Genomics

Dataset Information

240

H3K4me3 modification analysis comparing Lsh WT and Lsh-/- MEFs


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. Chromatin immunoprecipitation followed by genomic sequencing was used to compare H3K4me3 modifications between wild type murine embryonal fibroblast cell lines (MEFs) and Lsh-/-MEFs.

ORGANISM(S): Mus musculus  

SUBMITTER: Kathrin Muegge   Robert M Leighty  Eunice Y Lee  Keji Zhao  Jigui Shan  Anney Che  Theresa Geiman  Jiaqiang Huang  Alika Maunakea  Robert Stephens  Victorino Briones 

PROVIDER: E-GEOD-29393 | ArrayExpress | 2011-05-19

SECONDARY ACCESSION(S): SRP006814GSE29393PRJNA142995

REPOSITORIES: GEO, ArrayExpress, ENA

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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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