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E-GEOD-29392 - Gene expression array assay of Lsh WT and Knockout MEF cells

Status
Released on 19 May 2011, last updated on 27 March 2012
Organism
Mus musculus
Samples (2)
Array (1)
Protocols (8)
Description
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. We used microarrays to detail a correlation between cytosine methylation of murine genome modulated by Lsh at non-repetitive sequence and corresponding gene expression.
Experiment type
transcription profiling by array 
Contacts
Jigui Shan <shanj@mail.nih.gov>, Alika Maunakea, Anney Che, Eunice Y Lee, Jiaqiang Huang, Kathrin Muegge, Keji Zhao, Robert M Leighty, Robert Stephens, Theresa Geiman, Victorino Briones
Citation
Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences. Tao Y, Xi S, Shan J, Maunakea A, Che A, Briones V, Lee EY, Geiman T, Huang J, Stephens R, Leighty RM, Zhao K, Muegge K. , PMID:21427231
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-29392.idf.txt
Sample and data relationshipE-GEOD-29392.sdrf.txt
Raw data (1)E-GEOD-29392.raw.1.zip
Processed data (1)E-GEOD-29392.processed.1.zip
Array designA-GEOD-13621.adf.txt
R ExpressionSetE-GEOD-29392.eSet.r
Links