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| Status |
Public on Sep 03, 2013 |
| Title |
Gene body 5-hydroxymethylcytosine facilitates transcription in olfactory neurons |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
The modified DNA base 5-hydroxymethylcytosine (5hmC) is enriched in neurons where it may contribute to gene function and cellular identity. To address this issue in an in vivo neuronal population, we assessed the patterning, stability, and function of the base within gene bodies in olfactory sensory neurons. We find that gene body 5hmC linearly correlates with transcriptional output and is stable in fully mature neurons and those lacking de novo methyltransferase activity. Overexpression of Tet3, which oxidizes methylated cytosines (5mC) to 5hmC, markedly alters gene body 5hmC levels and provides evidence that 5hmC facilitates transcription. This manipulation disrupts olfactory receptor expression and the targeting of axons to the olfactory bulb, key molecular and anatomical features of the olfactory system that are necessary for proper physiology. Our results support a direct, positive and physiologically significant role for gene body 5hmC in transcriptional elongation and the maintenance of cellular identity independent of its function as an intermediate to demethylation.
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| Overall design |
We assessed the role of 5hmC in mature olfactory sensory neurons by assessing 5hmC levels in 2 month old neurons, olfactory epithelia lacking Dnmt3a, and mOSNs overexpressing Tet3. To determine genome-wide levels of 5hmC, we performed DNA immunoprecipitation coupled to Illumina sequencing. To determine transcript levels, we prepared and sequenced rRNA-depleted cDNA libraries.
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| Contributor(s) |
Colquitt BM, Lomvardas S |
| Citation(s) |
23969834 |
| Submission date |
Jan 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Brainard |
| E-mail(s) |
msb@phy.ucsf.edu
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| Organization name |
University of California, San Francisco
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| Street address |
675 Nelson Rising Ln
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA186825 |
| SRA |
SRP018035 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE43617_RAW.tar |
56.7 Mb |
(http)(custom) |
TAR (of WIG) |
| GSE43617_omp_ott3_rmrna_1log2.txt.gz |
624.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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