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Madrid A, Koueik J, Papale LA, Chebel R, Renteria I, Cannon E, Hogan KJ, Alisch RS, Iskandar BJ. Folate-mediated transgenerational inheritance of sperm DNA methylation patterns correlate with spinal axon regeneration. Epigenetics 2024; 19:2380930. [PMID: 39066680 PMCID: PMC11285217 DOI: 10.1080/15592294.2024.2380930] [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: 02/10/2024] [Revised: 06/01/2024] [Accepted: 07/11/2024] [Indexed: 07/30/2024] Open
Abstract
In mammals, the molecular mechanisms underlying transgenerational inheritance of phenotypic traits in serial generations of progeny after ancestral environmental exposures, without variation in DNA sequence, remain elusive. We've recently described transmission of a beneficial trait in rats and mice, in which F0 supplementation of methyl donors, including folic acid, generates enhanced axon regeneration after sharp spinal cord injury in untreated F1 to F3 progeny linked to differential DNA methylation levels in spinal cord tissue. To test whether the transgenerational effect of folic acid is transmitted via the germline, we performed whole-genome methylation sequencing on sperm DNA from F0 mice treated with either folic acid or vehicle control, and their F1, F2, and F3 untreated progeny. Transgenerational differentially methylated regions (DMRs) are observed in each consecutive generation and distinguish folic acid from untreated lineages, predominate outside of CpG islands and in regions of the genome that regulate gene expression, including promoters, and overlap at both the differentially methylated position (DMP) and gene levels. These findings indicate that molecular changes between generations are caused by ancestral folate supplementation. In addition, 29,719 DMPs exhibit serial increases or decreases in DNA methylation levels in successive generations of untreated offspring, correlating with a serial increase in the phenotype across generations, consistent with a 'wash-in' effect. Sibship-specific DMPs annotate to genes that participate in axon- and synapse-related pathways.
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Affiliation(s)
- Andy Madrid
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Joyce Koueik
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Ligia A. Papale
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Roy Chebel
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Isabelle Renteria
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Emily Cannon
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Kirk J. Hogan
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Reid S. Alisch
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Bermans J. Iskandar
- Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, USA
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Abbaszadeh F, Javadpour P, Mousavi Nasab MM, Jorjani M. The Role of Vitamins in Spinal Cord Injury: Mechanisms and Benefits. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2024; 2024:4293391. [PMID: 38938696 PMCID: PMC11211004 DOI: 10.1155/2024/4293391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/18/2024] [Accepted: 06/06/2024] [Indexed: 06/29/2024]
Abstract
Spinal cord injury (SCI) is a common neurological disease worldwide, often resulting in a substantial decrease in quality of life, disability, and in severe cases, even death. Unfortunately, there is currently no effective treatment for this disease. Nevertheless, current basic and clinical evidence suggests that vitamins, with their antioxidant properties and biological functions, may play a valuable role in improving the quality of life for individuals with SCI. They can promote overall health and facilitate the healing process. In this review, we discuss the mechanisms and therapeutic potential of vitamins in the treatment of SCI.
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Affiliation(s)
- Fatemeh Abbaszadeh
- Neurobiology Research CenterShahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pegah Javadpour
- Neuroscience Research CenterShahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Masoumeh Jorjani
- Neurobiology Research CenterShahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of PharmacologySchool of MedicineShahid Beheshti University of Medical Sciences, Tehran, Iran
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Zhou Y, Zhang Y, Botchway BOA, Wang X, Liu X. Curcumin can improve spinal cord injury by inhibiting DNA methylation. Mol Cell Biochem 2024; 479:351-362. [PMID: 37076656 DOI: 10.1007/s11010-023-04731-1] [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: 03/04/2023] [Accepted: 04/05/2023] [Indexed: 04/21/2023]
Abstract
Spinal cord injury (SCI) is a serious central nervous system disease. Traumatic SCI often causes persistent neurological deficits below the injury level. Epigenetic changes occur after SCI. Studies have shown DNA methylation to be a key player in nerve regeneration and remodeling, and in regulating some pathophysiological characteristics of SCI. Curcumin is a natural polyphenol from turmeric. It has anti-inflammatory, antioxidant, and neuroprotective effects, and can mitigate the cell and tissue damage caused by SCI. This report analyzed the specific functions of DNA methylation in central nervous system diseases, especially traumatic brain injury and SCI. DNA methylation can regulate the level of gene expressions in the central nervous system. Therefore, pharmacological interventions regulating DNA methylation may be promising for SCI.
