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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 11, 2014 |
| Title |
Environmental enrichment modulates 5-hydroxymethylcytosine dynamics in hippocampus |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Gene-environment interactions mediated at the epigenetic level may provide an initial step in delivering an appropriate response to environmental changes. 5-hydroxymethylcytosine (5hmC), a DNA base derived from 5-methylcytosine (5mC), accounts for ~40% of modified cytosine in brain and has been implicated in DNA methylation-related plasticity. To identify the role of 5hmC in gene-environment interactions, we exposed both young (6-week-old) and aged (18-month-old) mice to both an enriched environment and a standard environment. Exposure to EE significantly improves learning and memory in aged mice and reduces 5hmC abundance in mouse hippocampus. Furthermore, we mapped the genome-wide distribution of 5hmC and found that the alteration of 5hmC modification occurred mainly at gene bodies. In particular, genes involved in axon guidance are enriched among the genes with altered 5hmC modification. These results together suggest that environmental enrichment could modulate the dynamics of 5hmC in hippocampus, which could potentially contribute to improved learning and memory in aged animals.
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| Overall design |
To identify the role of 5hmC in gene-environment interactions, we exposed both young (6-week-old) and aged (18-month-old) C57B/6 mice to both an enriched environment (EE) and a standard environment. Exposure of mice to EE was achieved by keeping a group of mice in the EE chamber, which is larger than the standard cage, includes novel objects, such as toys of varied color and texture, tunnels, an exercise wheel for voluntary exercise, and extra bedding material, along with free access to food and water. Daily exposure to EE was kept at 5 hours during the daylight cycle for 4 consecutive weeks. Control animals were kept in their small cages that are used as standard housing cages (CE) containing bedding, food and access to water. YC, young mice exposing to control environment, YE, young mice exposing to enriched environment, AC, aged mice exposing to control environment, AE, aged mice exposed to enriched environment.
Please note that 5hmC-containing DNA enrichment method was inspired by a unique character of beta-glucotransferase that can specifically add glucose to 5hmC modification. With a modified glucose conjugated with biotin, we are able to purify the 5hmC-containing DNA by biotin-streptavidin-based immunoprecipitation.
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| Contributor(s) |
Jin P |
| Citation(s) |
25205305 |
| Submission date |
Sep 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Bing Yao |
| E-mail(s) |
bing.yao@emory.edu
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| Phone |
4047271725
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| Organization name |
Emory University
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| Department |
Human Genetics
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| Lab |
Bing Yao Lab
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| Street address |
615 Michael St. Rm 323
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platforms (1) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
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| Samples (8)
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| GSM1501646 |
Aged (Controlled Environment) Replicate 1 |
| GSM1501647 |
Aged (Controlled Environment) Replicate 2 |
| GSM1501648 |
Aged (Enriched Environment) Replicate 1 |
| GSM1501649 |
Aged (Enriched Environment) Replicate 2 |
| GSM1501650 |
Young (Controlled Environment) Replicate 1 |
| GSM1501651 |
Young (Controlled Environment) Replicate 2 |
| GSM1501652 |
Young (Enriched Environment) Replicate 1 |
| GSM1501653 |
Young (Enriched Environment) Replicate 2 |
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| Relations |
| BioProject |
PRJNA260671 |
| SRA |
SRP046767 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE61194_RAW.tar |
5.3 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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