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Series GSE29395 Query DataSets for GSE29395
Status Public on May 20, 2011
Title Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences
Organism Mus musculus
Experiment type Expression profiling by array
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by genome tiling array
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.

This SuperSeries is composed of the SubSeries listed below.
 
Overall design Refer to individual Series.
To investigate how genome-wide DNA methylation patterns are established in mice and how they may specifically depend on Lsh, we generated a comprehensive genomic map of cytosine methylation for wild-type (WT) and Lsh−/− mouse embryonic fibroblasts (MEFs) using methylated DNA immunoprecipitation (MeDIP) combined with whole-genome tiling microarray. In addition, we generated a histone 3 lysine 4 trimethylation (H3K4me3) chromatin map using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) and also evaluated genome-wide gene expression using cDNA microarrays
 
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
E-mail(s) shanj@mail.nih.gov
Organization name NCI-Frederick
Street address 430 Miller Dr
City Frederick
ZIP/Postal code 21702
Country USA
 
Platforms (40)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13567 NimbleGen Mouse 2006-07-17_MM8Tiling_Set01 [DESIGN_ID: 4072]
GPL13568 NimbleGen Mouse 2006-07-17_MM8Tiling_Set02 [DESIGN_ID: 4073]
Samples (80)
GSM726804 Lsh+/+ MEF
GSM726805 Lsh-/- MEF
GSM726806 Lsh+/+ H3K4me3
This SuperSeries is composed of the following SubSeries:
GSE29392 Gene expression array assay of Lsh WT and Knockout MEF cells
GSE29393 H3K4me3 modification analysis comparing Lsh WT and Lsh-/- MEFs
GSE29394 Comprehensive genomic map of cytosine methylation for wild-type (WT) and Lsh-/- mouse embryonic fibroblasts
Relations
BioProject PRJNA140163

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
GSE29395_RAW.tar 2.4 Gb (http)(custom) TAR (of CEL, GFF, PAIR, TXT)
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