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Xavier AM, Lin Q, Kang CJ, Cheadle L. A single-cell transcriptomic atlas of sensory-dependent gene expression in developing mouse visual cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600673. [PMID: 38979325 PMCID: PMC11230371 DOI: 10.1101/2024.06.25.600673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Sensory experience drives the refinement and maturation of neural circuits during postnatal brain development through molecular mechanisms that remain to be fully elucidated. One likely mechanism involves the sensory-dependent expression of genes that encode direct mediators of circuit remodeling within developing cells. However, while studies in adult systems have begun to uncover crucial roles for sensory-induced genes in modifying circuit connectivity, the gene programs induced by brain cells in response to sensory experience during development remain to be fully characterized. Here, we present a single-nucleus RNA-sequencing dataset describing the transcriptional responses of cells in mouse visual cortex to sensory deprivation or sensory stimulation during a developmental window when visual input is necessary for circuit refinement. We sequenced 118,529 individual nuclei across sixteen neuronal and non-neuronal cortical cell types isolated from control, sensory deprived, and sensory stimulated mice, identifying 1,268 unique sensory-induced genes within the developing brain. To demonstrate the utility of this resource, we compared the architecture and ontology of sensory-induced gene programs between cell types, annotated transcriptional induction and repression events based upon RNA velocity, and discovered Neurexin and Neuregulin signaling networks that underlie cell-cell interactions via CellChat . We find that excitatory neurons, especially layer 2/3 pyramidal neurons, are highly sensitive to sensory stimulation, and that the sensory-induced genes in these cells are poised to strengthen synapse-to-nucleus crosstalk by heightening protein serine/threonine kinase activity. Altogether, we expect this dataset to significantly broaden our understanding of the molecular mechanisms through which sensory experience shapes neural circuit wiring in the developing brain.
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2
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Liu Y, Flamier A, Bell GW, Diao AJ, Whitfield TW, Wang HC, Wu Y, Schulte F, Friesen M, Guo R, Mitalipova M, Liu XS, Vos SM, Young RA, Jaenisch R. MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons. Neuron 2024; 112:1943-1958.e10. [PMID: 38697112 DOI: 10.1016/j.neuron.2024.04.007] [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: 11/17/2023] [Revised: 03/08/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024]
Abstract
Mutations in the methyl-DNA-binding protein MECP2 cause the neurodevelopmental disorder Rett syndrome (RTT). How MECP2 contributes to transcriptional regulation in normal and disease states is unresolved; it has been reported to be an activator and a repressor. We describe here the first integrated CUT&Tag, transcriptome, and proteome analyses using human neurons with wild-type (WT) and mutant MECP2 molecules. MECP2 occupies CpG-rich promoter-proximal regions in over four thousand genes in human neurons, including a plethora of autism risk genes, together with RNA polymerase II (RNA Pol II). MECP2 directly interacts with RNA Pol II, and genes occupied by both proteins showed reduced expression in neurons with MECP2 patient mutations. We conclude that MECP2 acts as a positive cofactor for RNA Pol II gene expression at many neuronal genes that harbor CpG islands in promoter-proximal regions and that RTT is due, in part, to the loss of gene activity of these genes in neurons.
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Affiliation(s)
- Yi Liu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Anthony Flamier
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - George W Bell
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Annette Jun Diao
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Troy W Whitfield
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Hao-Che Wang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yizhe Wu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Fabian Schulte
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Max Friesen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ruisi Guo
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Maisam Mitalipova
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - X Shawn Liu
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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3
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Prince GS, Reynolds M, Martina V, Sun H. Gene-environmental regulation of the postnatal post-mitotic neuronal maturation. Trends Genet 2024; 40:480-494. [PMID: 38658255 PMCID: PMC11153025 DOI: 10.1016/j.tig.2024.03.006] [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: 01/30/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Embryonic neurodevelopment, particularly neural progenitor differentiation into post-mitotic neurons, has been extensively studied. While the number and composition of post-mitotic neurons remain relatively constant from birth to adulthood, the brain undergoes significant postnatal maturation marked by major property changes frequently disrupted in neural diseases. This review first summarizes recent characterizations of the functional and molecular maturation of the postnatal nervous system. We then review regulatory mechanisms controlling the precise gene expression changes crucial for the intricate sequence of maturation events, highlighting experience-dependent versus cell-intrinsic genetic timer mechanisms. Despite significant advances in understanding of the gene-environmental regulation of postnatal neuronal maturation, many aspects remain unknown. The review concludes with our perspective on exciting future research directions in the next decade.
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Affiliation(s)
- Gabrielle S Prince
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Molly Reynolds
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Verdion Martina
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - HaoSheng Sun
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA; Freeman Hrabowski Scholar, Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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4
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Nagai M, Porter RS, Hughes E, Saunders TL, Iwase S. Asynchronous microexon splicing of LSD1 and PHF21A during neurodevelopment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586181. [PMID: 38562691 PMCID: PMC10983945 DOI: 10.1101/2024.03.21.586181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
LSD1 histone H3K4 demethylase and its binding partner PHF21A, a reader protein for unmethylated H3K4, both undergo neuron-specific microexon splicing. The LSD1 neuronal microexon weakens H3K4 demethylation activity and can alter the substrate specificity to H3K9 or H4K20. Meanwhile, the PHF21A neuronal microexon interferes with nucleosome binding. However, the temporal expression patterns of LSD1 and PHF21A splicing isoforms during brain development remain unknown. In this work, we report that neuronal PHF21A isoform expression precedes neuronal LSD1 isoform expression during human neuron differentiation and mouse brain development. The asynchronous splicing events resulted in stepwise deactivation of the LSD1-PHF21A complex in reversing H3K4 methylation. We further show that the enzymatically inactive LSD1-PHF21A complex interacts with neuron-specific binding partners, including MYT1-family transcription factors and post-transcriptional mRNA processing proteins such as VIRMA. The interaction with the neuron-specific components, however, did not require the PHF21A microexon, indicating that the neuronal proteomic milieu, rather than the microexon-encoded PHF21A segment, is responsible for neuron-specific complex formation. These results indicate that the PHF21A microexon is dispensable for neuron-specific protein-protein interactions, yet the enzymatically inactive LSD1-PHF21A complex might have unique gene-regulatory roles in neurons.
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Affiliation(s)
- Masayoshi Nagai
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Robert S. Porter
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Elizabeth Hughes
- Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas L. Saunders
- Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
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5
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Shi J, Wang Z, Wang Z, Shao G, Li X. Epigenetic regulation in adult neural stem cells. Front Cell Dev Biol 2024; 12:1331074. [PMID: 38357000 PMCID: PMC10864612 DOI: 10.3389/fcell.2024.1331074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024] Open
Abstract
Neural stem cells (NSCs) exhibit self-renewing and multipotential properties. Adult NSCs are located in two neurogenic regions of adult brain: the ventricular-subventricular zone (V-SVZ) of the lateral ventricle and the subgranular zone of the dentate gyrus in the hippocampus. Maintenance and differentiation of adult NSCs are regulated by both intrinsic and extrinsic signals that may be integrated through expression of some key factors in the adult NSCs. A number of transcription factors have been shown to play essential roles in transcriptional regulation of NSC cell fate transitions in the adult brain. Epigenetic regulators have also emerged as key players in regulation of NSCs, neural progenitor cells and their differentiated progeny via epigenetic modifications including DNA methylation, histone modifications, chromatin remodeling and RNA-mediated transcriptional regulation. This minireview is primarily focused on epigenetic regulations of adult NSCs during adult neurogenesis, in conjunction with transcriptional regulation in these processes.
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Affiliation(s)
- Jiajia Shi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zilin Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhijun Wang
- Zhenhai Lianhua Hospital, Ningbo City, Zhejiang, China
| | - Guofeng Shao
- Department of Cardiothoracic Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo City, Zhejiang, China
| | - Xiajun Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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6
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Moore JR, Nemera MT, D’Souza RD, Hamagami N, Clemens AW, Beard DC, Urman A, Mendoza VR, Gabel HW. Non-CG DNA methylation and MeCP2 stabilize repeated tuning of long genes that distinguish closely related neuron types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.577861. [PMID: 38352532 PMCID: PMC10862856 DOI: 10.1101/2024.01.30.577861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
The extraordinary diversity of neuron types in the mammalian brain is delineated at the highest resolution by subtle gene expression differences that may require specialized molecular mechanisms to be maintained. Neurons uniquely express the longest genes in the genome and utilize neuron-enriched non-CG DNA methylation (mCA) together with the Rett syndrome protein, MeCP2, to control gene expression, but the function of these unique gene structures and machinery in regulating finely resolved neuron type-specific gene programs has not been explored. Here, we employ epigenomic and spatial transcriptomic analyses to discover a major role for mCA and MeCP2 in maintaining neuron type-specific gene programs at the finest scale of cellular resolution. We uncover differential susceptibility to MeCP2 loss in neuronal populations depending on global mCA levels and dissect methylation patterns and intragenic enhancer repression that drive overlapping and distinct gene regulation between neuron types. Strikingly, we show that mCA and MeCP2 regulate genes that are repeatedly tuned to differentiate neuron types at the highest cellular resolution, including spatially resolved, vision-dependent gene programs in the visual cortex. These repeatedly tuned genes display genomic characteristics, including long length, numerous intragenic enhancers, and enrichment for mCA, that predispose them to regulation by MeCP2. Thus, long gene regulation by the MeCP2 pathway maintains differential gene expression between closely-related neurons to facilitate the exceptional cellular diversity in the complex mammalian brain.
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Affiliation(s)
- J. Russell Moore
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Mati T. Nemera
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Rinaldo D. D’Souza
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Adam W. Clemens
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Diana C. Beard
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Alaina Urman
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Victoria Rodriguez Mendoza
- Opportunities in Genomic Research Program, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Harrison W. Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
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7
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Wallace JL, Pollen AA. Human neuronal maturation comes of age: cellular mechanisms and species differences. Nat Rev Neurosci 2024; 25:7-29. [PMID: 37996703 DOI: 10.1038/s41583-023-00760-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2023] [Indexed: 11/25/2023]
Abstract
The delayed and prolonged postmitotic maturation of human neurons, compared with neurons from other species, may contribute to human-specific cognitive abilities and neurological disorders. Here we review the mechanisms of neuronal maturation, applying lessons from model systems to understand the specific features of protracted human cortical maturation and species differences. We cover cell-intrinsic features of neuronal maturation, including transcriptional, epigenetic and metabolic mechanisms, as well as cell-extrinsic features, including the roles of activity and synapses, the actions of glial cells and the contribution of the extracellular matrix. We discuss evidence for species differences in biochemical reaction rates, the proposed existence of an epigenetic maturation clock and the contributions of both general and modular mechanisms to species-specific maturation timing. Finally, we suggest approaches to measure, improve and accelerate the maturation of human neurons in culture, examine crosstalk and interactions among these different aspects of maturation and propose conceptual models to guide future studies.
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Affiliation(s)
- Jenelle L Wallace
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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8
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Nettles SA, Ikeuchi Y, Lefton KB, Abbasi L, Erickson A, Agwu C, Papouin T, Bonni A, Gabel HW. MeCP2 represses the activity of topoisomerase IIβ in long neuronal genes. Cell Rep 2023; 42:113538. [PMID: 38096051 PMCID: PMC10844882 DOI: 10.1016/j.celrep.2023.113538] [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: 05/04/2022] [Revised: 08/31/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023] Open
Abstract
A unique signature of neurons is the high expression of the longest genes in the genome. These genes have essential neuronal functions, and disruption of their expression has been implicated in neurological disorders. DNA topoisomerases resolve DNA topological constraints and facilitate neuronal long gene expression. Conversely, the Rett syndrome protein, methyl-CpG-binding protein 2 (MeCP2), can transcriptionally repress long genes. How these factors regulate long genes is not well understood, and whether they interact is not known. Here, we identify and map a functional interaction between MeCP2 and topoisomerase IIβ (TOP2β) in mouse neurons. We profile neuronal TOP2β activity genome wide, detecting enrichment at regulatory regions and gene bodies of long genes, including MeCP2-regulated genes. We show that loss and overexpression of MeCP2 alter TOP2β activity at MeCP2-regulated genes. These findings uncover a mechanism of TOP2β inhibition by MeCP2 in neurons and implicate TOP2β dysregulation in disorders caused by MeCP2 disruption.
