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1.
Epigenetics ; 19(1): 2380930, 2024 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-39066680

RESUMEN

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.


Asunto(s)
Axones , Metilación de ADN , Ácido Fólico , Espermatozoides , Ácido Fólico/farmacología , Ácido Fólico/administración & dosificación , Animales , Masculino , Ratones , Espermatozoides/efectos de los fármacos , Espermatozoides/metabolismo , Axones/metabolismo , Axones/efectos de los fármacos , Traumatismos de la Médula Espinal/genética , Traumatismos de la Médula Espinal/metabolismo , Islas de CpG , Femenino , Regeneración Nerviosa/efectos de los fármacos , Epigénesis Genética , Médula Espinal/metabolismo , Médula Espinal/efectos de los fármacos , Médula Espinal/citología
2.
EBioMedicine ; 106: 105251, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-39024897

RESUMEN

BACKGROUND: DNA methylation integrates environmental signals with transcriptional programs. COVID-19 infection induces changes in the host methylome. While post-acute sequelae of COVID-19 (PASC) is a long-term complication of acute illness, its association with DNA methylation is unknown. No universal blood marker of PASC, superseding single organ dysfunctions, has yet been identified. METHODS: In this single centre prospective cohort study, PASC, post-COVID without PASC, and healthy participants were enrolled to investigate their symptoms association with peripheral blood DNA methylation data generated with state-of-the-art whole genome sequencing. PASC-induced quality-of-life deterioration was scored with a validated instrument, SF-36. Analyses were conducted to identify potential functional roles of differentially methylated loci, and machine learning algorithms were used to resolve PASC severity. FINDINGS: 103 patients with PASC (22.3% male, 77.7% female), 15 patients with previous COVID-19 infection but no PASC (40.0% male, 60.0% female), and 27 healthy volunteers (48.1% male, 51.9% female) were enrolled. Whole genome methylation sequencing revealed 39 differentially methylated regions (DMRs) specific to PASC, each harbouring an average of 15 consecutive positions, that differentiate patients with PASC from the two control groups. Motif analyses of PASC-regulated DMRs identify binding domains for transcription factors regulating circadian rhythm and others. Some DMRs annotated to protein coding genes were associated with changes of RNA expression. Machine learning support vector algorithm and random forest hierarchical clustering reveal 28 unique differentially methylated positions (DMPs) in the genome discriminating patients with better and worse quality of life. INTERPRETATION: Blood DNA methylation levels identify PASC, stratify PASC severity, and suggest that DNA motifs are targeted by circadian rhythm-regulating pathways in PASC. FUNDING: This project has been funded by the following agencies: NIH-AI173035 (A. Jaitovich and R. Alisch); and NIH-AG066179 (R. Alisch).


Asunto(s)
COVID-19 , Metilación de ADN , SARS-CoV-2 , Humanos , COVID-19/genética , COVID-19/sangre , COVID-19/virología , Femenino , Masculino , Persona de Mediana Edad , SARS-CoV-2/genética , Estudios Prospectivos , Adulto , Anciano , Síndrome Post Agudo de COVID-19 , Aprendizaje Automático , Secuenciación Completa del Genoma , Biomarcadores/sangre , Calidad de Vida , Betacoronavirus/genética
3.
Proc Natl Acad Sci U S A ; 121(3): e2317668121, 2024 Jan 16.
Artículo en Inglés | MEDLINE | ID: mdl-38194455

RESUMEN

Orofacial clefts of the lip and palate are widely recognized to result from complex gene-environment interactions, but inadequate understanding of environmental risk factors has stymied development of prevention strategies. We interrogated the role of DNA methylation, an environmentally malleable epigenetic mechanism, in orofacial development. Expression of the key DNA methyltransferase enzyme DNMT1 was detected throughout palate morphogenesis in the epithelium and underlying cranial neural crest cell (cNCC) mesenchyme, a highly proliferative multipotent stem cell population that forms orofacial connective tissue. Genetic and pharmacologic manipulations of DNMT activity were then applied to define the tissue- and timing-dependent requirement of DNA methylation in orofacial development. cNCC-specific Dnmt1 inactivation targeting initial palate outgrowth resulted in OFCs, while later targeting during palatal shelf elevation and elongation did not. Conditional Dnmt1 deletion reduced cNCC proliferation and subsequent differentiation trajectory, resulting in attenuated outgrowth of the palatal shelves and altered development of cNCC-derived skeletal elements. Finally, we found that the cellular mechanisms of cleft pathogenesis observed in vivo can be recapitulated by pharmacologically reducing DNA methylation in multipotent cNCCs cultured in vitro. These findings demonstrate that DNA methylation is a crucial epigenetic regulator of cNCC biology, define a critical period of development in which its disruption directly causes OFCs, and provide opportunities to identify environmental influences that contribute to OFC risk.


