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Series GSE29393 Query DataSets for GSE29393
Status Public on May 19, 2011
Title H3K4me3 modification analysis comparing Lsh WT and Lsh-/- MEFs
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary DNA methylation is critical for normal development and plays important roles in genome organization and transcriptional regulation. Although DNA methyltransferases have been identified, the factors that establish and contribute to genome-wide methylation patterns remain elusive. Here, we report a high-resolution cytosine methylation map of the murine genome modulated by Lsh, a chromatin remodeling family member that has previously been shown to regulate CpG methylation at repetitive sequences. We provide evidence that Lsh also controls genome-wide cytosine methylation at nonrepeat sequences and relate those changes to alterations in H4K4me3 modification and gene expression. Deletion of Lsh alters the allocation of cytosine methylation in chromosomal regions of 50 kb to 2 Mb and, in addition, leads to changes in the methylation profile at the 5′ end of genes. Furthermore, we demonstrate that loss of Lsh promotes—as well as prevents—cytosine methylation. Our data indicate that Lsh is an epigenetic modulator that is critical for normal distribution of cytosine methylation throughout the murine genome.
Overall design Chromatin immunoprecipitation followed by genomic sequencing was used to compare H3K4me3 modifications between wild type murine embryonal fibroblast cell lines (MEFs) and Lsh-/-MEFs.
Contributor(s) Maunakea A, Che A, Briones V, Lee EY, Geiman T, Huang J, Stephens R, Leighty RM, Zhao K, Muegge K
Citation(s) 21427231
Submission date May 19, 2011
Last update date May 15, 2019
Contact name Jigui Shan
Organization name NCI-Frederick
Street address 430 Miller Dr
City Frederick
ZIP/Postal code 21702
Country USA
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (2)
GSM726806 Lsh+/+ H3K4me3
GSM726807 Lsh-/- H3K4me3
This SubSeries is part of SuperSeries:
GSE29395 Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences
SRA SRP006814
BioProject PRJNA142995

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Supplementary file Size Download File type/resource
GSE29393_RAW.tar 233.8 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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