Genomics

Dataset Information

45

Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences


ABSTRACT: 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

INSTRUMENT(S): Illumina Genome Analyzer IIx (Mus musculus)

SUBMITTER: Jigui Shan  

PROVIDER: GSE29395 | GEO | 2011-05-20

SECONDARY ACCESSION(S): GSE29393PRJNA140163 GSE29392 GSE29394

REPOSITORIES: GEO

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Publications

Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences.

Tao Yongguang Y   Xi Sichuan S   Shan Jigui J   Maunakea Alika A   Che Anney A   Briones Victorino V   Lee Eunice Y EY   Geiman Theresa T   Huang Jiaqiang J   Stephens Robert R   Leighty Robert M RM   Zhao Keji K   Muegge Kathrin K  

Proceedings of the National Academy of Sciences of the United States of America 20110322 14


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. W  ...[more]

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