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Series GSE9568 Query DataSets for GSE9568
Status Public on Dec 05, 2007
Title Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary Mutations in MECP2 cause the autism-spectrum disorder Rett syndrome. MeCP2 is predicted to bind to methylated promoters and silence transcription. However, the first large-scale mapping of neuronal MeCP2-binding sites on 26.3 Mb of imprinted and nonimprinted loci revealed that 59% of MeCP2-binding sites are outside of genes and that only 6% are in CpG islands. Integrated genome-wide promoter analysis of MeCP2 binding, CpG methylation, and gene expression revealed that 63% of MeCP2-bound promoters are actively expressed and that only 6% are highly methylated. These results indicate that the primary function of MeCP2 is not the silencing of methylated promoters.
Keywords: ChIP-chip analysis
 
Overall design Experiments were performed using SH-SY5Y cells differentiated into a neuronal phenotype by 48 hour treatment with PMA. For custom genomic ChIP-chip analysis, chromatin from 3 biologic replicate cultures of SH-SY5Y neurons was crosslinked with formaldehyde, sonicated then immunoprecipitated with antibodies to MeCP2 and Pol2. Ligation mediated PCR amplified chromatin fragments were labeled then hybridized to a custom human genomic tiling array designed by Nimblegen along with differentially labeled total genomic DNA.
To examine the relationship of MeCP2 promoter binding to gene expression, MeCP2 ChIP amplicons from two biologic replicates of SH-SY5Y cells were hybridized to Nimblegen 1.5kb human promoter arrays along with total genomic DNA. MeCP2 promoter binding levels were then compared with identically treated SH-SY5Y RNA transcript levels as assayed by expression profiling analysis using Affymetrix human U133A Plus 2.0 microarrays performed from 3 biologic replicates.
To examine the relationship between MeCP2 binding and gene promoter methylation levels MeDIP analysis was performed again using SH-SY5Y cells differentiated with PMA. Genomic DNA was purified from SHSY-5Y cells, sonicated then immunoprecipitated with an anti-methylcytidine antibody. Selected fragments were then hybridized to Nimblegen 1.5kb human promoter arrays along with total genomic DNA. Methylcytidine levels of human promoters were then compared with MeCP2 binding levels determined in the analysis of MeCP2 promoter binding and gene expression levels.
 
Contributor(s) Yasui DH, Peddada S, Bieda MC, Vallero RO, Hogart A, Nagarajan RP, Thatcher KN, Farnham PJ, LaSalle JM
Citation(s) 18042715
Submission date Nov 08, 2007
Last update date Jan 18, 2013
Contact name Dag Yasui
E-mail(s) dhyasui@ucdavis.edu
Phone 530-754-7906
Organization name University of California at Davis
Department Medical Microbiology and Immunology
Lab Tupper Hall Room 3424
Street address 1 Shields Avenue
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platforms (3)
GPL4599 NimbleGen_1500b_Promoter_Array
GPL5962 LaSalle/UCDavis-Human custom tiling 26.3mb
GPL6183 NimbleGen 1500b Promoter Array
Samples (12)
GSM245264 MeCP2 ChIP-chip A
GSM245265 Pol2 ChIP-chip A
GSM245266 MeCP2 ChIP-chip B
Relations
BioProject PRJNA103391

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
GSE9568_RAW.tar 195.2 Mb (http)(custom) TAR (of PAIR, TXT)
Raw data provided as supplementary file
Processed data included within Sample table

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