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Affiliation(s)
- Sabin A Nettles
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yoshiho Ikeuchi
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katheryn B Lefton
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ladan Abbasi
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alyssa Erickson
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chibueze Agwu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thomas Papouin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Azad Bonni
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA.
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9
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Centeno MV, Alam MS, Haldar K, Apkarian AV. Long-range action of an HDAC inhibitor treats chronic pain in a spared nerve injury rat model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571583. [PMID: 38168166 PMCID: PMC10760082 DOI: 10.1101/2023.12.13.571583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Histone deacetylase inhibitors (HDACi) that modulate epigenetic regulation and are approved for treating rare cancers have, in disease models, also been shown to mitigate neurological conditions, including chronic pain. They are of interest as non-opioid treatments, but achieving long-term efficacy with limited dosing has remained elusive. Here we utilize a triple combination formulation (TCF) comprised of a pan-HDACi vorinostat (Vo at its FDA-approved daily dose of 50mg/Kg), the caging agent 2-hydroxypropyl-β-cyclodextrin (HPBCD) and polyethylene glycol (PEG) known to boost plasma and brain exposure and efficacy of Vo in mice and rats, of various ages, spared nerve injury (SNI) model of chronic neuropathic pain. Administration of the TCF (but not HPBCD and PEG) decreased mechanical allodynia for 4 weeks without antagonizing weight, anxiety, or mobility. This was achieved at less than 1% of the total dose of Vo approved for 4 weeks of tumor treatment and associated with decreased levels of major inflammatory markers and microglia in ipsilateral (but not contralateral) spinal cord regions. A single TCF injection was sufficient for 3-4 weeks of efficacy: this was mirrored in repeat injections, specific for the injured paw and not seen on sham treatment. Pharmacodynamics in an SNI mouse model suggested pain relief was sustained for days to weeks after Vo elimination. Doubling Vo in a single TCF injection proved effectiveness was limited to male rats, where the response amplitude tripled and remained effective for > 2 months, an efficacy that outperforms all currently available chronic pain pharmacotherapies. Together, these data suggest that through pharmacological modulation of Vo, the TCF enables single-dose effectiveness with extended action, reduces long-term HDACi dosage, and presents excellent potential to develop as a non-opioid treatment option for chronic pain.
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Affiliation(s)
- Maria Virginia Centeno
- Center for Translational Pain Research, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Md Suhail Alam
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556
| | - Kasturi Haldar
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556
| | - Apkar Vania Apkarian
- Center for Translational Pain Research, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
- Department of Anesthesia, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
- Physical Medicine and Rehabilitation, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
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10
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Beard DC, Zhang X, Wu DY, Martin JR, Erickson A, Boua JV, Hamagami N, Swift RG, McCullough KB, Ge X, Bell-Hensley A, Zheng H, Palmer CW, Fuhler NA, Lawrence AB, Hill CA, Papouin T, Noguchi KK, McAlinden A, Garbow JR, Dougherty JD, Maloney SE, Gabel HW. Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits. Cell Rep 2023; 42:113411. [PMID: 37952155 PMCID: PMC10843706 DOI: 10.1016/j.celrep.2023.113411] [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: 02/28/2023] [Revised: 09/06/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
Phenotypic heterogeneity in monogenic neurodevelopmental disorders can arise from differential severity of variants underlying disease, but how distinct alleles drive variable disease presentation is not well understood. Here, we investigate missense mutations in DNA methyltransferase 3A (DNMT3A), a DNA methyltransferase associated with overgrowth, intellectual disability, and autism, to uncover molecular correlates of phenotypic heterogeneity. We generate a Dnmt3aP900L/+ mouse mimicking a mutation with mild to moderate severity and compare phenotypic and epigenomic effects with a severe R878H mutation. P900L mutants exhibit core growth and behavioral phenotypes shared across models but show subtle epigenomic changes, while R878H mutants display extensive disruptions. We identify mutation-specific dysregulated genes that may contribute to variable disease severity. Shared transcriptomic disruption identified across mutations overlaps dysregulation observed in other developmental disorder models and likely drives common phenotypes. Together, our findings define central drivers of DNMT3A disorders and illustrate how variable epigenomic disruption contributes to phenotypic heterogeneity in neurodevelopmental disease.
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Affiliation(s)
- Diana C Beard
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiyun Zhang
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jenna R Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alyssa Erickson
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jane Valeriane Boua
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Raylynn G Swift
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine B McCullough
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xia Ge
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin Bell-Hensley
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63110, USA; Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hongjun Zheng
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Cory W Palmer
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole A Fuhler
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin B Lawrence
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Cheryl A Hill
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Thomas Papouin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kevin K Noguchi
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Audrey McAlinden
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joel R Garbow
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan E Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA.
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11
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Tooley KB, Chucair-Elliott AJ, Ocañas SR, Machalinski AH, Pham KD, Hoolehan W, Kulpa AM, Stanford DR, Freeman WM. Differential usage of DNA modifications in neurons, astrocytes, and microglia. Epigenetics Chromatin 2023; 16:45. [PMID: 37953264 PMCID: PMC10642035 DOI: 10.1186/s13072-023-00522-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Cellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used this model to assess epigenomic regulation, DNA modifications in particular, of gene expression between neurons and glia. RESULTS After validating the cell-specificity of the Camk2a-NuTRAP model, we performed TRAP-RNA-Seq and INTACT-whole genome oxidative bisulfite sequencing (WGoxBS) to assess the neuronal translatome and epigenome in the hippocampus of young mice (4 months old). WGoxBS findings were validated with enzymatic methyl-Seq (EM-Seq) and nanopore sequencing. Comparing neuronal data to microglial and astrocytic data from NuTRAP models, microglia had the highest global mCG levels followed by astrocytes and then neurons, with the opposite pattern observed for hmCG and mCH. Differentially modified regions between cell types were predominantly found within gene bodies and distal intergenic regions, rather than proximal promoters. Across cell types there was a negative correlation between DNA modifications (mCG, mCH, hmCG) and gene expression at proximal promoters. In contrast, a negative correlation of gene body mCG and a positive relationship between distal promoter and gene body hmCG with gene expression was observed. Furthermore, we identified a neuron-specific inverse relationship between mCH and gene expression across promoter and gene body regions. CONCLUSIONS Neurons, astrocytes, and microglia demonstrate different genome-wide levels of mCG, hmCG, and mCH that are reproducible across analytical methods. However, modification-gene expression relationships are conserved across cell types. Enrichment of differential modifications across cell types in gene bodies and distal regulatory elements, but not proximal promoters, highlights epigenomic patterning in these regions as potentially greater determinants of cell identity. These findings also demonstrate the importance of differentiating between mC and hmC in neuroepigenomic analyses, as up to 30% of what is conventionally interpreted as mCG can be hmCG, which often has a different relationship to gene expression than mCG.
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Affiliation(s)
- Kyla B Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Ana J Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Sarah R Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Adeline H Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Kevin D Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Walker Hoolehan
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Adam M Kulpa
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - David R Stanford
- Center for Biomedical Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Willard M Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
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12
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Porter RS, Nagai M, An S, Gavilan MC, Murata-Nakamura Y, Bonefas KM, Zhou B, Dionne O, Manuel JM, St-Germain J, Browning L, Laurent B, Cho US, Iwase S. A neuron-specific microexon ablates the novel DNA-binding function of a histone H3K4me0 reader PHF21A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563357. [PMID: 37904995 PMCID: PMC10614952 DOI: 10.1101/2023.10.20.563357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
How cell-type-specific chromatin landscapes emerge and progress during metazoan ontogenesis remains an important question. Transcription factors are expressed in a cell-type-specific manner and recruit chromatin-regulatory machinery to specific genomic loci. In contrast, chromatin-regulatory proteins are expressed broadly and are assumed to exert the same intrinsic function across cell types. However, human genetics studies have revealed an unexpected vulnerability of neurodevelopment to chromatin factor mutations with unknown mechanisms. Here, we report that 14 chromatin regulators undergo evolutionary-conserved neuron-specific splicing events involving microexons. Of the 14 chromatin regulators, two are integral components of a histone H3K4 demethylase complex; the catalytic subunit LSD1 and an H3K4me0-reader protein PHF21A adopt neuron-specific forms. We found that canonical PHF21A (PHF21A-c) binds to DNA by AT-hook motif, and the neuronal counterpart PHF21A-n lacks this DNA-binding function yet maintains H3K4me0 recognition intact. In-vitro reconstitution of the canonical and neuronal PHF21A-LSD1 complexes identified the neuronal complex as a hypomorphic H3K4 demethylating machinery with reduced nucleosome engagement. Furthermore, an autism-associated PHF21A missense mutation, 1285 G>A, at the last nucleotide of the common exon immediately upstream of the neuronal microexon led to impaired splicing of PHF21A -n. Thus, ubiquitous chromatin regulatory complexes exert unique intrinsic functions in neurons via alternative splicing of their subunits and potentially contribute to faithful human brain development.
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13
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Roethler O, Zohar E, Cohen-Kashi Malina K, Bitan L, Gabel HW, Spiegel I. Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex. Neuron 2023; 111:2693-2708.e8. [PMID: 37354902 DOI: 10.1016/j.neuron.2023.05.026] [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: 10/03/2022] [Revised: 03/29/2023] [Accepted: 05/30/2023] [Indexed: 06/26/2023]
Abstract
Experience-dependent plasticity of synapses modulates information processing in neural circuits and is essential for cognitive functions. The genome, via non-coding enhancers, was proposed to control information processing and circuit plasticity by regulating experience-induced transcription of genes that modulate specific sets of synapses. To test this idea, we analyze here the cellular and circuit functions of the genomic mechanisms that control the experience-induced transcription of Igf1 (insulin-like growth factor 1) in vasoactive intestinal peptide (VIP) interneurons (INs) in the visual cortex of adult mice. We find that two sensory-induced enhancers selectively and cooperatively drive the activity-induced transcription of Igf1 to thereby promote GABAergic inputs onto VIP INs and to homeostatically control the ratio between excitation and inhibition (E/I ratio)-in turn, this restricts neural activity in VIP INs and principal excitatory neurons and maintains spatial frequency tuning. Thus, enhancer-mediated activity-induced transcription maintains sensory processing in the adult cortex via homeostatic modulation of E/I ratio.
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Affiliation(s)
- Ori Roethler
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Zohar
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Katayun Cohen-Kashi Malina
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Lidor Bitan
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Harrison Wren Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Ivo Spiegel
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.
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14
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Liu R, Zhao E, Yu H, Yuan C, Abbas MN, Cui H. Methylation across the central dogma in health and diseases: new therapeutic strategies. Signal Transduct Target Ther 2023; 8:310. [PMID: 37620312 PMCID: PMC10449936 DOI: 10.1038/s41392-023-01528-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 08/26/2023] Open
Abstract
The proper transfer of genetic information from DNA to RNA to protein is essential for cell-fate control, development, and health. Methylation of DNA, RNAs, histones, and non-histone proteins is a reversible post-synthesis modification that finetunes gene expression and function in diverse physiological processes. Aberrant methylation caused by genetic mutations or environmental stimuli promotes various diseases and accelerates aging, necessitating the development of therapies to correct the disease-driver methylation imbalance. In this Review, we summarize the operating system of methylation across the central dogma, which includes writers, erasers, readers, and reader-independent outputs. We then discuss how dysregulation of the system contributes to neurological disorders, cancer, and aging. Current small-molecule compounds that target the modifiers show modest success in certain cancers. The methylome-wide action and lack of specificity lead to undesirable biological effects and cytotoxicity, limiting their therapeutic application, especially for diseases with a monogenic cause or different directions of methylation changes. Emerging tools capable of site-specific methylation manipulation hold great promise to solve this dilemma. With the refinement of delivery vehicles, these new tools are well positioned to advance the basic research and clinical translation of the methylation field.
