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Series GSE43617 Query DataSets for GSE43617
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
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.
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.
Contributor(s) Colquitt BM, Lomvardas S
Citation(s) 23969834
Submission date Jan 18, 2013
Last update date May 15, 2019
Contact name Michael Brainard
Organization name University of California, San Francisco
Street address 675 Nelson Rising Ln
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (3)
GSM1067215 Tet3-tg 5hmC
GSM1067216 mOSN ribominus RNA
GSM1067217 O/Tet3 ribominus RNA
BioProject PRJNA186825
SRA SRP018035

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

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
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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