GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE25930 Query DataSets for GSE25930
Status Public on Jun 23, 2011
Title Large-scale methylation domains mark a functional subset of neuronally expressed genes
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary DNA methylation is essential for embryonic and neuronal differentiation, but the function of most genomic DNA methylation marks are poorly understood. Generally the human genome is highly methylated (>70%) except for CpG islands and gene promoters. However, it was recently shown that the IMR90 human fetal lung fibroblast cells have large regions of the genome with partially methylated domains (PMDs, <70% average methylation), in contrast to the rest of the genome which is in highly methylated domains (HMDs, >70% average methylation). Using bisulfite conversion followed by high-throughput sequencing (MethylC-seq), we discovered that human SH-SY5Y neuronal cells also contain PMDs. We developed a novel hidden Markov model (HMM) to computationally map the genomic locations of PMDs in both cell types and found that autosomal PMDs can be over 9 Mb in length and cover 41% of the IMR90 genome and 19% of the SH-SY5Y genome. Genomic regions marked by cell line specific PMDs contain genes that are expressed in a tissue-specific manner, with PMDs being a mark of repressed transcription. Genes contained within N-HMDs (neuronal HMDs, defined as a PMD in IMR90 but HMD in SH-SY5Y) were significantly enriched for calcium signaling, synaptic transmission and neuron differentiation functions. Autism candidate genes were enriched within PMDs and the largest PMD observed in SH-SY5Y cells marked a 10 Mb cluster of cadherin genes with strong genetic association to autism. Our results suggest that these large-scale methylation domain maps could be relevant to interpreting and directing future investigations into the elusive etiology of autism.
Overall design Examined DNA methylation in a human neuronal cell line and cerebral cortex
Contributor(s) Schroeder DI, LaSalle JM
Citation(s) 21784875
Submission date Dec 08, 2010
Last update date May 15, 2019
Contact name Janine LaSalle
Organization name UC Davis
Street address Medical Microbiology and Immunology
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (2)
GSM636908 SH-SY5Y_MethylC-seq
GSM636909 cortex_MethylC-seq
SRA SRP004775
BioProject PRJNA135679

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE25930_RAW.tar 138.4 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap