| |
Collapse
|
30
|
McNally AG, Poplawski SG, Mayweather BA, White KM, Abel T. Characterization of a Novel Chromatin Sorting Tool Reveals Importance of Histone Variant H3.3 in Contextual Fear Memory and Motor Learning. Front Mol Neurosci 2016; 9:11. [PMID: 26903803 PMCID: PMC4746260 DOI: 10.3389/fnmol.2016.00011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/25/2016] [Indexed: 01/02/2023] Open
Abstract
The consolidation of short-term labile memories for long-term storage requires transcription and there is growing interest in defining the epigenetic mechanisms regulating these transcriptional events. In particular, it has been hypothesized that combinations of histone post-translational modifications (PTMs) have the potential to store memory by dynamically defining the transcriptional status of any given gene loci. Studying epigenetic phenomena during long-term memory consolidation, however, is complicated by the complex cellular heterogeneity of the brain, in which epigenetic signal from memory-relevant cells can be obscured or diluted by the surrounding milieu. To address this issue, we have developed a transgenic mouse line expressing a tetO-regulated, hemagglutinin (HA)-tagged histone H3.3 exclusively in excitatory neurons of the forebrain. Unlike canonical histones, histone H3.3 is incorporated at promoter regions of transcriptionally active genes in a DNA replication-independent manner, stably “barcoding” active regions of the genome in post-mitotic cells. Immunoprecipitating H3.3-HA containing nucleosomes from the hippocampus will therefore enrich for memory-relevant chromatin by isolating actively transcribed regions of the excitatory neuron genome. To evaluate the validity of using H3.3 “barcoding” to sort chromatin, we performed a molecular and behavioral characterization of the H3.3-HA transgenic mouse line. Expectedly, we find that H3.3-HA is incorporated preferentially at promoter regions of actively-transcribed neuronal genes and that expression can be effectively regulated by doxycycline. Additionally, H3.3-HA overexpression does not adversely affect exploratory or anxiety-related behaviors, nor does it affect spatial memory. Transgenic animals do, however, exhibit deficits in contextual memory and motor learning, revealing the importance of this histone isoform in the brain. Future studies in the H3.3-HA transgenic mouse line will define the combinatorial histone PTM landscape during spatial memory consolidation and will investigate the important contributions of histone H3.3 to the normal functioning of the brain.
Collapse
Affiliation(s)
- Anna G McNally
- Pharmacology Graduate Group, University of Pennsylvania Philadelphia, PA, USA
| | - Shane G Poplawski
- Pharmacology Graduate Group, University of Pennsylvania Philadelphia, PA, USA
| | | | - Kyle M White
- Department of Biology, University of Pennsylvania Philadelphia, PA, USA
| | - Ted Abel
- Department of Biology, University of Pennsylvania Philadelphia, PA, USA
| |
Collapse
|
31
|
Persistent variations in neuronal DNA methylation following cocaine self-administration and protracted abstinence in mice. ACTA ACUST UNITED AC 2015; 4:1-11. [PMID: 27213137 DOI: 10.1016/j.nepig.2015.10.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Continued vulnerability to relapse during abstinence is characteristic of cocaine addiction and suggests that drug-induced neuroadaptations persist during abstinence. However, the precise cellular and molecular attributes of these adaptations remain equivocal. One possibility is that cocaine self-administration leads to enduring changes in DNA methylation. To address this possibility, we isolated neurons from medial prefrontal cortex and performed high throughput DNA sequencing to examine changes in DNA methylation following cocaine self-administration. Twenty-nine genomic regions became persistently differentially methylated during cocaine self-administration, and an additional 28 regions became selectively differentially methylated during abstinence. Altered DNA methylation was associated with isoform-specific changes in the expression of co-localizing genes. These results provide the first neuron-specific, genome-wide profile of changes in DNA methylation induced by cocaine self-administration and protracted abstinence. Moreover, our findings suggest that altered DNA methylation facilitates long-term behavioral adaptation in a manner that extends beyond the perpetuation of altered transcriptional states.
Collapse
|