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Affiliation(s)
- Ruochen Liu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Erhu Zhao
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Huijuan Yu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Chaoyu Yuan
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Muhammad Nadeem Abbas
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China.
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China.
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15
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Tooley KB, Chucair-Elliott AJ, Ocañas SR, Machalinski AH, Pham KD, Stanford DR, Freeman WM. Differential usage of DNA modifications in neurons, astrocytes, and microglia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543497. [PMID: 37333391 PMCID: PMC10274634 DOI: 10.1101/2023.06.05.543497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background Cellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. This is especially true as for DNA modifications where most data are derived from bisulfite sequencing that cannot differentiate between DNA methylation and hydroxymethylation. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used this model to assess epigenomic regulation of gene expression between neurons and glia. Results After validating the cell-specificity of the Camk2a-NuTRAP model, we performed TRAP-RNA-Seq and INTACT whole genome oxidative bisulfite sequencing to assess the neuronal translatome and epigenome in the hippocampus of young mice (3 months old). These data were then compared to microglial and astrocytic data from NuTRAP models. When comparing the different cell types, microglia had the highest global mCG levels followed by astrocytes and then neurons, with the opposite pattern observed for hmCG and mCH. Differentially modified regions between cell types were predominantly found within gene bodies and distal intergenic regions, with limited differences occurring within proximal promoters. Across cell types there was a negative correlation between DNA modifications (mCG, mCH, hmCG) and gene expression at proximal promoters. In contrast, a negative correlation of mCG with gene expression within the gene body while a positive relationship between distal promoter and gene body hmCG and gene expression was observed. Furthermore, we identified a neuron-specific inverse relationship between mCH and gene expression across promoter and gene body regions. Conclusions In this study, we identified differential usage of DNA modifications across CNS cell types, and assessed the relationship between DNA modifications and gene expression in neurons and glia. Despite having different global levels, the general modification-gene expression relationship was conserved across cell types. The enrichment of differential modifications in gene bodies and distal regulatory elements, but not proximal promoters, across cell types highlights epigenomic patterning in these regions as potentially greater determinants of cell identity.
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Affiliation(s)
- Kyla B. Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Ana J. Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Sarah R. Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Adeline H. Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Kevin D. Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - David R. Stanford
- Center for Biomedical Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Willard M. Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK USA
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16
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Hamagami N, Wu DY, Clemens AW, Nettles SA, Li A, Gabel HW. NSD1 deposits histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons. Mol Cell 2023; 83:1412-1428.e7. [PMID: 37098340 PMCID: PMC10230755 DOI: 10.1016/j.molcel.2023.04.001] [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: 09/13/2022] [Revised: 02/16/2023] [Accepted: 03/30/2023] [Indexed: 04/27/2023]
Abstract
During postnatal development, the DNA methyltransferase DNMT3A deposits high levels of non-CG cytosine methylation in neurons. This methylation is critical for transcriptional regulation, and loss of this mark is implicated in DNMT3A-associated neurodevelopmental disorders (NDDs). Here, we show in mice that genome topology and gene expression converge to shape histone H3 lysine 36 dimethylation (H3K36me2) profiles, which in turn recruit DNMT3A and pattern neuronal non-CG methylation. We show that NSD1, an H3K36 methyltransferase mutated in NDD, is required for the patterning of megabase-scale H3K36me2 and non-CG methylation in neurons. We find that brain-specific deletion of NSD1 causes altered DNA methylation that overlaps with DNMT3A disorder models to drive convergent dysregulation of key neuronal genes that may underlie shared phenotypes in NSD1- and DNMT3A-associated NDDs. Our findings indicate that H3K36me2 deposited by NSD1 is important for neuronal non-CG DNA methylation and suggest that the H3K36me2-DNMT3A-non-CG-methylation pathway is likely disrupted in NSD1-associated NDDs.
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Affiliation(s)
- Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Adam W Clemens
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Sabin A Nettles
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Aidan Li
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA.
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17
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Martin S, Poppe D, Olova N, O'Leary C, Ivanova E, Pflueger J, Dechka J, Simmons RK, Cooper HM, Reik W, Lister R, Wolvetang EJ. Embryonic Stem Cell-Derived Neurons as a Model System for Epigenome Maturation during Development. Genes (Basel) 2023; 14:genes14050957. [PMID: 37239317 DOI: 10.3390/genes14050957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
DNA methylation in neurons is directly linked to neuronal genome regulation and maturation. Unlike other tissues, vertebrate neurons accumulate high levels of atypical DNA methylation in the CH sequence context (mCH) during early postnatal brain development. Here, we investigate to what extent neurons derived in vitro from both mouse and human pluripotent stem cells recapitulate in vivo DNA methylation patterns. While human ESC-derived neurons did not accumulate mCH in either 2D culture or 3D organoid models even after prolonged culture, cortical neurons derived from mouse ESCs acquired in vivo levels of mCH over a similar time period in both primary neuron cultures and in vivo development. mESC-derived neuron mCH deposition was coincident with a transient increase in Dnmt3a, preceded by the postmitotic marker Rbfox3 (NeuN), was enriched at the nuclear lamina, and negatively correlated with gene expression. We further found that methylation patterning subtly differed between in vitro mES-derived and in vivo neurons, suggesting the involvement of additional noncell autonomous processes. Our findings show that mouse ESC-derived neurons, in contrast to those of humans, can recapitulate the unique DNA methylation landscape of adult neurons in vitro over experimentally tractable timeframes, which allows their use as a model system to study epigenome maturation over development.
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Affiliation(s)
- Sally Martin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Daniel Poppe
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Nelly Olova
- Epigenetics ISP, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Conor O'Leary
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Elena Ivanova
- Epigenetics ISP, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Jahnvi Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Jennifer Dechka
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rebecca K Simmons
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Helen M Cooper
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Wolf Reik
- Epigenetics ISP, The Babraham Institute, Cambridge CB22 3AT, UK
- The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Ernst J Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
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18
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Ramabadran R, Wang JH, Reyes JM, Guzman AG, Gupta S, Rosas C, Brunetti L, Gundry MC, Tovy A, Long H, Gu T, Cullen SM, Tyagi S, Rux D, Kim JJ, Kornblau SM, Kyba M, Stossi F, Rau RE, Takahashi K, Westbrook TF, Goodell MA. DNMT3A-coordinated splicing governs the stem state switch towards differentiation in embryonic and haematopoietic stem cells. Nat Cell Biol 2023; 25:528-539. [PMID: 37024683 PMCID: PMC10337578 DOI: 10.1038/s41556-023-01109-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/17/2023] [Indexed: 04/08/2023]
Abstract
Upon stimulation by extrinsic stimuli, stem cells initiate a programme that enables differentiation or self-renewal. Disruption of the stem state exit has catastrophic consequences for embryogenesis and can lead to cancer. While some elements of this stem state switch are known, major regulatory mechanisms remain unclear. Here we show that this switch involves a global increase in splicing efficiency coordinated by DNA methyltransferase 3α (DNMT3A), an enzyme typically involved in DNA methylation. Proper activation of murine and human embryonic and haematopoietic stem cells depends on messenger RNA processing, influenced by DNMT3A in response to stimuli. DNMT3A coordinates splicing through recruitment of the core spliceosome protein SF3B1 to RNA polymerase and mRNA. Importantly, the DNA methylation function of DNMT3A is not required and loss of DNMT3A leads to impaired splicing during stem cell turnover. Finally, we identify the spliceosome as a potential therapeutic target in DNMT3A-mutated leukaemias. Together, our results reveal a modality through which DNMT3A and the spliceosome govern exit from the stem state towards differentiation.
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Affiliation(s)
- Raghav Ramabadran
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Interdepartmental Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Jarey H Wang
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jaime M Reyes
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Anna G Guzman
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Sinjini Gupta
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Carina Rosas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Lorenzo Brunetti
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael C Gundry
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ayala Tovy
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hali Long
- Interdepartmental Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Tianpeng Gu
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Sean M Cullen
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Siddhartha Tyagi
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Danielle Rux
- Lillehei Heart Institute and Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Jean J Kim
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Kyba
- Lillehei Heart Institute and Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Rachel E Rau
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Thomas F Westbrook
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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19
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Li Q, Perera D, Cao C, He J, Bian J, Chen X, Azeem F, Howe A, Au B, Wu J, Yan J, Long Q. Interaction-integrated linear mixed model reveals 3D-genetic basis underlying Autism. Genomics 2023; 115:110575. [PMID: 36758877 DOI: 10.1016/j.ygeno.2023.110575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023]
Abstract
Genetic interactions play critical roles in genotype-phenotype associations. We developed a novel interaction-integrated linear mixed model (ILMM) that integrates a priori knowledge into linear mixed models. ILMM enables statistical integration of genetic interactions upfront and overcomes the problems of searching for combinations. To demonstrate its utility, with 3D genomic interactions (assessed by Hi-C experiments) as a priori, we applied ILMM to whole-genome sequencing data for Autism Spectrum Disorders (ASD) and brain transcriptome data, revealing the 3D-genetic basis of ASD and 3D-expression quantitative loci (3D-eQTLs) for brain tissues. Notably, we reported a potential mechanism involving distal regulation between FOXP2 and DNMT3A, conferring the risk of ASD.
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Affiliation(s)
- Qing Li
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Deshan Perera
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Chen Cao
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Jingni He
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Jiayi Bian
- Department of Mathematics and Statistics, University of Calgary, Alberta T2N 1N4, Canada
| | - Xingyu Chen
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Feeha Azeem
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada
| | - Aaron Howe
- Heritage Youth Researcher Summer Program, University of Calgary, Alberta T2N 1N4, Canada
| | - Billie Au
- Department of Medical Genetics, University of Calgary, Alberta T2N 1N4, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Alberta T2N 1N4, Canada
| | - Jingjing Wu
- Department of Mathematics and Statistics, University of Calgary, Alberta T2N 1N4, Canada
| | - Jun Yan
- Department of Physiology and Pharmacology, University of Calgary, Alberta T2N 1N4, Canada; Hotchkiss Brain Institute, University of Calgary, Alberta T2N 1N4, Canada.
| | - Quan Long
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta T2N 1N4, Canada; Department of Medical Genetics, University of Calgary, Alberta T2N 1N4, Canada; Department of Mathematics and Statistics, University of Calgary, Alberta T2N 1N4, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Alberta T2N 1N4, Canada; Hotchkiss Brain Institute, University of Calgary, Alberta T2N 1N4, Canada.
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20
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Beard DC, Zhang X, Wu DY, Martin JR, Hamagami N, Swift RG, McCullough KB, Ge X, Bell-Hensley A, Zheng H, Lawrence AB, Hill CA, Papouin T, McAlinden A, Garbow JR, Dougherty JD, Maloney SE, Gabel HW. Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530041. [PMID: 36909558 PMCID: PMC10002657 DOI: 10.1101/2023.02.27.530041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Phenotypic heterogeneity is a common feature of monogenic neurodevelopmental disorders that can arise from differential severity of missense variants underlying disease, but how distinct alleles impact molecular mechanisms to drive variable disease presentation is not well understood. Here, we investigate missense mutations in the DNA methyltransferase DNMT3A associated with variable overgrowth, intellectual disability, and autism, to uncover molecular correlates of phenotypic heterogeneity in neurodevelopmental disease. We generate a DNMT3A P900L/+ mouse model mimicking a disease mutation with mild-to-moderate severity and compare phenotypic and epigenomic effects with a severe R878H mutation. We show that the P900L mutation leads to disease-relevant overgrowth, obesity, and social deficits shared across DNMT3A disorder models, while the R878H mutation causes more extensive epigenomic disruption leading to differential dysregulation of enhancers elements. We identify distinct gene sets disrupted in each mutant which may contribute to mild or severe disease, and detect shared transcriptomic disruption that likely drives common phenotypes across affected individuals. Finally, we demonstrate that core gene dysregulation detected in DNMT3A mutant mice overlaps effects in other developmental disorder models, highlighting the importance of DNMT3A-deposited methylation in neurodevelopment. Together, these findings define central drivers of DNMT3A disorders and illustrate how variable disruption of transcriptional mechanisms can drive the spectrum of phenotypes in neurodevelopmental disease.