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Affiliation(s)
- Yu Zhou
- Department of Histology and Embryology, Medical College, Shaoxing University, Shaoxing, 312000, Zhejiang, China
| | - Yong Zhang
- Department of Histology and Embryology, Medical College, Shaoxing University, Shaoxing, 312000, Zhejiang, China
| | - Benson O A Botchway
- Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, China
- Bupa Cromwell Hospital, London, UK
| | - Xichen Wang
- Department of Histology and Embryology, Medical College, Shaoxing University, Shaoxing, 312000, Zhejiang, China
| | - Xuehong Liu
- Department of Histology and Embryology, Medical College, Shaoxing University, Shaoxing, 312000, Zhejiang, China.
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Kim HN, McCrea MR, Li S. Advances in molecular therapies for targeting pathophysiology in spinal cord injury. Expert Opin Ther Targets 2023; 27:171-187. [PMID: 37017093 PMCID: PMC10148912 DOI: 10.1080/14728222.2023.2194532] [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: 01/23/2023] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 04/06/2023]
Abstract
INTRODUCTION Spinal cord injury (SCI) affects 25,000-50,000 people around the world each year and there is no cure for SCI patients currently. The primary injury damages spinal cord tissues and secondary injury mechanisms, including ischemia, apoptosis, inflammation, and astrogliosis, further exacerbate the lesions to the spinal cord. Recently, researchers have designed various therapeutic approaches for SCI by targeting its major cellular or molecular pathophysiology. AREAS COVERED Some strategies have shown promise in repairing injured spinal cord for functional recoveries, such as administering neuroprotective reagents, targeting specific genes to promote robust axon regeneration of disconnected spinal fiber tracts, targeting epigenetic factors to enhance cell survival and neural repair, and facilitating neuronal relay pathways and neuroplasticity for restoration of function after SCI. This review focuses on the major advances in preclinical molecular therapies for SCI reported in recent years. EXPERT OPINION Recent progress in developing novel and effective repairing strategies for SCI is encouraging, but many challenges remain for future design of effective treatments, including developing highly effective neuroprotectants for early interventions, stimulating robust neuronal regeneration with functional synaptic reconnections among disconnected neurons, maximizing the recovery of lost neural functions with combination strategies, and translating the most promising therapies into human use.
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Affiliation(s)
- Ha Neui Kim
- Shriners Hospitals Pediatric Research Center, Department of Neural Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Madeline R. McCrea
- Shriners Hospitals Pediatric Research Center, Department of Neural Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Shuxin Li
- Shriners Hospitals Pediatric Research Center, Department of Neural Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
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Rizk E, Madrid A, Koueik J, Sun D, Stewart K, Chen D, Luo S, Hong F, Papale LA, Hariharan N, Alisch RS, Iskandar BJ. Purified regenerating retinal neurons reveal regulatory role of DNA methylation-mediated Na+/K+-ATPase in murine axon regeneration. Commun Biol 2023; 6:120. [PMID: 36717618 PMCID: PMC9886953 DOI: 10.1038/s42003-023-04463-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
While embryonic mammalian central nervous system (CNS) axons readily grow and differentiate, only a minority of fully differentiated mature CNS neurons are able to regenerate injured axons, leading to stunted functional recovery after injury and disease. To delineate DNA methylation changes specifically associated with axon regeneration, we used a Fluorescent-Activated Cell Sorting (FACS)-based methodology in a rat optic nerve transection model to segregate the injured retinal ganglion cells (RGCs) into regenerating and non-regenerating cell populations. Whole-genome DNA methylation profiling of these purified neurons revealed genes and pathways linked to mammalian RGC regeneration. Moreover, whole-methylome sequencing of purified uninjured adult and embryonic RGCs identified embryonic molecular profiles reactivated after injury in mature neurons, and others that correlate specifically with embryonic or adult axon growth, but not both. The results highlight the contribution to both embryonic growth and adult axon regeneration of subunits encoding the Na+/K+-ATPase. In turn, both biochemical and genetic inhibition of the Na+/K+-ATPase pump significantly reduced RGC axon regeneration. These data provide critical molecular insights into mammalian CNS axon regeneration, pinpoint the Na+/K+-ATPase as a key regulator of regeneration of injured mature CNS axons, and suggest that successful regeneration requires, in part, reactivation of embryonic signals.