Asunto(s)
Labio Leporino , Fisura del Paladar , Animales , Ratones , Labio Leporino/genética , Metilación de ADN , Fisura del Paladar/genética , Cresta Neural , Metilasas de Modificación del ADN , Proliferación Celular
4.
Alzheimers Dement ; 20(2): 1050-1062, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-37856321

RESUMEN

INTRODUCTION: DNA microarray-based studies report differentially methylated positions (DMPs) in blood between late-onset dementia due to Alzheimer's disease (AD) and cognitively unimpaired individuals, but interrogate < 4% of the genome. METHODS: We used whole genome methylation sequencing (WGMS) to quantify DNA methylation levels at 25,409,826 CpG loci in 281 blood samples from 108 AD and 173 cognitively unimpaired individuals. RESULTS: WGMS identified 28,038 DMPs throughout the human methylome, including 2707 differentially methylated genes (e.g., SORCS3, GABA, and PICALM) encoding proteins in biological pathways relevant to AD such as synaptic membrane, cation channel complex, and glutamatergic synapse. One hundred seventy-three differentially methylated blood-specific enhancers interact with the promoters of 95 genes that are differentially expressed in blood from persons with and without AD. DISCUSSION: WGMS identifies differentially methylated CpGs in known and newly detected genes and enhancers in blood from persons with and without AD. HIGHLIGHTS: Whole genome DNA methylation levels were quantified in blood from persons with and without Alzheimer's disease (AD). Twenty-eight thousand thirty-eight differentially methylated positions (DMPs) were identified. Two thousand seven hundred seven genes comprise DMPs. Forty-eight of 75 independent genetic risk loci for AD have DMPs. One thousand five hundred sixty-eight blood-specific enhancers comprise DMPs, 173 of which interact with the promoters of 95 genes that are differentially expressed in blood from persons with and without AD.


Asunto(s)
Enfermedad de Alzheimer , Metilación de ADN , Humanos , Enfermedad de Alzheimer/genética , Enfermedad de Alzheimer/metabolismo , Epigénesis Genética , Secuenciación Completa del Genoma
5.
Hum Mol Genet ; 32(24): 3312-3322, 2023 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-37658766

RESUMEN

Autism spectrum disorders (ASD) are polygenic multifactorial disorders influenced by environmental factors. ASD-related differential DNA methylation has been found in human peripheral tissues, such as placenta, paternal sperm, buccal epithelium, and blood. However, these data lack direct comparison of DNA methylation levels with brain tissue from the same individual to determine the extent that peripheral tissues are surrogates for behavior-related disorders. Here, whole genome methylation profiling at all the possible sites throughout the mouse genome (>25 million) from both brain and blood tissues revealed novel insights into the systemic contributions of DNA methylation to ASD. Sixty-six differentially methylated regions (DMRs) share the same genomic coordinates in these two tissues, many of which are linked to risk genes for neurodevelopmental disorders and intellectual disabilities (e.g. Prkch, Ptn, Hcfc1, Mid1, and Nfia). Gene ontological pathways revealed a significant number of common terms between brain and blood (N = 65 terms), and nearly half (30/65) were associated with brain/neuronal development. Furthermore, seven DMR-associated genes among these terms contain methyl-sensitive transcription factor sequence motifs within the DMRs of both tissues; four of them (Cux2, Kcnip2, Fgf13, and Mrtfa) contain the same methyl-sensitive transcription factor binding sequence motifs (HES1/2/5, TBX2 and TFAP2C), suggesting DNA methylation influences the binding of common transcription factors required for gene expression. Together, these findings suggest that peripheral blood is a good surrogate tissue for brain and support that DNA methylation contributes to altered gene regulation in the pathogenesis of ASD.