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Affiliation(s)
- Diana C. Beard
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiyun Zhang
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dennis Y. Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jenna R. Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Raylynn G. Swift
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine B. McCullough
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xia Ge
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin Bell-Hensley
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63110, USA
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hongjun Zheng
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin B. Lawrence
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Cheryl A. Hill
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Thomas Papouin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Audrey McAlinden
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joel R. Garbow
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D. Dougherty
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan E. Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W. Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
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21
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Hamagami N, Wu DY, Clemens AW, Nettles SA, Gabel HW. NSD1 deposits histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.528965. [PMID: 36824816 PMCID: PMC9949142 DOI: 10.1101/2023.02.17.528965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
During postnatal development the DNA methyltransferase DNMT3A deposits high levels of non-CG cytosine methylation in neurons. This unique methylation is critical for transcriptional regulation in the mature mammalian brain, and loss of this mark is implicated in DNMT3A-associated neurodevelopmental disorders (NDDs). The mechanisms determining genomic non-CG methylation profiles are not well defined however, and it is unknown if this pathway is disrupted in additional NDDs. Here we show that genome topology and gene expression converge to shape histone H3 lysine 36 dimethylation (H3K36me2) profiles, which in turn recruit DNMT3A and pattern neuronal non-CG methylation. We show that NSD1, the H3K36 methyltransferase mutated in the NDD, Sotos syndrome, is required for megabase-scale patterning of H3K36me2 and non-CG methylation in neurons. We find that brain-specific deletion of NSD1 causes alterations in DNA methylation that overlap with models of DNMT3A disorders and define convergent disruption in the expression of key neuronal genes in these models that may contribute to shared phenotypes in NSD1- and DNMT3A-associated NDD. Our findings indicate that H3K36me2 deposited by NSD1 is an important determinant of neuronal non-CG DNA methylation and implicates disruption of this methylation in Sotos syndrome. Highlights Topology-associated DNA methylation and gene expression independently contribute to neuronal gene body and enhancer non-CG DNA methylation patterns.Topology-associated H3K36me2 patterns and local enrichment of H3K4 methylation impact deposition of non-CG methylation by DNMT3A. Disruption of NSD1 in vivo leads to alterations in H3K36me2, DNA methylation, and gene expression that overlap with models of DNMT3A disorders.
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Affiliation(s)
- Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
- These authors contributed equally
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
- These authors contributed equally
| | - Adam W Clemens
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
| | - Sabin A Nettles
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
- Lead contact
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22
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Panayotis N, Ehinger Y, Felix MS, Roux JC. State-of-the-art therapies for Rett syndrome. Dev Med Child Neurol 2023; 65:162-170. [PMID: 36056801 PMCID: PMC10087176 DOI: 10.1111/dmcn.15383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/04/2023]
Abstract
Rett syndrome (RTT) is an X-linked neurogenetic disorder caused by mutations of the MECP2 (methyl-CpG-binding protein 2) gene. Over two decades of work established MeCP2 as a protein with pivotal roles in the regulation of the epigenome, neuronal physiology, synaptic maintenance, and behaviour. Given the genetic aetiology of RTT and the proof of concept of its reversal in a mouse model, considerable efforts have been made to design therapeutic approaches to re-express MeCP2. By being at the forefront of the development of innovative gene therapies, research on RTT is of paramount importance for the treatment of monogenic neurological diseases. Here we discuss the recent advances and challenges of promising genetic strategies for the treatment of RTT including gene replacement therapies, gene/RNA editing strategies, and reactivation of the silenced X chromosome. WHAT THIS PAPER ADDS: Recent advances shed light on the promises of gene replacement therapy with new vectors designed to control the levels of MeCP2 expression. New developments in DNA/RNA editing approaches or reactivation of the silenced X chromosome open the possibility to re-express the native MeCP2 locus at endogenous levels. Current strategies still face limitations in transduction efficiency and future work is needed to improve brain delivery.
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Affiliation(s)
- Nicolas Panayotis
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.,Université Paris Cité, CNRS, Saints-Pères Paris Institute for the Neurosciences, Paris, France
| | - Yann Ehinger
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
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23
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Raus AM, Fuller TD, Nelson NE, Valientes DA, Bayat A, Ivy AS. Early-life exercise primes the murine neural epigenome to facilitate gene expression and hippocampal memory consolidation. Commun Biol 2023; 6:18. [PMID: 36611093 PMCID: PMC9825372 DOI: 10.1038/s42003-022-04393-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023] Open
Abstract
Aerobic exercise is well known to promote neuroplasticity and hippocampal memory. In the developing brain, early-life exercise (ELE) can lead to persistent improvements in hippocampal function, yet molecular mechanisms underlying this phenomenon have not been fully explored. In this study, transgenic mice harboring the "NuTRAP" (Nuclear tagging and Translating Ribosome Affinity Purification) cassette in Emx1 expressing neurons ("Emx1-NuTRAP" mice) undergo ELE during adolescence. We then simultaneously isolate and sequence translating mRNA and nuclear chromatin from single hippocampal homogenates containing Emx1-expressing neurons. This approach allowed us to couple translatomic with epigenomic sequencing data to evaluate the influence of histone modifications H4K8ac and H3K27me3 on translating mRNA after ELE. A subset of ELE mice underwent a hippocampal learning task to determine the gene expression and epigenetic underpinnings of ELE's contribution to improved hippocampal memory performance. From this experiment, we discover gene expression - histone modification relationships that may play a critical role in facilitated memory after ELE. Our data reveal candidate gene-histone modification interactions and implicate gene regulatory pathways involved in ELE's impact on hippocampal memory.
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Affiliation(s)
- Anthony M Raus
- Physiology/Biophysics, Anatomy/Neurobiology, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - Tyson D Fuller
- Pediatrics, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - Nellie E Nelson
- Physiology/Biophysics, Anatomy/Neurobiology, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - David A Valientes
- Pediatrics, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - Anita Bayat
- Pediatrics, University of California- Irvine School of Medicine, Irvine, CA, USA
| | - Autumn S Ivy
- Physiology/Biophysics, Anatomy/Neurobiology, University of California- Irvine School of Medicine, Irvine, CA, USA.
- Pediatrics, University of California- Irvine School of Medicine, Irvine, CA, USA.
- Neurobiology/Behavior, University of California- Irvine School of Biological Sciences, Irvine, CA, USA.
- Anatomy/Neurobiology, University of California- Irvine School of Medicine, Irvine, CA, USA.
- Division of Neurology, Children's Hospital Orange County, Orange, CA, USA.
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24
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Luo S, Zhang H, Xie Y, Huang J, Luo D, Zhang Q. Decreased SUV39H1 at the promoter region leads to increased CREMα and accelerates autoimmune response in CD4 + T cells from patients with systemic lupus erythematosus. Clin Epigenetics 2022; 14:181. [PMID: 36536372 PMCID: PMC9764740 DOI: 10.1186/s13148-022-01411-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Overproduction of cAMP-responsive element modulator α (CREMα) in total T cells from patients with systemic lupus erythematosus (SLE) can inhibit IL-2 and increase IL-17A. These ultimately promote progression of SLE. This study aims to investigate the expression of CREMα in SLE CD4+ T cells and find out the mechanisms for the regulation of CREMα in SLE CD4+ T cells. RESULTS CREMα mRNA was overexpressed in CD4+ T cells from SLE patients. The levels of histone H3 lysine 9 trimethylation (H3K9me3) and suppressor of variation 3-9 homolog 1 (SUV39H1) at the CREMα promoter of SLE CD4+ T cells were markedly decreased. Down-regulating SUV39H1 in normal CD4+ T cells elevated the levels of CREMα, IL-17A, and histone H3 lysine 4 trimethylation (H3K4me3) in the CREMα promoter region, and lowered IL-2, H3K9me3, DNA methylation, and DNA methyltransferase 3a (DNMT3a) enrichments within the CREMα promoter, while no sharp change in SET domain containing 1 (Set1) at the CREMα promoter. Up-regulating SUV39H1 in SLE CD4+ T cells had the opposite effects. The DNA methylation and DNMT3a levels were obviously reduced, and H3K4me3 enrichment was greatly increased at the CREMα promoter of CD4+ T cells from SLE patients. The Set1 binding in the CREMα promoter region upgraded significantly, and knocking down Set1 in SLE CD4+ T cells alleviated the H3K4me3 enrichment within this region, suppressed CREMα and IL-17A productions, and promoted the levels of IL-2, CREMα promoter DNA methylation, and DNMT3a. But there were no obviously alterations in H3K9me3 and SUV39H1 amounts in the region after transfection. CONCLUSIONS Decreased SUV39H1 in the CREMα promoter region of CD4+ T cells from SLE patients contributes to under-expression of H3K9me3 at this region. In the meantime, the Set1 binding at the CREMα promoter of SLE CD4+ T cells is up-regulated. As a result, DNMT3a and DNA methylation levels alleviate, and H3K4me3 binding increases. All these lead to overproduction of CREMα. Thus, the secretion of IL-2 down-regulates and the concentration of IL-17A up-regulates, ultimately promoting SLE.
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Affiliation(s)
- Shuangyan Luo
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Rd, Changsha, 410011 Hunan People’s Republic of China
| | - Huilin Zhang
- grid.216417.70000 0001 0379 7164Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Rd, Changsha, 410011 Hunan People’s Republic of China
| | - Yuming Xie
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Rd, Changsha, 410011 Hunan People’s Republic of China
| | - Junke Huang
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Rd, Changsha, 410011 Hunan People’s Republic of China
| | - Danhong Luo
- Department of Dermatology, The Fifth People’s Hospital of Hainan Province, #49 Longkun South Rd, Haikou, 570206 Hainan People’s Republic of China
| | - Qing Zhang
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Rd, Changsha, 410011 Hunan People’s Republic of China
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25
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Aversano S, Caiazza C, Caiazzo M. Induced pluripotent stem cell-derived and directly reprogrammed neurons to study neurodegenerative diseases: The impact of aging signatures. Front Aging Neurosci 2022; 14:1069482. [PMID: 36620769 PMCID: PMC9810544 DOI: 10.3389/fnagi.2022.1069482] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Many diseases of the central nervous system are age-associated and do not directly result from genetic mutations. These include late-onset neurodegenerative diseases (NDDs), which represent a challenge for biomedical research and drug development due to the impossibility to access to viable human brain specimens. Advancements in reprogramming technologies have allowed to obtain neurons from induced pluripotent stem cells (iPSCs) or directly from somatic cells (iNs), leading to the generation of better models to understand the molecular mechanisms and design of new drugs. Nevertheless, iPSC technology faces some limitations due to reprogramming-associated cellular rejuvenation which resets the aging hallmarks of donor cells. Given the prominent role of aging for the development and manifestation of late-onset NDDs, this suggests that this approach is not the most suitable to accurately model age-related diseases. Direct neuronal reprogramming, by which a neuron is formed via direct conversion from a somatic cell without going through a pluripotent intermediate stage, allows the possibility to generate patient-derived neurons that maintain aging and epigenetic signatures of the donor. This aspect may be advantageous for investigating the role of aging in neurodegeneration and for finely dissecting underlying pathological mechanisms. Here, we will compare iPSC and iN models as regards the aging status and explore how this difference is reported to affect the phenotype of NDD in vitro models.
