Comment[ArrayExpressAccession] E-GEOD-43430 MAGE-TAB Version 1.1 Public Release Date 2013-01-24 Investigation Title Extensive changes in DNA methylation are associated with expression of mutant huntingtin [MeDIP-seq] Comment[Submitted Name] Extensive changes in DNA methylation are associated with expression of mutant huntingtin [MeDIP-seq] Experiment Description The earliest stages of Huntington’s disease are marked by changes in gene expression that are caused in an indirect and poorly understood manner by polyglutamine expansions in the huntingtin protein (HTT). To explore the hypothesis DNA methylation may be altered in cells expressing mutated HTT, we use reduced-representation bisulfite sequencing (RRBS) to map sites of DNA methylation in cells carrying either wild-type or mutant HTT. We find that a large fraction of the genes that change in expression in the presence of mutant huntingtin demonstrate significant changes in DNA methylation. Regions with low CpG content, which have previously been shown to undergo methylation changes in response to neuronal activity, are disproportionately affected. Based on the sequence of regions that change in methylation, we identify AP-1 and SOX2 as transcriptional regulators associated with DNA methylation changes, and we confirm these hypotheses using genome-wide chromatin immunoprecipitation (ChIP-Seq). Our findings suggest new mechanisms for the effects of polyglutamine-expanded HTT. These results also raise important questions about the potential effects of changes in DNA methylation on neurogenesis and at later stages, cognitive decline in Huntington’s patients. MeDIP-seq in STHdhQ7/Q7 and STHdhQ111/Q111 cells Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Ng Ng Fraenkel Person First Name Christopher Christopher Ernest Person Mid Initials W Person Email geo@ncbi.nlm.nih.gov Person Affiliation Massachusetts Institute of Technology Person Address Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts, USA Person Roles submitter Protocol Name P-GSE43430-3 P-GSE43430-2 P-GSE43430-1 Protocol Description MeDIP-Seq reads were aligned to the reference mouse genome (mm9) using Bowtie (v0.12.7). MACS (v1.4) was used to shift positive and negative strand reads and generate*.wig format files. Genome_build: MGSCv37 5ug of genomic DNA was sheared using Covaris S2 and standard Illumina libraries were constructed. 500ng of DNA library was then immunoprecipitated and enriched for DNA fragments containing 5-methylcytosine using the MeDIP kit according to the manufacturer’s recommended protocol (Active Motif cat. 55009). 18 cycles of PCR were then carried out and libraries were size selected using a 2% TBE agarose gel from 200-300bp. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). STHdhQ7 and STHdhQ111 cell lines were cultured according as described previously (Trettel et al, Hum Mol Genet, 2000). In order to stop cell division and mitigate cell cycle differences, the culture is maintained at 33oC and raised to 39oC for two days prior to each experiment. Protocol Type normalization data transformation protocol nucleic acid library construction protocol growth protocol Experimental Factor Name GENOTYPE Experimental Factor Type genotype Publication Title Extensive changes in DNA methylation are associated with expression of mutant huntingtin. Publication Author List Ng CW, Yildirim F, Yap YS, Dalin S, Matthews BJ, Velez PJ, Labadorf A, Housman DE, Fraenkel E PubMed ID 23341638 Publication DOI 10.1073/pnas.1221292110 Comment[SecondaryAccession] GSE43430 Comment[GEOReleaseDate] 2013-01-24 Comment[ArrayExpressSubmissionDate] 2013-01-10 Comment[GEOLastUpdateDate] 2013-07-23 Comment[AEExperimentType] methylation profiling by high throughput sequencing Comment[SecondaryAccession] SRP017912 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR647726-SRR647729 SDRF File E-GEOD-43430.sdrf.txt