Asunto(s)
Trastorno Autístico , Metilación de ADN , Embarazo , Femenino , Masculino , Humanos , Animales , Ratones , Metilación de ADN/genética , Trastorno Autístico/genética , Epigénesis Genética , Semen , Factores de Transcripción/genética , Hipocampo
7.
Environ Epigenet ; 9(1): dvad002, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36843857

RESUMEN

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.

8.
Commun Biol ; 6(1): 120, 2023 01 30.
Artículo en Inglés | MEDLINE | ID: mdl-36717618

RESUMEN

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.


Asunto(s)
Axones , Metilación de ADN , Animales , Ratas , Adenosina Trifosfatasas/metabolismo , Axones/metabolismo , Regeneración Nerviosa/genética , Células Ganglionares de la Retina/fisiología
9.
Sci Rep ; 12(1): 17177, 2022 10 20.
Artículo en Inglés | MEDLINE | ID: mdl-36266402

RESUMEN

Adverse childhood experiences (ACEs, i.e., abuse, neglect, household dysfunction) represent a potential risk factor for a wide range of long-lasting diseases and shorter life expectancy. We recently described a 1-week residential group program, based on mindfulness training, artistic expression and EMDR group therapy, that significantly reduced PTSD-related symptoms and increased attention/awareness-related outcomes in adolescent girls with multiple ACEs in a randomized controlled study. Since epigenetic mechanisms (i.e., DNA methylation) have been associated with the long-lasting effects of ACEs, the present report extends these prior findings by exploring genome-wide DNA methylation changes following the program. Saliva samples from all participants (n = 44) were collected and genomic DNA was extracted prior (T1) and following (T2) the intervention. Genome-wide DNA methylation analysis using the MethylationEPIC beadchip array (Illumina) revealed 49 differentially methylated loci (DML; p value < 0.001; methylation change > 10%) that were annotated to genes with roles in biological processes linked to early childhood adversity (i.e., neural, immune, and endocrine pathways, cancer and cardiovascular disease). DNA sequences flanking these DML showed significant enrichment of transcription factor binding sites involved in inflammation, cancer, cardiovascular disease, and brain development. Methylation changes in SIRT5 and TRAPPC2L genes showed associations with changes in trauma-related psychological measures. Results presented here suggest that this multimodal group program for adolescents with multiple victimization modulates the DNA methylome at sites of potential relevance for health and behavioral disorders associated with ACEs.


Asunto(s)
Experiencias Adversas de la Infancia , Epigénesis Genética , Adolescente , Femenino , Humanos , Enfermedades Cardiovasculares/genética , Metilación de ADN , Factores de Transcripción/genética , Inflamación/genética , Neoplasias/genética
10.
Clin Epigenetics ; 14(1): 94, 2022 07 23.
Artículo en Inglés | MEDLINE | ID: mdl-35871090

RESUMEN

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.


Asunto(s)
COVID-19 , Metilación de ADN , Enfermedad Aguda , COVID-19/genética , Islas de CpG , Humanos , SARS-CoV-2
11.
Nat Immunol ; 23(4): 581-593, 2022 04.
Artículo en Inglés | MEDLINE | ID: mdl-35347285

RESUMEN

Meningeal lymphatics near the cribriform plate undergo lymphangiogenesis during neuroinflammation to drain excess fluid. Here, we hypothesized that lymphangiogenic vessels may acquire an altered phenotype to regulate immunity. Using single-cell RNA sequencing of meningeal lymphatics near the cribriform plate from healthy and experimental autoimmune encephalomyelitis in the C57BL/6 model, we report that neuroinflammation induces the upregulation of genes involved in antigen presentation such as major histocompatibility complex class II, adhesion molecules including vascular cell adhesion protein 1 and immunoregulatory molecules such as programmed cell death 1 ligand 1, where many of these changes are mediated by interferon-γ. The inflamed lymphatics retain CD11c+ cells and CD4 T cells where they capture and present antigen, creating an immunoregulatory niche that represents an underappreciated interface in the regulation of neuroinflammation. We also found discontinuity of the arachnoid membrane near the cribriform plate, which provides unrestricted access to the cerebrospinal fluid. These findings highlight a previously unknown function of local meningeal lymphatics in regulating immunity that has only previously been characterized in draining lymph nodes.