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Affiliation(s)
- Simona Aversano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Carmen Caiazza
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Massimiliano Caiazzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy,Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, Netherlands,*Correspondence: Massimiliano Caiazzo,
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26
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Nayak M, Das D, Pradhan J, Ahmed R, Laureano-Melo R, Dandapat J. Epigenetic signature in neural plasticity: the journey so far and journey ahead. Heliyon 2022; 8:e12292. [PMID: 36590572 PMCID: PMC9798197 DOI: 10.1016/j.heliyon.2022.e12292] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/31/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Neural plasticity is a remarkable characteristic of the brain which allows neurons to rewire their structure in response to internal and external stimuli. Many external stimuli collectively referred to as 'epigenetic factors' strongly influence structural and functional reorganization of the brain, thereby acting as a potential driver of neural plasticity. DNA methylation and demethylation, histone acetylation, and deacetylation are some of the frontline epigenetic mechanisms behind neural plasticity. Epigenetic signature molecules (mostly proteins) play a pivotal role in epigenetic reprogramming. Though neuro-epigenetics is an incredibly important field of emerging research, the critical role of signature proteins associated with epigenetic alteration and their involvement in neural plasticity needs further attention. This study gives an integrated and systematic overview of the current state of knowledge with a clear idea of types of neural plasticity and the context-dependent role of epigenetic signature molecules and their modulation by some natural bioactive compounds.
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Affiliation(s)
- Madhusmita Nayak
- Post-Graduate Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India,Centre of Excellence in Integrated Omics and Computational Biology, Utkal University, Bhubaneswar 751004, Odisha, India
| | - Diptimayee Das
- Post-Graduate Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India,Faculty of Allied Health Science, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Chennai India
| | - Jyotsnarani Pradhan
- Post-Graduate Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India,Corresponding author.
| | - R.G. Ahmed
- Division of Anatomy and Embryology, Zoology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Roberto Laureano-Melo
- Barra Mansa University Center, R. Ver. Pinho de Carvalho, 267, 27330-550, Barra Mansa, Rio de Janeiro, Brazil
| | - Jagneshwar Dandapat
- Post-Graduate Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India,Centre of Excellence in Integrated Omics and Computational Biology, Utkal University, Bhubaneswar 751004, Odisha, India,Corresponding author.
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27
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Wei A, Wu H. Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers. Development 2022; 149:dev182683. [PMID: 36519514 PMCID: PMC10108609 DOI: 10.1242/dev.182683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA methylation is a highly conserved epigenetic modification that plays essential roles in mammalian gene regulation, genome stability and development. Despite being primarily considered a stable and heritable epigenetic silencing mechanism at heterochromatic and repetitive regions, whole genome methylome analysis reveals that DNA methylation can be highly cell-type specific and dynamic within proximal and distal gene regulatory elements during early embryonic development, stem cell differentiation and reprogramming, and tissue maturation. In this Review, we focus on the mechanisms and functions of regulated DNA methylation and demethylation, highlighting how these dynamics, together with crosstalk between DNA methylation and histone modifications at distinct regulatory regions, contribute to mammalian development and tissue maturation. We also discuss how recent technological advances in single-cell and long-read methylome sequencing, along with targeted epigenome-editing, are enabling unprecedented high-resolution and mechanistic dissection of DNA methylome dynamics.
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Affiliation(s)
- Alex Wei
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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28
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Adami R, Bottai D. NSC Physiological Features in Spinal Muscular Atrophy: SMN Deficiency Effects on Neurogenesis. Int J Mol Sci 2022; 23:ijms232315209. [PMID: 36499528 PMCID: PMC9736802 DOI: 10.3390/ijms232315209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/20/2022] [Accepted: 11/30/2022] [Indexed: 12/08/2022] Open
Abstract
While the U.S. Food and Drug Administration and the European Medicines Evaluation Agency have recently approved new drugs to treat spinal muscular atrophy 1 (SMA1) in young patients, they are mostly ineffective in older patients since many motor neurons have already been lost. Therefore, understanding nervous system (NS) physiology in SMA patients is essential. Consequently, studying neural stem cells (NSCs) from SMA patients is of significant interest in searching for new treatment targets that will enable researchers to identify new pharmacological approaches. However, studying NSCs in these patients is challenging since their isolation damages the NS, making it impossible with living patients. Nevertheless, it is possible to study NSCs from animal models or create them by differentiating induced pluripotent stem cells obtained from SMA patient peripheral tissues. On the other hand, therapeutic interventions such as NSCs transplantation could ameliorate SMA condition. This review summarizes current knowledge on the physiological properties of NSCs from animals and human cellular models with an SMA background converging on the molecular and neuronal circuit formation alterations of SMA fetuses and is not focused on the treatment of SMA. By understanding how SMA alters NSC physiology, we can identify new and promising interventions that could help support affected patients.
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29
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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.
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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
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30
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Li J, Pinto-Duarte A, Zander M, Cuoco MS, Lai CY, Osteen J, Fang L, Luo C, Lucero JD, Gomez-Castanon R, Nery JR, Silva-Garcia I, Pang Y, Sejnowski TJ, Powell SB, Ecker JR, Mukamel EA, Behrens MM. Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3. eLife 2022; 11:e66909. [PMID: 35604009 PMCID: PMC9170249 DOI: 10.7554/elife.66909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/22/2022] [Indexed: 11/13/2022] Open
Abstract
Two epigenetic pathways of transcriptional repression, DNA methylation and polycomb repressive complex 2 (PRC2), are known to regulate neuronal development and function. However, their respective contributions to brain maturation are unknown. We found that conditional loss of the de novo DNA methyltransferase Dnmt3a in mouse excitatory neurons altered expression of synapse-related genes, stunted synapse maturation, and impaired working memory and social interest. At the genomic level, loss of Dnmt3a abolished postnatal accumulation of CG and non-CG DNA methylation, leaving adult neurons with an unmethylated, fetal-like epigenomic pattern at ~222,000 genomic regions. The PRC2-associated histone modification, H3K27me3, increased at many of these sites. Our data support a dynamic interaction between two fundamental modes of epigenetic repression during postnatal maturation of excitatory neurons, which together confer robustness on neuronal regulation.
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Affiliation(s)
- Junhao Li
- Department of Cognitive Science, University of California, San DiegoLa JollaUnited States
| | - Antonio Pinto-Duarte
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Mark Zander
- Genomic Analysis Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Michael S Cuoco
- Bioinformatics and Systems Biology Graduate Program, University of California, San DiegoLa JollaUnited States
| | - Chi-Yu Lai
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Julia Osteen
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Linjing Fang
- Waitt Advanced Biophotonics Core, Salk Institute for Biological StudiesLa JollaUnited States
| | - Chongyuan Luo
- Genomic Analysis Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
- Howard Hughes Medical Institute, Salk Institute for Biological StudiesLa JollaUnited States
| | - Jacinta D Lucero
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Rosa Gomez-Castanon
- Genomic Analysis Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Joseph R Nery
- Genomic Analysis Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
- Howard Hughes Medical Institute, Salk Institute for Biological StudiesLa JollaUnited States
| | - Isai Silva-Garcia
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Yan Pang
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Terrence J Sejnowski
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Susan B Powell
- Department of Psychiatry, University of California, San DiegoLa JollaUnited States
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San DiegoLa JollaUnited States
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
- Department of Psychiatry, University of California, San DiegoLa JollaUnited States
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31
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Pumo GM, Kitazawa T, Rijli FM. Epigenetic and Transcriptional Regulation of Spontaneous and Sensory Activity Dependent Programs During Neuronal Circuit Development. Front Neural Circuits 2022; 16:911023. [PMID: 35664458 PMCID: PMC9158562 DOI: 10.3389/fncir.2022.911023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Spontaneous activity generated before the onset of sensory transduction has a key role in wiring developing sensory circuits. From axonal targeting, to synapse formation and elimination, to the balanced integration of neurons into developing circuits, this type of activity is implicated in a variety of cellular processes. However, little is known about its molecular mechanisms of action, especially at the level of genome regulation. Conversely, sensory experience-dependent activity implements well-characterized transcriptional and epigenetic chromatin programs that underlie heterogeneous but specific genomic responses that shape both postnatal circuit development and neuroplasticity in the adult. In this review, we focus on our knowledge of the developmental processes regulated by spontaneous activity and the underlying transcriptional mechanisms. We also review novel findings on how chromatin regulates the specificity and developmental induction of the experience-dependent program, and speculate their relevance for our understanding of how spontaneous activity may act at the genomic level to instruct circuit assembly and prepare developing neurons for sensory-dependent connectivity refinement and processing.
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Affiliation(s)
- Gabriele M. Pumo
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department Biozentrum, University of Basel, Basel, Switzerland
| | - Taro Kitazawa
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Filippo M. Rijli
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department Biozentrum, University of Basel, Basel, Switzerland
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32
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The disordered N-terminal domain of DNMT3A recognizes H2AK119ub and is required for postnatal development. Nat Genet 2022; 54:625-636. [PMID: 35534561 PMCID: PMC9295050 DOI: 10.1038/s41588-022-01063-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/28/2022] [Indexed: 02/03/2023]
Abstract
DNA methyltransferase 3a (DNMT3A) plays a crucial role during mammalian development. Two isoforms of DNMT3A are differentially expressed from stem cells to somatic tissues, but their individual functions remain largely uncharacterized. Here we report that the long isoform DNMT3A1, but not the short DNMT3A2, is essential for mouse postnatal development. DNMT3A1 binds to and regulates bivalent neurodevelopmental genes in the brain. Strikingly, Dnmt3a1 knockout perinatal lethality could be partially rescued by DNMT3A1 restoration in the nervous system. We further show that the intrinsically disordered N terminus of DNMT3A1 is required for normal development and DNA methylation at DNMT3A1-enriched regions. Mechanistically, a ubiquitin-interacting motif embedded in a putative α-helix within the N terminus binds to mono-ubiquitinated histone H2AK119, probably mediating recruitment of DNMT3A1 to Polycomb-regulated regions. These data demonstrate an isoform-specific role for DNMT3A1 in mouse postnatal development and reveal the N terminus as a necessary regulatory domain for DNMT3A1 chromatin occupancy and functions in the nervous system.
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33
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Janssen SM, Lorincz MC. Interplay between chromatin marks in development and disease. Nat Rev Genet 2022; 23:137-153. [PMID: 34608297 DOI: 10.1038/s41576-021-00416-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 02/07/2023]
Abstract
DNA methylation (DNAme) and histone post-translational modifications (PTMs) have important roles in transcriptional regulation. Although many reports have characterized the functions of such chromatin marks in isolation, recent genome-wide studies reveal surprisingly complex interactions between them. Here, we focus on the interplay between DNAme and methylation of specific lysine residues on the histone H3 tail. We describe the impact of genetic perturbation of the relevant methyltransferases in the mouse on the landscape of chromatin marks as well as the transcriptome. In addition, we discuss the specific neurodevelopmental growth syndromes and cancers resulting from pathogenic mutations in the human orthologues of these genes. Integrating these observations underscores the fundamental importance of crosstalk between DNA and histone H3 methylation in development and disease.
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Affiliation(s)
- Sanne M Janssen
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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34
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Tian Q, Zou J, Tang J, Liang L, Cao X, Fan S. scMelody: An Enhanced Consensus-Based Clustering Model for Single-Cell Methylation Data by Reconstructing Cell-to-Cell Similarity. Front Bioeng Biotechnol 2022; 10:842019. [PMID: 35284424 PMCID: PMC8905497 DOI: 10.3389/fbioe.2022.842019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell DNA methylation sequencing technology has brought new perspectives to investigate epigenetic heterogeneity, supporting a need for computational methods to cluster cells based on single-cell methylation profiles. Although several methods have been developed, most of them cluster cells based on single (dis)similarity measures, failing to capture complete cell heterogeneity and resulting in locally optimal solutions. Here, we present scMelody, which utilizes an enhanced consensus-based clustering model to reconstruct cell-to-cell methylation similarity patterns and identifies cell subpopulations with the leveraged information from multiple basic similarity measures. Besides, benefitted from the reconstructed cell-to-cell similarity measure, scMelody could conveniently leverage the clustering validation criteria to determine the optimal number of clusters. Assessments on distinct real datasets showed that scMelody accurately recapitulated methylation subpopulations and outperformed existing methods in terms of both cluster partitions and the number of clusters. Moreover, when benchmarking the clustering stability of scMelody on a variety of synthetic datasets, it achieved significant clustering performance gains over existing methods and robustly maintained its clustering accuracy over a wide range of number of cells, number of clusters and CpG dropout proportions. Finally, the real case studies demonstrated the capability of scMelody to assess known cell types and uncover novel cell clusters.
