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Series GSE43429 Query DataSets for GSE43429
Status Public on Jan 24, 2013
Title Extensive changes in DNA methylation are associated with expression of mutant huntingtin [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
Overall design ChIP-seq for FRA-2, JUND, and SOX2 in STHdhQ7/Q7 and STHdhQ111/Q111 cells
Contributor(s) Ng CW, Fraenkel E
Citation(s) 23341638
Submission date Jan 10, 2013
Last update date May 15, 2019
Contact name Christopher Ng
Organization name Massachusetts Institute of Technology
Street address 77 Massachusetts Ave.
City Cambridge
State/province Massachusetts
ZIP/Postal code 02139
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (7)
GSM1062362 ChIP_STHdhQ7_FRA2_reps1and2
GSM1062363 ChIP_STHdhQ111_FRA2_reps1and2
GSM1062364 ChIP_STHdhQ7_JUND_reps1and2
This SubSeries is part of SuperSeries:
GSE43433 Extensive changes in DNA methylation are associated with expression of mutant huntingtin
BioProject PRJNA186415
SRA SRP017911

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Supplementary file Size Download File type/resource
GSE43429_ChIP_STHdhQ7_SOX2_GPS_significant.txt.gz 338.0 Kb (ftp)(http) TXT
GSE43429_ChIP_STHdhQ7_STHdhQ111_FRA2_GPS_significant.txt.gz 2.2 Mb (ftp)(http) TXT
GSE43429_ChIP_STHdhQ7_STHdhQ111_JUND_GPS_significant.txt.gz 1.5 Mb (ftp)(http) TXT
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