Asunto(s)
Hueso Etmoides , Vasos Linfáticos , Animales , Hueso Etmoides/fisiología , Linfangiogénesis/fisiología , Sistema Linfático , Enfermedades Neuroinflamatorias
12.
Genome Res ; 32(2): 266-279, 2022 02.
Artículo en Inglés | MEDLINE | ID: mdl-34949667

RESUMEN

Mouse knockouts of Cntnap2 show altered neurodevelopmental behavior, deficits in striatal GABAergic signaling, and a genome-wide disruption of an environmentally sensitive DNA methylation modification (5-hydroxymethylcytosine [5hmC]) in the orthologs of a significant number of genes implicated in human neurodevelopmental disorders. We tested adult Cntnap2 heterozygous mice (Cntnap2 +/-; lacking behavioral or neuropathological abnormalities) subjected to a prenatal stress and found that prenatally stressed Cntnap2 +/- female mice show repetitive behaviors and altered sociability, similar to the homozygote phenotype. Genomic profiling revealed disruptions in hippocampal and striatal 5hmC levels that are correlated to altered transcript levels of genes linked to these phenotypes (e.g., Reln, Dst, Trio, and Epha5). Chromatin immunoprecipitation coupled with high-throughput sequencing and hippocampal nuclear lysate pull-down data indicated that 5hmC abundance alters the binding of the transcription factor CLOCK near the promoters of these genes (e.g., Palld, Gigyf1, and Fry), providing a mechanistic role for 5hmC in gene regulation. Together, these data support gene-by-environment hypotheses for the origins of mental illness and provide a means to identify the elusive factors contributing to complex human diseases.


Asunto(s)
Interacción Gen-Ambiente , Trastornos del Neurodesarrollo , 5-Metilcitosina/análogos & derivados , 5-Metilcitosina/metabolismo , Animales , Metilación de ADN , Epigénesis Genética , Femenino , Proteínas de la Membrana/metabolismo , Ratones , Proteínas del Tejido Nervioso/metabolismo , Embarazo
13.
Sleep ; 44(10)2021 10 11.
Artículo en Inglés | MEDLINE | ID: mdl-34145460

RESUMEN

STUDY OBJECTIVES: Patients with unexplained hypersomnolence have significant impairment related to daytime sleepiness and excessive sleep duration, the biological bases of which are poorly understood. This investigation sought to examine relationships between objectively measured hypersomnolence phenotypes and epigenetic modification of candidate hypersomnolence genes to advance this line of inquiry. METHODS: Twenty-eight unmedicated clinical patients with unexplained hypersomnolence were evaluated using overnight ad libitum polysomnography, multiple sleep latency testing, infrared pupillometry, and the psychomotor vigilance task. DNA methylation levels on CpG sites annotated to 11 a priori hypersomnolence candidate genes were assessed for statistical association with hypersomnolence measures using independent regression models with adjusted local index of significance (aLIS) P-value threshold of 0.05. RESULTS: Nine CpG sites exhibited significant associations between DNA methylation levels and total sleep time measured using ad libitum polysomnography (aLIS p-value < .05). All nine differentially methylated CpG sites were annotated to the paired box 8 (PAX8) gene and its related antisense gene (PAX8-AS1). Among these nine differentially methylated positions was a cluster of five CpG sites located in the body of the PAX8 gene and promoter of PAX8-AS1. CONCLUSIONS: This study demonstrates that PAX8/PAX8-AS1 DNA methylation levels are associated with total sleep time in persons with unexplained hypersomnolence. Given prior investigations that have implicated single nucleotide polymorphisms in PAX8/PAX8-AS1 with habitual sleep duration, further research that clarifies the role of DNA methylation levels on these genes in the phenotypic expression of total sleep time is warranted.