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Affiliation(s)
- Elias Rizk
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA ,grid.240473.60000 0004 0543 9901Department of Neurological Surgery, Penn State Milton S. Hershey Medical Center, Hershey, PA 17033 USA
| | - Andy Madrid
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Joyce Koueik
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Dandan Sun
- grid.21925.3d0000 0004 1936 9000Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Krista Stewart
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - David Chen
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Susan Luo
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Felissa Hong
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Ligia A. Papale
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Nithya Hariharan
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Reid S. Alisch
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
| | - Bermans J. Iskandar
- grid.14003.360000 0001 2167 3675Department of Neurological Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53792 USA
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Madrid A, Alisch RS, Rizk E, Papale LA, Hogan KJ, Iskandar BJ. Transgenerational epigenetic inheritance of axonal regeneration after spinal cord injury. ENVIRONMENTAL EPIGENETICS 2023; 9:dvad002. [PMID: 36843857 PMCID: PMC9949995 DOI: 10.1093/eep/dvad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/01/2023] [Accepted: 01/14/2023] [Indexed: 05/14/2023]
Abstract
Human epidemiological studies reveal that dietary and environmental alterations influence the health of the offspring and that the effect is not limited to the F1 or F2 generations. Non-Mendelian transgenerational inheritance of traits in response to environmental stimuli has been confirmed in non-mammalian organisms including plants and worms and are shown to be epigenetically mediated. However, transgenerational inheritance beyond the F2 generation remains controversial in mammals. Our lab previously discovered that the treatment of rodents (rats and mice) with folic acid significantly enhances the regeneration of injured axons following spinal cord injury in vivo and in vitro, and the effect is mediated by DNA methylation. The potential heritability of DNA methylation prompted us to investigate the following question: Is the enhanced axonal regeneration phenotype inherited transgenerationally without exposure to folic acid supplementation in the intervening generations? In the present review, we condense our findings showing that a beneficial trait (i.e., enhanced axonal regeneration after spinal cord injury) and accompanying molecular alterations (i.e., DNA methylation), triggered by an environmental exposure (i.e., folic acid supplementation) to F0 animals only, are inherited transgenerationally and beyond the F3 generation.
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Affiliation(s)
- Andy Madrid
- Department of Neurological Surgery, University of Wisconsin—Madison, Madison, WI 53719, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin—Madison, Madison, WI 53719, USA
| | - Elias Rizk
- Department of Neurosurgery, Penn State Children’s Hospital, Hershey, PA 17033, USA
| | - Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin—Madison, Madison, WI 53719, USA
| | - Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin—Madison, Madison, WI 53719, USA
- Wisconsin Alzheimer’s Institute, University of Wisconsin—Madison, Madison, WI 53719, USA
| | - Bermans J Iskandar
- Department of Neurological Surgery, University of Wisconsin—Madison, Madison, WI 53719, USA
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Balnis J, Madrid A, Hogan KJ, Drake LA, Adhikari A, Vancavage R, Singer HA, Alisch RS, Jaitovich A. Persistent blood DNA methylation changes one year after SARS-CoV-2 infection. Clin Epigenetics 2022; 14:94. [PMID: 35871090 PMCID: PMC9308917 DOI: 10.1186/s13148-022-01313-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/11/2022] [Indexed: 11/29/2022] Open
Abstract
We recently reported the COVID-19-induced circulating leukocytes DNA methylation profile. Here, we hypothesized that some of these genes would persist differentially methylated after disease resolution. Fifteen participants previously hospitalized for SARS-CoV-2 infection were epityped one year after discharge. Of the 1505 acute illness-induced differentially methylated regions (DMRs) previously identified, we found 71 regions with persisted differentially methylated, with an average of 7 serial CpG positions per DMR. Sixty-four DMRs persisted hypermethylated, and 7 DMR persisted hypomethylated. These data are the first reported evidence that DNA methylation changes in circulating leukocytes endure long after recovery from acute illness.
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Affiliation(s)
- Joseph Balnis
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, USA.,Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC91, Albany, New York, 12208, USA
| | - Andy Madrid
- Department of Neurological Surgery, Albany Medical College, Madison, Wisconsin, USA
| | - Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Lisa A Drake
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, USA
| | - Anish Adhikari
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, USA.,Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC91, Albany, New York, 12208, USA
| | - Rachel Vancavage
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, USA.,Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC91, Albany, New York, 12208, USA
| | - Harold A Singer
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, USA
| | - Reid S Alisch
- Department of Neurological Surgery, Albany Medical College, Madison, Wisconsin, USA
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, USA. .,Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC91, Albany, New York, 12208, USA.
