Alcohol alters DNA methylation patterns and inhibits neural stem cell differentiation.
paper
Cited
Public
- Authors
- Zhou, Feng C; Balaraman, Yokesh; Teng, MingXiang; Liu, Yunlong; Singh, Rabindra P; Nephew, Kenneth P
- Year
- 2011
- Journal
- Alcoholism, clinical and experimental research
- PMID
- 21223309
- DOI
- 10.1111/j.1530-0277.2010.01391.x
- PMCID
- PMC3076804
BACKGROUND: Potential epigenetic mechanisms underlying fetal alcohol syndrome (FAS) include alcohol-induced alterations of methyl metabolism, resulting in aberrant patterns of DNA methylation and gene expression during development. Having previously demonstrated an essential role for epigenetics in neural stem cell (NSC) development and that inhibiting DNA methylation prevents NSC differentiation, here we investigated the effect of alcohol exposure on genome-wide DNA methylation patterns and NSC differentiation. METHODS: Neural stem cells in culture were treated with or without a 6-hour 88 mM ("binge-like") alcohol exposure and examined at 48 hours, for migration, growth, and genome-wide DNA methylation. The DNA methylation was examined using DNA-methylation immunoprecipitation followed by microarray analysis. Further validation was performed using Independent Sequenom analysis. RESULTS: Neural stem cell differentiated in 24 to 48 hours with migration, neuronal expression, and morphological transformation. Alcohol exposure retarded the migration, neuronal formation, and growth processes of NSC, similar to treatment with the methylation inhibitor 5-aza-cytidine. When NSC departed from the quiescent state, a genome-wide diversification of DNA methylation was observed-that is, many moderately methylated genes altered methylation levels and became hyper- and hypomethylated. Alcohol prevented many genes from such diversification, including genes related to neural development, neuronal receptors, and olfaction, while retarding differentiation. Validation of specific genes by Sequenom analysis demonstrated that alcohol exposure prevented methylation of specific genes associated with neural development [cut-like 2 (cutl2), insulin-like growth factor 1 (Igf1), epidermal growth factor-containing fibulin-like extracellular matrix protein 1 (Efemp1), and SRY-box-containing gene 7 (Sox 7)]; eye development, lens intrinsic membrane protein 2 (Lim 2); the epigenetic mark Smarca2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2); and developmental disorder [DiGeorge syndrome critical region gene 2 (Dgcr2)]. Specific sites altered by DNA methylation also correlated with transcription factor binding sites known to be critical for regulating neural development. CONCLUSION: The data indicate that alcohol prevents normal DNA methylation programming of key neural stem cell genes and retards NSC differentiation. Thus, the role of DNA methylation in FAS warrants further investigation.
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| Name | Type |
|---|---|
| 5-AZA local | drug |
| 5-aza-cytidine local | drug |
| 5-azacytidine local | drug |
| 5-MeC local | drug |
| 5-methylcytidine local | drug |
| 5-methyl-cytosine local | drug |
| 5-methylcytosine antibody local | drug |
| ADH4 | gene |
| Adra1a | gene |
| Adult DRG-NSCs local | cohort |
| alcohol | phenotype |
| Alcohol-differentiated local | cohort |
| Alcohol-treated NSCs local | cohort |
| alcohol-treated samples local | cohort |
| Alexa 635 | drug |
| Alexa Fluor 488 | drug |
| AQP8 local | gene |
| AQP9 local | gene |
| Ascl1 | gene |
| B27 supplement | drug |
| basic fibroblast growth factor | drug |
| bFGF | drug |
| brain development | phenotype |
| Branson sonifier local | drug |
| BRG1 | gene |
| cell proliferation | phenotype |
| Chrm1 | gene |
| Chromatin remodeling local | phenotype |
| CLCF1 local | gene |
| control | cohort |
| Control-differentiated local | cohort |
| Control NSCs local | cohort |
| controls | cohort |
| Control-undifferentiated local | cohort |
| core | anatomy |
| Cortical ventricular zone local | anatomy |
| Crabp1 local | gene |
| culture medium | drug |
| CUX2 | gene |
| Cy3 | drug |
| Cy5 | drug |
| DAPI | drug |
| Decreased migration local | phenotype |
| Differentiated + alcohol local | cohort |
| Differentiated cells with alcohol treatment local | cohort |
| Differentiated cells without treatment local | cohort |
| Differentiated DRG cells local | cohort |
| Differentiated neurospheres local | phenotype |
| Differentiated NSC local | phenotype |
| Differentiated NSCs local | phenotype |
| Differentiating ALC group local | cohort |
| Differentiating AZA group local | cohort |
| Differentiating Control group local | cohort |
| differentiation status local | phenotype |
| DLX3 local | gene |