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Affiliation(s)
- Qi Tian
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Jianxiao Zou
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, China
- Intelligent Terminal Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu, China
- Shenzhen Institute for Advanced Study, University of Electronic Science and Technology of China, Shenzhen, China
| | - Jianxiong Tang
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Liang Liang
- Cancer Center, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaohong Cao
- Department of Geriatric Endocrinology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Shicai Fan
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, China
- Intelligent Terminal Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu, China
- Shenzhen Institute for Advanced Study, University of Electronic Science and Technology of China, Shenzhen, China
- *Correspondence: Shicai Fan,
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35
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Gauvrit T, Benderradji H, Buée L, Blum D, Vieau D. Early-Life Environment Influence on Late-Onset Alzheimer’s Disease. Front Cell Dev Biol 2022; 10:834661. [PMID: 35252195 PMCID: PMC8891536 DOI: 10.3389/fcell.2022.834661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/27/2022] [Indexed: 12/30/2022] Open
Abstract
With the expand of the population’s average age, the incidence of neurodegenerative disorders has dramatically increased over the last decades. Alzheimer disease (AD) which is the most prevalent neurodegenerative disease is mostly sporadic and primarily characterized by cognitive deficits and neuropathological lesions such as amyloid -β (Aβ) plaques and neurofibrillary tangles composed of hyper- and/or abnormally phosphorylated Tau protein. AD is considered a complex disease that arises from the interaction between environmental and genetic factors, modulated by epigenetic mechanisms. Besides the well-described cognitive decline, AD patients also exhibit metabolic impairments. Metabolic and cognitive perturbations are indeed frequently observed in the Developmental Origin of Health and Diseases (DOHaD) field of research which proposes that environmental perturbations during the perinatal period determine the susceptibility to pathological conditions later in life. In this review, we explored the potential influence of early environmental exposure to risk factors (maternal stress, malnutrition, xenobiotics, chemical factors … ) and the involvement of epigenetic mechanisms on the programming of late-onset AD. Animal models indicate that offspring exposed to early-life stress during gestation and/or lactation increase both AD lesions, lead to defects in synaptic plasticity and finally to cognitive impairments. This long-lasting epigenetic programming could be modulated by factors such as nutriceuticals, epigenetic modifiers or psychosocial behaviour, offering thus future therapeutic opportunity to protect from AD development.
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Affiliation(s)
- Thibaut Gauvrit
- Inserm, CHU Lille, U1172 LilNCog—Lille Neuroscience and Cognition, Université de Lille, Lille, France
- Alzheimer and Tauopathies, LabEx DISTALZ, Lille, France
| | - Hamza Benderradji
- Inserm, CHU Lille, U1172 LilNCog—Lille Neuroscience and Cognition, Université de Lille, Lille, France
- Alzheimer and Tauopathies, LabEx DISTALZ, Lille, France
| | - Luc Buée
- Inserm, CHU Lille, U1172 LilNCog—Lille Neuroscience and Cognition, Université de Lille, Lille, France
- Alzheimer and Tauopathies, LabEx DISTALZ, Lille, France
| | - David Blum
- Inserm, CHU Lille, U1172 LilNCog—Lille Neuroscience and Cognition, Université de Lille, Lille, France
- Alzheimer and Tauopathies, LabEx DISTALZ, Lille, France
| | - Didier Vieau
- Inserm, CHU Lille, U1172 LilNCog—Lille Neuroscience and Cognition, Université de Lille, Lille, France
- Alzheimer and Tauopathies, LabEx DISTALZ, Lille, France
- *Correspondence: Didier Vieau,
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36
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Fang H, Luo Z, Lin C. Epigenetic reorganization during early embryonic lineage specification. Genes Genomics 2022; 44:379-387. [PMID: 35133623 DOI: 10.1007/s13258-021-01213-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Dynamic chromatin reorganization occurs during two waves of cell lineage specification process, blastocyst formation and gastrulation, to generate distinct cell types. Epigenetic defects have been associated with severe developmental defects and diseases. How epigenetic remodeling coordinates the two lineage specification waves is becoming uncovered, benefiting from the development and application of new technologies including low-input or single-cell epigenome analysis approached in the past few years. OBJECTIVE In this review, we aim to highlight the most recent findings on epigenetic remodeling in cell lineage specification during blastocyst formation and gastrulation. METHODS First, we introduce how DNA methylation dynamically changes in blastocyst formation and gastrulation and its function in transcriptional regulation lineage-specific genes. Then, we discuss widespread remodeling of histone modification at promoters and enhancers in orchestrating the trajectory of cell lineage specification. Finally, we review dynamics of chromatin accessibility and 3D structure regulating developmental gene expression and associating with specific transcription factor binding events at stage specific manner. We also highlight the key questions that remain to be answered to fully understand chromatin regulation and reorganization in lineage specification. CONCLUSION Here, we summarize the recent advances and discoveries on epigenetic reorganization and its roles in blastocyst formation and gastrulation, and how it cooperates with the lineage specification, painting from global sequencing data from mouse in vivo tissues.
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Affiliation(s)
- Haitong Fang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China.
| | - Zhuojuan Luo
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Chengqi Lin
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China. .,Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China.
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37
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Kaplan G, Xu H, Abreu K, Feng J. DNA Epigenetics in Addiction Susceptibility. Front Genet 2022; 13:806685. [PMID: 35145550 PMCID: PMC8821887 DOI: 10.3389/fgene.2022.806685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/06/2022] [Indexed: 12/22/2022] Open
Abstract
Addiction is a chronically relapsing neuropsychiatric disease that occurs in some, but not all, individuals who use substances of abuse. Relatively little is known about the mechanisms which contribute to individual differences in susceptibility to addiction. Neural gene expression regulation underlies the pathogenesis of addiction, which is mediated by epigenetic mechanisms, such as DNA modifications. A growing body of work has demonstrated distinct DNA epigenetic signatures in brain reward regions that may be associated with addiction susceptibility. Furthermore, factors that influence addiction susceptibility are also known to have a DNA epigenetic basis. In the present review, we discuss the notion that addiction susceptibility has an underlying DNA epigenetic basis. We focus on major phenotypes of addiction susceptibility and review evidence of cell type-specific, time dependent, and sex biased effects of drug use. We highlight the role of DNA epigenetics in these diverse processes and propose its contribution to addiction susceptibility differences. Given the prevalence and lack of effective treatments for addiction, elucidating the DNA epigenetic mechanism of addiction vulnerability may represent an expeditious approach to relieving the addiction disease burden.
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38
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Abellán-Álvaro M, Stork O, Agustín-Pavón C, Santos M. MeCP2 haplodeficiency and early-life stress interaction on anxiety-like behavior in adolescent female mice. J Neurodev Disord 2021; 13:59. [PMID: 34895132 PMCID: PMC8903671 DOI: 10.1186/s11689-021-09409-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/30/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Early-life stress can leave persistent epigenetic marks that may modulate vulnerability to psychiatric conditions later in life, including anxiety, depression and stress-related disorders. These are complex disorders with both environmental and genetic influences contributing to their etiology. Methyl-CpG Binding Protein 2 (MeCP2) has been attributed a key role in the control of neuronal activity-dependent gene expression and is a master regulator of experience-dependent epigenetic programming. Moreover, mutations in the MECP2 gene are the primary cause of Rett syndrome and, to a lesser extent, of a range of other major neurodevelopmental disorders. Here, we aim to study the interaction of MeCP2 with early-life stress in variables known to be affected by this environmental manipulation, namely anxiety-like behavior and activity of the underlying neural circuits. METHODS Using Mecp2 heterozygous and wild-type female mice we investigated the effects of the interaction of Mecp2 haplodeficiency with maternal separation later in life, by assessing anxiety-related behaviors and measuring concomitant c-FOS expression in stress- and anxiety-related brain regions of adolescent females. Moreover, arginine vasopressin and corticotropin-releasing hormone neurons of the paraventricular hypothalamic nucleus were analyzed for neuronal activation. RESULTS In wild-type mice, maternal separation caused a reduction in anxiety-like behavior and in the activation of the hypothalamic paraventricular nucleus, specifically in corticotropin-releasing hormone-positive cells, after the elevated plus maze. This effect of maternal separation was not observed in Mecp2 heterozygous females that per se show decreased anxiety-like behavior and concomitant decreased paraventricular nuclei activation. CONCLUSIONS Our data supports that MeCP2 is an essential component of HPA axis reprogramming and underlies the differential response to anxiogenic situations later in life.
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Affiliation(s)
- María Abellán-Álvaro
- Unitat Mixta d'Investigació en Neuroanatomia Funcional, Departamento de Biologia Cel·lular, Biologia Funcional i Antropologia Física, Universitat de València, 46100 Burjassot, València, Spain
| | - Oliver Stork
- Department of Genetics and Molecular Neurobiology, Institute of Biology, Otto-von-Guericke University, 39120, Magdeburg, Germany
| | - Carmen Agustín-Pavón
- Unitat Mixta d'Investigació en Neuroanatomia Funcional, Departamento de Biologia Cel·lular, Biologia Funcional i Antropologia Física, Universitat de València, 46100 Burjassot, València, Spain
| | - Mónica Santos
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal.
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39
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Abstract
Epigenetic mechanisms such as DNA methylation (DNAm) have been associated with stress responses and increased vulnerability to depression. Abnormal DNAm is observed in stressed animals and depressed individuals. Antidepressant treatment modulates DNAm levels and regulates gene expression in diverse tissues, including the brain and the blood. Therefore, DNAm could be a potential therapeutic target in depression. Here, we reviewed the current knowledge about the involvement of DNAm in the behavioural and molecular changes associated with stress exposure and depression. We also evaluated the possible use of DNAm changes as biomarkers of depression. Finally, we discussed current knowledge limitations and future perspectives.
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40
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Liu H, Zhou J, Tian W, Luo C, Bartlett A, Aldridge A, Lucero J, Osteen JK, Nery JR, Chen H, Rivkin A, Castanon RG, Clock B, Li YE, Hou X, Poirion OB, Preissl S, Pinto-Duarte A, O'Connor C, Boggeman L, Fitzpatrick C, Nunn M, Mukamel EA, Zhang Z, Callaway EM, Ren B, Dixon JR, Behrens MM, Ecker JR. DNA methylation atlas of the mouse brain at single-cell resolution. Nature 2021; 598:120-128. [PMID: 34616061 PMCID: PMC8494641 DOI: 10.1038/s41586-020-03182-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/23/2020] [Indexed: 12/14/2022]
Abstract
Mammalian brain cells show remarkable diversity in gene expression, anatomy and function, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly understood. Here we carry out a comprehensive assessment of the epigenomes of mouse brain cell types by applying single-nucleus DNA methylation sequencing1,2 to profile 103,982 nuclei (including 95,815 neurons and 8,167 non-neuronal cells) from 45 regions of the mouse cortex, hippocampus, striatum, pallidum and olfactory areas. We identified 161 cell clusters with distinct spatial locations and projection targets. We constructed taxonomies of these epigenetic types, annotated with signature genes, regulatory elements and transcription factors. These features indicate the potential regulatory landscape supporting the assignment of putative cell types and reveal repetitive usage of regulators in excitatory and inhibitory cells for determining subtypes. The DNA methylation landscape of excitatory neurons in the cortex and hippocampus varied continuously along spatial gradients. Using this deep dataset, we constructed an artificial neural network model that precisely predicts single neuron cell-type identity and brain area spatial location. Integration of high-resolution DNA methylomes with single-nucleus chromatin accessibility data3 enabled prediction of high-confidence enhancer-gene interactions for all identified cell types, which were subsequently validated by cell-type-specific chromatin conformation capture experiments4. By combining multi-omic datasets (DNA methylation, chromatin contacts, and open chromatin) from single nuclei and annotating the regulatory genome of hundreds of cell types in the mouse brain, our DNA methylation atlas establishes the epigenetic basis for neuronal diversity and spatial organization throughout the mouse cerebrum.
