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E-GEOD-38604 - The developmental patterning of 5-hydroxymethylcytosine during neuronal differentiation

Status
Released on 3 September 2013, last updated on 3 May 2014
Organism
Mus musculus
Samples (9)
Protocols (4)
Description
Recent analyses of 5-hydroxymethylcytosine (5hmC) suggest that the modified base influences transcription by acting as an intermediate to demethylation. However, elevated levels of 5hmC within neural tissues suggest that the mark is stable and may directly contribute to gene regulation. Here, we characterize the in vivo genomic patterning and stability of 5hmC in three defined developmental states of the mouse main olfactory epithelium – multipotent stem cells, neuronal progenitors, and mature olfactory sensory neurons. 5hmC is globally enriched in neuronal progenitors and neurons relative to the stem population with significant enrichment on the bodies of transcriptionally active genes and intergenic enhancers. Although gene body 5hmC levels are positively correlated with cell type-specific gene expression in all developmental stages, genes that are commonly expressed within both neuronal progenitors and mature neurons experience the greatest increases in 5hmC levels. Moreover, enriched levels of the modified base on intergenic conserved regions correlate with cell type-specific expression of nearby genes and coincide with developmentally regulated enhancer-promoter interaction at one locus examined. Finally, an analysis of two-month old neurons indicates that elevated 5hmC levels persist in fully differentiated neurons. Together, these data suggest that 5hmC stabilizes the expression of developmentally active genes through effects at both gene bodies and intergenic regulatory elements. 9 Samples
Experiment types
methylation profiling by high throughput sequencing, RNA-seq of coding RNA 
Contacts
Bradley Colquitt <bradley.colquitt@ucsf.edu>, Bradley M Colquitt, Stavros Lomvardas
Citation
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-38604.idf.txt
Sample and data relationshipE-GEOD-38604.sdrf.txt
Processed data (2)E-GEOD-38604.processed.1.zip, E-GEOD-38604.processed.2.zip
Links