| D-MEM/F-12 local | drug |
| DNA | drug |
| DNA methylation | drug |
| DNA methylation level local | phenotype |
| DNA methyltransferase | drug |
| DNeasy blood and tissue kit local | drug |
| DNMT1 | gene |
| DNMTs | gene |
| dorsal root ganglion | anatomy |
| dorsal root ganglion neural stem cells local | anatomy |
| DRG | anatomy |
| DRG stem cells local | cohort |
| E2F local | gene |
| early embryonic development | phenotype |
| EDG6 local | gene |
| EGF | drug |
| Embryonic DRG-NSCs local | cohort |
| endogenous peroxide local | drug |
| epidermal growth factor | drug |
| EpiTYPER local | drug |
| ER-ALPHA local | gene |
| ethanol consumption | phenotype |
| Fetal Alcohol Spectrum Disorder | phenotype |
| fetal bovine serum | drug |
| folate | drug |
| full sample | cohort |
| genomic DNA | drug |
| GRIA3 | gene |
| Grip1 local | gene |
| GRIP1 local | gene |
| growth retardation | phenotype |
| Histone deacetylase local | drug |
| HISTONE DEACETYLASE local | drug |
| Histone methyl transferase local | drug |
| HISTONE METHYL TRANSFERASE local | drug |
| hydrogen peroxide | drug |
| hyper methylation local | phenotype |
| hypomethylation local | phenotype |
| IGF2 | gene |
| Immunocytochemistry local | drug |
| Immunodeficiency centromeric instability and facial syndrome local | phenotype |
| Kcna1 | gene |
| laminin | drug |
| LIM2 local | gene |
| MALDI-TOF local | drug |
| MAP2 | gene |
| MassARRAY local | drug |
| MassCLEAVE | drug |
| MeDIP analysis local | drug |
| methionine | drug |
| Methionine adenosyltransferase local | gene |
| Methionine synthase local | gene |
| Methyl donors local | drug |
| Methylene tetrahydrofolate local | drug |
| migrated local | anatomy |
| migrated zone local | anatomy |
| migration | phenotype |
| Migration of differentiated NSCs local | phenotype |
| moderate methylation local | phenotype |
| N2 supplement | drug |
| Nanodrop spectrophotometer local | drug |
| neural patterning | phenotype |
| neural phenotype expression local | phenotype |
| Neural progenitor development local | phenotype |
| Neural stem cell local | phenotype |
| Neural stem cell differentiation local | phenotype |
| Neural stem cell growth local | phenotype |
| Neural stem cell patterning local | phenotype |
| Neural stem cell proliferation local | phenotype |
| neural stem cells | cohort |
| neural tube defect local | phenotype |
| Neural tube development | phenotype |
| neurobasal medium | drug |
| Neurodevelopmental deficit local | phenotype |
| neuronal differentiation | phenotype |
| Neuronal transmission local | phenotype |
| neurosphere | cohort |
| NimbleGen CpG island array local | drug |
| NimbleGen promoter plus CpG island tiling array local | drug |
| normal | phenotype |
| NSC neurospheres local | cohort |
| Oct4 | gene |
| olfaction | phenotype |
| olfactory bulb | anatomy |
| olfactory genes local | gene |
| Olr1139 local | gene |
| OLR1139 local | gene |
| Olr1646 local | gene |
| OLR1646 local | gene |
| Olr214 local | gene |
| OLR214 local | gene |
| Olr304 local | gene |
| OLR304 local | gene |
| Olr408 local | gene |
| OLR408 local | gene |
| Olr611 local | gene |
| OLR611 local | gene |
| P107 local | gene |
| penicillin-streptomycin | drug |
| Peripheral area local | anatomy |
| periphery local | anatomy |
| phenotype expression local | phenotype |
| phosphate-buffered saline | drug |
| PIK3R1 | gene |
| pluripotency | phenotype |
| poly-D-lysine | drug |
| Postmitotic neurons local | phenotype |
| POU4F2 local | gene |
| POU4F3 | gene |
| Prader-Willi/Angelman syndrome local | phenotype |
| process growth local | phenotype |
| Proteinase K local | drug |
| PTPRC | gene |
| Qiagen | drug |
| rat promoters and CpG islands local | gene |
| RefSeq gene | gene |
| retinoic acid | drug |
| Rett's syndrome local | phenotype |
| RN34 Promoter plus CpG island microarray local | drug |
| SAM | drug |
| sensory deficits | phenotype |
| Sequenom | drug |
| serine | drug |
| SH3BP2 local | gene |
| SMARCA2 | gene |
| sodium bisulfite | drug |
| SOX7 local | gene |
| Sp1 | gene |
| spinal cord | anatomy |
| stem-cell-ness local | phenotype |
| T2r140 local | gene |
| T2R140 local | gene |
| T2r18 local | gene |
| T2R18 local | gene |
| T7 promoter local | drug |
| Tas2r123 local | gene |
| TAS2R123 local | gene |
| Tas2r7 local | gene |
| TAS2R7 local | gene |
| taste sensitivity | phenotype |
| Thymidine local | drug |
| TNF | gene |
| Triton X-100 | drug |
| Undifferentiated cells without treatment local | cohort |
| Undifferentiated neurospheres local | phenotype |
| Undifferentiated NSC local | phenotype |
| vitamin B12 | drug |
| Wnt16 | gene |
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