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Balnis J, Madrid A, Hogan KJ, Drake LA, Chieng HC, Tiwari A, Vincent CE, Chopra A, Vincent PA, Robek MD, Singer HA, Alisch RS, Jaitovich A. Blood DNA methylation and COVID-19 outcomes. Clin Epigenetics 2021; 13:118. [PMID: 34034806 PMCID: PMC8148415 DOI: 10.1186/s13148-021-01102-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/11/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND There are no prior reports that compare differentially methylated regions of DNA in blood samples from COVID-19 patients to samples collected before the SARS-CoV-2 pandemic using a shared epigenotyping platform. We performed a genome-wide analysis of circulating blood DNA CpG methylation using the Infinium Human MethylationEPIC BeadChip on 124 blood samples from hospitalized COVID-19-positive and COVID-19-negative patients and compared these data with previously reported data from 39 healthy individuals collected before the pandemic. Prospective outcome measures such as COVID-19-GRAM risk-score and mortality were combined with methylation data. RESULTS Global mean methylation levels did not differ between COVID-19 patients and healthy pre-pandemic controls. About 75% of acute illness-associated differentially methylated regions were located near gene promoter regions and were hypo-methylated in comparison with healthy pre-pandemic controls. Gene ontology analyses revealed terms associated with the immune response to viral infections and leukocyte activation; and disease ontology analyses revealed a predominance of autoimmune disorders. Among COVID-19-positive patients, worse outcomes were associated with a prevailing hyper-methylated status. Recursive feature elimination identified 77 differentially methylated positions predictive of COVID-19 severity measured by the GRAM-risk score. CONCLUSION Our data contribute to the awareness that DNA methylation may influence the expression of genes that regulate COVID-19 progression and represent a targetable process in that setting.
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Affiliation(s)
- Joseph Balnis
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin, Madison, WI, USA
| | - Lisa A Drake
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Hau C Chieng
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Anupama Tiwari
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Catherine E Vincent
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Amit Chopra
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Peter A Vincent
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Michael D Robek
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, USA
| | - Harold A Singer
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA.
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA.
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA.
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Madrid A, Borth LE, Hogan KJ, Hariharan N, Papale LA, Alisch RS, Iskandar BJ. DNA methylation and hydroxymethylation have distinct genome-wide profiles related to axonal regeneration. Epigenetics 2021; 16:64-78. [PMID: 32633672 PMCID: PMC7889172 DOI: 10.1080/15592294.2020.1786320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/04/2020] [Accepted: 05/28/2020] [Indexed: 12/23/2022] Open
Abstract
Alterations in environmentally sensitive epigenetic mechanisms (e.g., DNA methylation) influence axonal regeneration in the spinal cord following sharp injury. Conventional DNA methylation detection methods using sodium bisulphite treatment do not distinguish between methylated and hydroxymethylated forms of cytosine, meaning that past studies report a composite of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). To identify the distinct contributions of DNA methylation modifications to axonal regeneration, we collected spinal cord tissue after sharp injury from untreated adult F3 male rats with enhanced regeneration of injured spinal axons or controls, derived from folate- or water-treated F0 lineages, respectively. Genomic DNA was profiled for genome-wide 5hmC levels, revealing 658 differentially hydroxymethylated regions (DhMRs). Genomic profiling with whole genome bisulphite sequencing disclosed regeneration-related alterations in composite 5mC + 5hmC DNA methylation levels at 2,260 differentially methylated regions (DMRs). While pathway analyses revealed that differentially hydroxymethylated and methylated genes are linked to biologically relevant axon developmental pathways, only 22 genes harbour both DhMR and DMRs. Since these differential modifications were more than 60 kilobases on average away from each other, the large majority of differential hydroxymethylated and methylated regions are unique with distinct functions in the axonal regeneration phenotype. These data highlight the importance of distinguishing independent contributions of 5mC and 5hmC levels in the central nervous system, and denote discrete roles for DNA methylation modifications in spinal cord injury and regeneration in the context of transgenerational inheritance.
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Affiliation(s)
- Andy Madrid
- Department of Neurological Surgery, University of Wisconsin – Madison, Madison, WI, USA
- Neuroscience Training Program, University of Wisconsin – Madison, Madison, WI, USA
| | - Laura E. Borth
- Department of Neurological Surgery, University of Wisconsin – Madison, Madison, WI, USA
- Interdepartmental Graduate Program in Nutritional Science, University of Wisconsin – Madison, Madison, WI, USA
| | - Kirk J. Hogan
- Department of Anesthesiology, University of Wisconsin – Madison, Madison, WI, USA
| | - Nithya Hariharan
- Department of Neurological Surgery, University of Wisconsin – Madison, Madison, WI, USA
| | - Ligia A. Papale
- Department of Neurological Surgery, University of Wisconsin – Madison, Madison, WI, USA
| | - Reid S. Alisch
- Department of Neurological Surgery, University of Wisconsin – Madison, Madison, WI, USA
| | - Bermans J. Iskandar
- Department of Neurological Surgery, University of Wisconsin – Madison, Madison, WI, USA
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