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Affiliation(s)
- Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jingtian Zhou
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Wei Tian
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Chongyuan Luo
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Andrew Aldridge
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jacinta Lucero
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Julia K Osteen
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Huaming Chen
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Angeline Rivkin
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ben Clock
- Peptide Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yang Eric Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Xiaomeng Hou
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Olivier B Poirion
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Antonio Pinto-Duarte
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Carolyn O'Connor
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Lara Boggeman
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Conor Fitzpatrick
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Michael Nunn
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | - Zhuzhu Zhang
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Edward M Callaway
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jesse R Dixon
- Peptide Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA.
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Carleial S, Nätt D, Unternährer E, Elbert T, Robjant K, Wilker S, Vukojevic V, Kolassa IT, Zeller AC, Koebach A. DNA methylation changes following narrative exposure therapy in a randomized controlled trial with female former child soldiers. Sci Rep 2021; 11:18493. [PMID: 34531495 PMCID: PMC8445994 DOI: 10.1038/s41598-021-98067-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/02/2021] [Indexed: 02/08/2023] Open
Abstract
The aftermath of traumatization lives on in the neural and epigenetic traces creating a momentum of affliction in the psychological and social realm. Can psychotherapy reorganise these memories through changes in DNA methylation signatures? Using a randomised controlled parallel group design, we examined methylome-wide changes in saliva samples of 84 female former child soldiers from Eastern DR Congo before and six months after Narrative Exposure Therapy. Treatment predicted differentially methylated positions (DMPs) related to ALCAM, RIPOR2, AFAP1 and MOCOS. In addition, treatment associations overlapped at gene level with baseline clinical and social outcomes. Treatment related DMPs are involved in memory formation-the key agent in trauma focused treatments-and enriched for molecular pathways commonly affected by trauma related disorders. Results were partially replicated in an independent sample of 53 female former child soldiers from Northern Uganda. Our results suggest a molecular impact of psychological treatment in women with war-related childhood trauma.Trial registration: Addressing Heightened Levels of Aggression in Traumatized Offenders With Psychotherapeutic Means (ClinicalTrials.gov Identifier: NCT02992561, 14/12/2016).
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Affiliation(s)
- Samuel Carleial
- grid.9811.10000 0001 0658 7699Department of Psychology, Centre for Psychiatry, University of Konstanz, Feuerstein-Strasse. 55, Haus 22, 78479 Konstanz, Germany
| | - Daniel Nätt
- grid.5640.70000 0001 2162 9922Division of Neurobiology, Department of Biomedical and Clinical Sciences, University of Linköping, Building 463, Room 12.023, Linköping, Sweden
| | - Eva Unternährer
- grid.9811.10000 0001 0658 7699Department of Psychology, Centre for Psychiatry, University of Konstanz, Feuerstein-Strasse. 55, Haus 22, 78479 Konstanz, Germany ,grid.6612.30000 0004 1937 0642Child- and Adolescent Research Department, Psychiatric University Hospitals Basel (UPK), University of Basel, Basel, Switzerland
| | - Thomas Elbert
- grid.9811.10000 0001 0658 7699Department of Psychology, Centre for Psychiatry, University of Konstanz, Feuerstein-Strasse. 55, Haus 22, 78479 Konstanz, Germany ,Vivo International E.V., Postbox 5108, 78430 Konstanz, Germany
| | - Katy Robjant
- Vivo International E.V., Postbox 5108, 78430 Konstanz, Germany
| | - Sarah Wilker
- Vivo International E.V., Postbox 5108, 78430 Konstanz, Germany ,grid.7491.b0000 0001 0944 9128Department of Psychology and Sports Science, University of Bielefeld, 33501 Bielefeld, Germany
| | - Vanja Vukojevic
- grid.6612.30000 0004 1937 0642Psychiatric University Clinics, Transfaculty Research Platform, University of Basel, Wilhelm Klein-Strasse 27, CH-4012 Basel, Switzerland
| | - Iris-Tatjana Kolassa
- Vivo International E.V., Postbox 5108, 78430 Konstanz, Germany ,grid.6582.90000 0004 1936 9748Department of Clinical and Biological Psychology, Institute of Psychology & Education, University of Ulm, Ulm University, Ulm, Germany
| | - Anja C. Zeller
- grid.9811.10000 0001 0658 7699Department of Psychology, Centre for Psychiatry, University of Konstanz, Feuerstein-Strasse. 55, Haus 22, 78479 Konstanz, Germany ,Vivo International E.V., Postbox 5108, 78430 Konstanz, Germany
| | - Anke Koebach
- grid.9811.10000 0001 0658 7699Department of Psychology, Centre for Psychiatry, University of Konstanz, Feuerstein-Strasse. 55, Haus 22, 78479 Konstanz, Germany ,Vivo International E.V., Postbox 5108, 78430 Konstanz, Germany
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42
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Kopp ND, Nygaard KR, Liu Y, McCullough KB, Maloney SE, Gabel HW, Dougherty JD. Functions of Gtf2i and Gtf2ird1 in the developing brain: transcription, DNA binding and long-term behavioral consequences. Hum Mol Genet 2021; 29:1498-1519. [PMID: 32313931 DOI: 10.1093/hmg/ddaa070] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/19/2020] [Accepted: 04/13/2020] [Indexed: 12/13/2022] Open
Abstract
Gtf2ird1 and Gtf2i are two transcription factors (TFs) among the 28 genes deleted in Williams syndrome, and prior mouse models of each TF show behavioral phenotypes. Here we identify their genomic binding sites in the developing brain and test for additive effects of their mutation on transcription and behavior. GTF2IRD1 binding targets were enriched for transcriptional and chromatin regulators and mediators of ubiquitination. GTF2I targets were enriched for signal transduction proteins, including regulators of phosphorylation and WNT. Both TFs are highly enriched at promoters, strongly overlap CTCF binding and topological associating domain boundaries and moderately overlap each other, suggesting epistatic effects. Shared TF targets are enriched for reactive oxygen species-responsive genes, synaptic proteins and transcription regulators such as chromatin modifiers, including a significant number of highly constrained genes and known ASD genes. We next used single and double mutants to test whether mutating both TFs will modify transcriptional and behavioral phenotypes of single Gtf2ird1 mutants, though with the caveat that our Gtf2ird1 mutants, like others previously reported, do produce low levels of a truncated protein product. Despite little difference in DNA binding and transcriptome-wide expression, homozygous Gtf2ird1 mutation caused balance, marble burying and conditioned fear phenotypes. However, mutating Gtf2i in addition to Gtf2ird1 did not further modify transcriptomic or most behavioral phenotypes, suggesting Gtf2ird1 mutation alone was sufficient for the observed phenotypes.
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Affiliation(s)
- Nathan D Kopp
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kayla R Nygaard
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine B McCullough
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan E Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.,Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.,Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
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43
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Ibrahim A, Papin C, Mohideen-Abdul K, Le Gras S, Stoll I, Bronner C, Dimitrov S, Klaholz BP, Hamiche A. MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion. Science 2021; 372:372/6549/eabd5581. [PMID: 34324427 DOI: 10.1126/science.abd5581] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 05/06/2021] [Indexed: 12/14/2022]
Abstract
The Rett syndrome protein MeCP2 was described as a methyl-CpG-binding protein, but its exact function remains unknown. Here we show that mouse MeCP2 is a microsatellite binding protein that specifically recognizes hydroxymethylated CA repeats. Depletion of MeCP2 alters chromatin organization of CA repeats and lamina-associated domains and results in nucleosome accumulation on CA repeats and genome-wide transcriptional dysregulation. The structure of MeCP2 in complex with a hydroxymethylated CA repeat reveals a characteristic DNA shape, with considerably modified geometry at the 5-hydroxymethylcytosine, which is recognized specifically by Arg133, a key residue whose mutation causes Rett syndrome. Our work identifies MeCP2 as a microsatellite DNA binding protein that targets the 5hmC-modified CA-rich strand and maintains genome regions nucleosome-free, suggesting a role for MeCP2 dysfunction in Rett syndrome.
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Affiliation(s)
- Abdulkhaleg Ibrahim
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France.,Department of Functional Genomics and Cancer, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France.,Biotechnology Research Center (BTRC), 30303 Tripoli, Libya
| | - Christophe Papin
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France.,Department of Functional Genomics and Cancer, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Kareem Mohideen-Abdul
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France.,Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France
| | - Stéphanie Le Gras
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Isabelle Stoll
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France.,Department of Functional Genomics and Cancer, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Christian Bronner
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France.,Department of Functional Genomics and Cancer, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Stefan Dimitrov
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France. .,Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Bruno P Klaholz
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France. .,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France.,Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France
| | - Ali Hamiche
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France. .,Department of Functional Genomics and Cancer, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U964, 67404 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France.,Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch, France.,Center of Excellence in Bionanoscience Research, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
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44
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Altered neurodevelopmental DNA methylation status after fetal growth restriction with brain-sparing. J Dev Orig Health Dis 2021; 13:378-389. [PMID: 34325767 DOI: 10.1017/s2040174421000374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
It is under debate how preferential perfusion of the brain (brain-sparing) in fetal growth restriction (FGR) relates to long-term neurodevelopmental outcome. Epigenetic modification of neurotrophic genes by altered fetal oxygenation may be involved. To explore this theory, we performed a follow-up study of 21 FGR children, in whom we prospectively measured the prenatal cerebroplacental ratio (CPR) with Doppler sonography. At 4 years of age, we tested their neurodevelopmental outcome using the Wechsler Preschool and Primary Scale of Intelligence, the Child Behavior Checklist, and the Behavior Rating Inventory of Executive Function. In addition, we collected their buccal DNA to determine the methylation status at predefined genetic regions within the genes hypoxia-inducible factor-1 alpha (HIF1A), vascular endothelial growth factor A (VEGFA), erythropoietin (EPO), EPO-receptor (EPOR), brain-derived neurotrophic factor (BDNF), and neurotrophic tyrosine kinase, receptor, type 2 (NTRK2) by pyrosequencing. We found that FGR children with fetal brain-sparing (CPR <1, n = 8) demonstrated a trend (0.05 < p < 0.1) toward hypermethylation of HIF1A and VEGFA at their hypoxia-response element (HRE) compared with FGR children without fetal brain-sparing. Moreover, in cases with fetal brain-sparing, we observed statistically significant hypermethylation at a binding site for cyclic adenosine monophophate response element binding protein (CREB) of BDNF promoter exon 4 and hypomethylation at an HRE located within the NTRK2 promoter (both p <0.05). Hypermethylation of VEGFA was associated with a poorer Performance Intelligence Quotient, while hypermethylation of BDNF was associated with better inhibitory self-control (both p <0.05). These results led us to formulate the hypothesis that early oxygen-dependent epigenetic alterations due to hemodynamic alterations in FGR may be associated with altered neurodevelopmental outcome in later life. We recommend further studies to test this hypothesis.