Asunto(s)
Metilación de ADN , Trastornos de Somnolencia Excesiva/genética , Factor de Transcripción PAX8/genética , ARN Largo no Codificante/genética , Humanos , Polisomnografía , Latencia del Sueño , Vigilia
14.
Sci Rep ; 11(1): 12181, 2021 06 09.
Artículo en Inglés | MEDLINE | ID: mdl-34108589

RESUMEN

Maternal and environmental factors influence brain networks and architecture via both physiological pathways and epigenetic modifications. In particular, prenatal maternal depression and anxiety symptoms appear to impact infant white matter (WM) microstructure, leading us to investigate whether epigenetic modifications (i.e., DNA methylation) contribute to these WM differences. To determine if infants of women with depression and anxiety symptoms exhibit epigenetic modifications linked to neurodevelopmental changes, 52 umbilical cord bloods (CBs) were profiled. We observed 219 differentially methylated genomic positions (DMPs; FDR p < 0.05) in CB that were associated with magnetic resonance imaging measures of WM microstructure at 1 month of age and in regions previously described to be related to maternal depression and anxiety symptoms. Genomic characterization of these associated DMPs revealed 143 unique genes with significant relationships to processes involved in neurodevelopment, GTPase activity, or the canonical Wnt signaling pathway. Separate regression models for female (n = 24) and male (n = 28) infants found 142 associated DMPs in females and 116 associated DMPs in males (nominal p value < 0.001, R > 0.5), which were annotated to 98 and 81 genes, respectively. Together, these findings suggest that umbilical CB DNA methylation levels at birth are associated with 1-month WM microstructure.


Asunto(s)
Trastornos de Ansiedad/fisiopatología , Encéfalo/patología , Metilación de ADN , Trastorno Depresivo/fisiopatología , Sangre Fetal/química , Efectos Tardíos de la Exposición Prenatal/patología , Sustancia Blanca/patología , Adolescente , Adulto , Encéfalo/metabolismo , Epigénesis Genética , Femenino , Humanos , Recién Nacido , Masculino , Embarazo , Efectos Tardíos de la Exposición Prenatal/etiología , Efectos Tardíos de la Exposición Prenatal/metabolismo , Sustancia Blanca/metabolismo , Adulto Joven
15.
Clin Epigenetics ; 13(1): 118, 2021 05 25.
Artículo en Inglés | MEDLINE | ID: mdl-34034806

RESUMEN

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.


Asunto(s)
COVID-19/sangre , COVID-19/mortalidad , Metilación de ADN/fisiología , Anciano , Anciano de 80 o más Años , Femenino , Humanos , Masculino , Persona de Mediana Edad , New York/epidemiología , Estudios Prospectivos , SARS-CoV-2
16.
Epigenetics ; 16(1): 64-78, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-32633672

RESUMEN

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.


Asunto(s)
Axones/metabolismo , Metilación de ADN , Regeneración Nerviosa/genética , 5-Metilcitosina/análogos & derivados , 5-Metilcitosina/metabolismo , Animales , Epigénesis Genética , Femenino , Masculino , Ratas , Ratas Sprague-Dawley , Transcriptoma
17.
Epigenetics ; 16(10): 1085-1101, 2021 10.
Artículo en Inglés | MEDLINE | ID: mdl-33172347

RESUMEN

Maternal malnutrition remains one of the major adversities affecting brain development and long-term mental health outcomes, increasing the risk to develop anxiety and depressive disorders. We have previously shown that malnutrition-induced anxiety-like behaviours can be rescued by a social and sensory stimulation (enriched environment) in male mice. Here, we expand these findings to adult female mice and profiled genome-wide ventral hippocampal 5hmC levels related to malnutrition-induced anxiety-like behaviours and their rescue by an enriched environment. This approach revealed 508 differentially hydroxymethylated genes associated with protein malnutrition and that several genes (N = 34) exhibited a restored 5hmC abundance to control levels following exposure to an enriched environment, including genes involved in neuronal functions like dendrite outgrowth, axon guidance, and maintenance of neuronal circuits (e.g. Fltr3, Itsn1, Lman1, Lsamp, Nav, and Ror1) and epigenetic mechanisms (e.g. Hdac9 and Dicer1). Sequence motif predictions indicated that 5hmC may be modulating the binding of transcription factors for several of these transcripts, suggesting a regulatory role for 5hmC in response to perinatal malnutrition and exposure to an enriched environment. Together, these findings establish a role for 5hmC in early-life malnutrition and reveal genes linked to malnutrition-induced anxious behaviours that are mitigated by an enriched environment.


