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| Status |
Public on Aug 24, 2012 |
| Title |
5-hmC in the brain: abundance in synaptic genes and differences at the exon-intron boundary (MRE-Seq) |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
5-hydroxymethylcytosine (5-hmC), a derivative of 5-methylcytosine (5-mC), is abundant in the brain for unknown reasons. We mapped the genomic distribution of 5-hmC and 5-mC in human and mouse tissues using glucosylation of 5-hmC coupled with restriction enzyme digestion, and interrogation on microarrays. We detected 5-hmC enrichment in genes with synapse-related functions in the brain.
We also identified significant, tissue-specific differential distributions of these DNA modifications at the exon-intron boundary, in both human and mouse. This boundary change was mainly due to 5-hmC in the brain, but due to 5-mC in non-neural contexts. This pattern was replicated in multiple independent datasets, and the brain-specific change in 5-hmC was validated using single-molecule sequencing. Moreover, in the brain, constitutive exons contained higher levels of 5-hmC, relative to alternatively-spliced exons. Our study suggests a novel role for 5-hmC in RNA splicing and synaptic function in the brain
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| Overall design |
The β-glucosyltransferase (BGT) enzyme transfers a glucose molecule specifically to the hydroxymethyl group of 5-hmC, thus rendering it resistant to digestion by the methylation insensitive MspI enzyme at the ChmCGG target site; 5-hmC is thus detected by differential resistance to MspI-digestion with and without glucosylation of genomic DNA (gDNA). HpaII (targets the same site, CCGG) cannot cut CmCGG or ChmCGG, and conceptually its difference with MspI digestion is a measure of both 5-mC and 5-hmC. Subtraction of 5-hmC from the HpaII-based estimate therefore measures 5-mC. These estimates were measured on respective Affymetrix whole-genome tiling arrays (2.0 R )
MspI - APRIL_fc1.ch02_coverage.bed
Undigested DNA - APRIL_fc1.ch01_coverage.bed
GluMspI - APRIL_fc1.ch04_coverage_NONTARGET.bed
GluMspI - APRIL_fc1.ch04_coverage.bed
MspI - APRIL_fc1.ch02_coverage_NONTARGET.bed
Undigested DNA - APRIL_fc1.ch01_coverage_NONTARGET.bed
MspI - MARCH_fc1.ch02_coverage_NONTARGET.bed
Undigested DNA - MARCH_fc1.ch01_coverage_NONTARGET.bed
GluMspI - MARCH_fc1.ch04_coverage_NONTARGET.bed
GluMspI - MARCH_fc1.ch04_coverage.bed
MspI - MARCH_fc1.ch02_coverage.bed
Undigested DNA - MARCH_fc1.ch01_coverage.bed
MspI - MAY_fc1.ch02_coverage.bed
GluMspI - MAY_fc1.ch04_coverage_NONTARGET.bed
GluMspI - MAY_fc1.ch04_coverage.bed
Undigested DNA - MAY_fc1.ch01_coverage.bed
MspI - MAY_fc1.ch02_coverage_NONTARGET.bed
Undigested DNA - MAY_fc1.ch01_coverage_NONTARGET.bed
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| Contributor(s) |
Pai S, Khare T, Klimasauskas S, Petronis A |
| Citation(s) |
22961382 |
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| Submission date |
Aug 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Shraddha Pai |
| E-mail(s) |
shraddha.pai@utoronto.ca
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| Organization name |
University of Toronto
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| Street address |
160 College Street, Room 602
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| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5S 3E1 |
| Country |
Canada |
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| Platforms (1) |
| GPL14761 |
Helicos HeliScope (Homo sapiens) |
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| Samples (9)
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| GSM986482 |
Sample 71, GluMspI, Replicate 1 |
| GSM986483 |
Sample 71, Undigested DNA, Replicate 1 |
| GSM986484 |
Sample 71, MspI, Replicate 1 |
| GSM986485 |
Sample 71, MspI, Replicate 3 |
| GSM986486 |
Sample 71, GluMspI, Replicate 3 |
| GSM986487 |
Sample 71, Undigested DNA, Replicate 3 |
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| This SubSeries is part of SuperSeries: |
| GSE40167 |
5-hmC in the brain: abundance in synaptic genes and differences at the exon-intron boundary |
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| Relations |
| SRA |
SRP014879 |
| BioProject |
PRJNA173641 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40158_RAW.tar |
47.8 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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