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45
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Zocher S, Overall RW, Lesche M, Dahl A, Kempermann G. Environmental enrichment preserves a young DNA methylation landscape in the aged mouse hippocampus. Nat Commun 2021; 12:3892. [PMID: 34162876 PMCID: PMC8222384 DOI: 10.1038/s41467-021-23993-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 05/20/2021] [Indexed: 02/05/2023] Open
Abstract
The decline of brain function during aging is associated with epigenetic changes, including DNA methylation. Lifestyle interventions can improve brain function during aging, but their influence on age-related epigenetic changes is unknown. Using genome-wide DNA methylation sequencing, we here show that experiencing a stimulus-rich environment counteracts age-related DNA methylation changes in the hippocampal dentate gyrus of mice. Specifically, environmental enrichment prevented the aging-induced CpG hypomethylation at target sites of the methyl-CpG-binding protein Mecp2, which is critical to neuronal function. The genes at which environmental enrichment counteracted aging effects have described roles in neuronal plasticity, neuronal cell communication and adult hippocampal neurogenesis and are dysregulated with age-related cognitive decline in the human brain. Our results highlight the stimulating effects of environmental enrichment on hippocampal plasticity at the level of DNA methylation and give molecular insights into the specific aspects of brain aging that can be counteracted by lifestyle interventions.
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Affiliation(s)
- Sara Zocher
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Rupert W Overall
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Mathias Lesche
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
- DRESDEN-concept Genome Center c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Andreas Dahl
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
- DRESDEN-concept Genome Center c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Gerd Kempermann
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Dresden, Germany.
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany.
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46
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Dick A, Chen A. The role of TET proteins in stress-induced neuroepigenetic and behavioural adaptations. Neurobiol Stress 2021; 15:100352. [PMID: 34189192 PMCID: PMC8220100 DOI: 10.1016/j.ynstr.2021.100352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 05/21/2021] [Accepted: 06/05/2021] [Indexed: 12/27/2022] Open
Abstract
Over the past decade, critical, non-redundant roles of the ten-eleven translocation (TET) family of dioxygenase enzymes have been identified in the brain during developmental and postnatal stages. Specifically, TET-mediated active demethylation, involving the iterative oxidation of 5-methylcytosine to 5-hydroxymethylcytosine and subsequent oxidative derivatives, is dynamically regulated in response to environmental stimuli such as neuronal activity, learning and memory processes, and stressor exposure. Such changes may therefore perpetuate stable and dynamic transcriptional patterns within neuronal populations required for neuroplasticity and behavioural adaptation. In this review, we will highlight recent evidence supporting a role of TET protein function and active demethylation in stress-induced neuroepigenetic and behavioural adaptations. We further explore potential mechanisms by which TET proteins may mediate both the basal and pathological embedding of stressful life experiences within the brain of relevance to stress-related psychiatric disorders.
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Affiliation(s)
- Alec Dick
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
- Corresponding author.
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
- The Ruhman Family Laboratory for Research on the Neurobiology of Stress, Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
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47
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Deng P, Yuan Q, Cheng Y, Li J, Liu Z, Liu Y, Li Y, Su T, Wang J, Salvo ME, Wang W, Fan G, Lyons K, Yu B, Wang CY. Loss of KDM4B exacerbates bone-fat imbalance and mesenchymal stromal cell exhaustion in skeletal aging. Cell Stem Cell 2021; 28:1057-1073.e7. [PMID: 33571444 PMCID: PMC8178178 DOI: 10.1016/j.stem.2021.01.010] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/27/2020] [Accepted: 01/14/2021] [Indexed: 12/20/2022]
Abstract
Skeletal aging is a complex process, characterized by a decrease in bone formation, an increase in marrow fat, and stem cell exhaustion. Loss of H3K9me3, a heterochromatin mark, has been proposed to be associated with aging. Here, we report that loss of KDM4B in mesenchymal stromal cells (MSCs) exacerbated skeletal aging and osteoporosis by reducing bone formation and increasing marrow adiposity via increasing H3K9me3. KDM4B epigenetically coordinated β-catenin/Smad1-mediated transcription by removing repressive H3K9me3. Importantly, KDM4B ablation impaired MSC self-renewal and promoted MSC exhaustion by inducing senescence-associated heterochromatin foci formation, providing a mechanistic explanation for stem cell exhaustion with aging. Moreover, while KDM4B was required for parathyroid hormone-mediated bone anabolism, KDM4B depletion accelerated bone loss and marrow adiposity induced by a high-fat diet. Our results suggest that the epigenetic rejuvenation and reversing bone-fat imbalance might be new strategies for preventing and treating skeletal aging and osteoporosis by activating KDM4B in MSCs.
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Affiliation(s)
- Peng Deng
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
| | - Quan Yuan
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
| | - Yingduan Cheng
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
| | - Jiong Li
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
| | - Zhenqing Liu
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
| | - Yan Liu
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
| | - Ye Li
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
| | - Trent Su
- Institute for Quantitative and Computational Biology and Department of Biological Chemistry, UCLA, Los Angeles, CA 90095, USA
| | - Jing Wang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles Young Drive South, Los Angeles, CA 90095, USA
| | - Mari Ekimyan Salvo
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
| | - Weiguang Wang
- Department of Orthopaedic Surgery, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Guoping Fan
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles Young Drive South, Los Angeles, CA 90095, USA
| | - Karen Lyons
- Department of Orthopaedic Surgery, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Bo Yu
- Division of Constitutive and Regenerative Science, School of Dentistry, UCLA, Los Angeles, CA 90095, USA
| | - Cun-Yu Wang
- Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Department of Bioengineering, Henry Samueli School of Engineering and Applied Science, UCLA, Los Angeles, CA 90095, USA.
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48
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INTACT vs. FANS for Cell-Type-Specific Nuclei Sorting: A Comprehensive Qualitative and Quantitative Comparison. Int J Mol Sci 2021; 22:ijms22105335. [PMID: 34069481 PMCID: PMC8159132 DOI: 10.3390/ijms22105335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 12/15/2022] Open
Abstract
Increasing numbers of studies seek to characterize the different cellular sub-populations present in mammalian tissues. The techniques “Isolation of Nuclei Tagged in Specific Cell Types” (INTACT) or “Fluorescence-Activated Nuclei Sorting” (FANS) are frequently used for isolating nuclei of specific cellular subtypes. These nuclei are then used for molecular characterization of the cellular sub-populations. Despite the increasing popularity of both techniques, little is known about their isolation efficiency, advantages, and disadvantages or downstream molecular effects. In our study, we compared the physical and molecular attributes of sfGFP+ nuclei isolated by the two methods—INTACT and FANS—from the neocortices of Arc-CreERT2 × CAG-Sun1/sfGFP animals. We identified differences in efficiency of sfGFP+ nuclei isolation, nuclear size as well as transcriptional (RNA-seq) and chromatin accessibility (ATAC-seq) states. Therefore, our study presents a comprehensive comparison between the two widely used nuclei sorting techniques, identifying the advantages and disadvantages for both INTACT and FANS. Our conclusions are summarized in a table to guide researchers in selecting the most suitable methodology for their individual experimental design.
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Rizzardi LF, Hickey PF, Idrizi A, Tryggvadóttir R, Callahan CM, Stephens KE, Taverna SD, Zhang H, Ramazanoglu S, Hansen KD, Feinberg AP. Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits. Genome Biol 2021; 22:116. [PMID: 33888138 PMCID: PMC8061076 DOI: 10.1186/s13059-021-02335-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 03/30/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND DNA methylation dynamics in the brain are associated with normal development and neuropsychiatric disease and differ across functionally distinct brain regions. Previous studies of genome-wide methylation differences among human brain regions focus on limited numbers of individuals and one to two brain regions. RESULTS Using GTEx samples, we generate a resource of DNA methylation in purified neuronal nuclei from 8 brain regions as well as lung and thyroid tissues from 12 to 23 donors. We identify differentially methylated regions between brain regions among neuronal nuclei in both CpG (181,146) and non-CpG (264,868) contexts, few of which were unique to a single pairwise comparison. This significantly expands the knowledge of differential methylation across the brain by 10-fold. In addition, we present the first differential methylation analysis among neuronal nuclei from basal ganglia tissues and identify unique CpG differentially methylated regions, many associated with ion transport. We also identify 81,130 regions of variably CpG methylated regions, i.e., variable methylation among individuals in the same brain region, which are enriched in regulatory regions and in CpG differentially methylated regions. Many variably methylated regions are unique to a specific brain region, with only 202 common across all brain regions, as well as lung and thyroid. Variably methylated regions identified in the amygdala, anterior cingulate cortex, and hippocampus are enriched for heritability of schizophrenia. CONCLUSIONS These data suggest that epigenetic variation in these particular human brain regions could be associated with the risk for this neuropsychiatric disorder.
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Affiliation(s)
- Lindsay F. Rizzardi
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | - Peter F. Hickey
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St, Baltimore, MD 21205 USA
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria Australia
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
| | - Rakel Tryggvadóttir
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
| | - Colin M. Callahan
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
| | - Kimberly E. Stephens
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- Department of Pediatrics, Division of Infectious Diseases, University of Arkansas for Medical Sciences, 13 Children’s Way, Little Rock, AR 72202 USA
- Arkansas Children’s Research Institute, Little Rock, AR 72202 USA
| | - Sean D. Taverna
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD 21205 USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205 USA
| | - Sinan Ramazanoglu
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
| | - GTEx Consortium
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St, Baltimore, MD 21205 USA
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria Australia
- Department of Pediatrics, Division of Infectious Diseases, University of Arkansas for Medical Sciences, 13 Children’s Way, Little Rock, AR 72202 USA
- Arkansas Children’s Research Institute, Little Rock, AR 72202 USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD 21205 USA
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205 USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Departments of Biomedical Engineering and Mental Health, Johns Hopkins University Schools of Engineering and Public Health, Baltimore, MD USA
| | - Kasper D. Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe St, Baltimore, MD 21205 USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Andrew P. Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, 855 N. Wolfe St., Baltimore, MD 21205 USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Departments of Biomedical Engineering and Mental Health, Johns Hopkins University Schools of Engineering and Public Health, Baltimore, MD USA
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50
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Swahari V, Nakamura A, Hollville E, Stroud H, Simon JM, Ptacek TS, Beck MV, Flowers C, Guo J, Plestant C, Liang J, Kurtz CL, Kanke M, Hammond SM, He YW, Anton ES, Sethupathy P, Moy SS, Greenberg ME, Deshmukh M. MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation. Cell Rep 2021; 35:108946. [PMID: 33826889 PMCID: PMC8103628 DOI: 10.1016/j.celrep.2021.108946] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/09/2020] [Accepted: 03/14/2021] [Indexed: 11/27/2022] Open
Abstract
Although embryonic brain development and neurodegeneration have received considerable attention, the events that govern postnatal brain maturation are less understood. Here, we identify the miR-29 family to be strikingly induced during the late stages of brain maturation. Brain maturation is associated with a transient, postnatal period of de novo non-CG (CH) DNA methylation mediated by DNMT3A. We examine whether an important function of miR-29 during brain maturation is to restrict the period of CH methylation via its targeting of Dnmt3a. Deletion of miR-29 in the brain, or knockin mutations preventing miR-29 to specifically target Dnmt3a, result in increased DNMT3A expression, higher CH methylation, and repression of genes associated with neuronal activity and neuropsychiatric disorders. These mouse models also develop neurological deficits and premature lethality. Our results identify an essential role for miR-29 in restricting CH methylation in the brain and illustrate the importance of CH methylation regulation for normal brain maturation.
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Affiliation(s)
- Vijay Swahari
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA.
| | - Ayumi Nakamura
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA
| | - Emilie Hollville
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Hume Stroud
- Department of Neurobiology, Harvard University, Boston, MA, USA
| | - Jeremy M Simon
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | - Travis S Ptacek
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | - Matthew V Beck
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Cornelius Flowers
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jiami Guo
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Jie Liang
- Department of Immunology, Duke University, Durham, NC, USA
| | - C Lisa Kurtz
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Matt Kanke
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Scott M Hammond
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - You-Wen He
- Department of Immunology, Duke University, Durham, NC, USA
| | - E S Anton
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Praveen Sethupathy
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA; Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Sheryl S Moy
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | | | - Mohanish Deshmukh
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA.
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