Asunto(s)
Metilación de ADN , Desnutrición , 5-Metilcitosina/análogos & derivados , Animales , Epigénesis Genética , Femenino , Masculino , Ratones
19.
Mol Neurobiol ; 57(4): 2048-2071, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-31919777

RESUMEN

Folate supplementation in F0 mating rodents increases regeneration of injured spinal axons in vivo in 4 or more generations of progeny (F1-F4) in the absence of interval folate administration to the progeny. Transmission of the enhanced regeneration phenotype to untreated progeny parallels axonal growth in neuron culture after in vivo folate administration to the F0 ancestors alone, in correlation with differential patterns of genomic DNA methylation and RNA transcription in treated lineages. Enhanced axonal regeneration phenotypes are observed with diverse folate preparations and routes of administration, in outbred and inbred rodent strains, and in two rodent genera comprising rats and mice, and are reversed in F4-F5 progeny by pretreatment with DNA demethylating agents prior to phenotyping. Uniform transmission of the enhanced regeneration phenotype to progeny together with differential patterns of DNA methylation and RNA expression is consistent with a non-Mendelian mechanism. The capacity of an essential nutritional co-factor to induce a beneficial transgenerational phenotype in untreated offspring carries broad implications for the diagnosis, prevention, and treatment of inborn and acquired disorders.


Asunto(s)
Ácido Fólico/farmacología , Regeneración Nerviosa/efectos de los fármacos , Neuronas/fisiología , Administración Oral , Animales , Axones/efectos de los fármacos , Axones/patología , Azacitidina/farmacología , Metilación de ADN/genética , Femenino , Ácido Fólico/administración & dosificación , Genoma , Inhibidores de Histona Desacetilasas/farmacología , Ácidos Hidroxámicos/farmacología , Inyecciones Intraperitoneales , Masculino , Neuronas/efectos de los fármacos , Fenotipo , Ratas Sprague-Dawley , Transcripción Genética/efectos de los fármacos
20.
Curr Protoc Hum Genet ; 101(1): e81, 2019 04.
Artículo en Inglés | MEDLINE | ID: mdl-30620135

RESUMEN

Mapping patterns of DNA methylation throughout the epigenome are critical to our understanding of several important biological and regulatory functions, such as transcriptional regulation, genomic imprinting, and embryonic development. The development and rapid advancement of next-generation sequencing (NGS) technologies have provided clinicians and researchers with accurate and reliable read-outs of genomic and epigenomic information at the nucleotide level. Such improvements have significantly lowered the cost required for genome-wide sequencing, facilitating the vast acquisition of data that has led to many improvements in patient care. However, the torrid rate of NGS data generation has left targeted validation approaches behind, including the confirmation of epigenetic marks such as DNA methylation. To overcome these shortcomings, we present a rapid and robust protocol for the parallel examination of multiple methylated sequences that we have termed simultaneous targeted methylation sequencing (sTM-Seq). Key features of this technique include the elimination of the need for large amounts of high-molecular weight DNA and the nucleotide specific distinction of both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Moreover, sTM-Seq is scalable and can be used to investigate multiple loci in dozens of samples within a single sequencing run. By utilizing freely available web-based software and universal primers for multipurpose barcoding, library preparation, and customized sequencing, sTM-Seq is affordable, efficient, and widely applicable. Together, these features enable sTM-Seq to have wide-reaching clinical applications that will greatly improve turnaround rates for same-day procedures and allow clinicians to collect high-resolution data that can be used in a variety of patient settings. © 2019 by John Wiley & Sons, Inc.


Asunto(s)
Metilación de ADN/genética , Genoma/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Análisis de Secuencia de ADN/métodos , 5-Metilcitosina/análogos & derivados , 5-Metilcitosina/química , 5-Metilcitosina/metabolismo , ADN/genética , Cartilla de ADN/química , Cartilla de ADN/genética , Epigénesis Genética , Genómica/tendencias , Humanos , Programas Informáticos
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