Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

DNA methylation in B cells

ABSTRACT: Using a methylated-DNA enrichment technique (MIRA) in combination with whole genome tiling arrays, we have characterized by MIRA-chip the entire B cell ‘methylome’ of an individual human at 100 base pair resolution. Methylated fragments in genomic DNA extracted from B cells were enriched with the MIRA assay and hybridized together with input genomic DNA to NimbleGen's whole genomc tiling array.

ORGANISM(S): Homo sapiens

SUBMITTER: Xiwei Wu

PROVIDER: E-GEOD-13700 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A human B cell methylome at 100-base pair resolution.

Rauch Tibor A TA Wu Xiwei X Zhong Xueyan X Riggs Arthur D AD Pfeifer Gerd P GP

Proceedings of the National Academy of Sciences of the United States of America 20090112 3

Using a methylated-DNA enrichment technique (methylated CpG island recovery assay, MIRA) in combination with whole-genome tiling arrays, we have characterized by MIRA-chip the entire B cell "methylome" of an individual human at 100-bp resolution. We find that at the chromosome level high CpG methylation density is correlated with subtelomeric regions and Giemsa-light bands (R bands). The majority of the most highly methylated regions that could be identified on the tiling arrays were associated ...[more]

PMID: 19139413

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Project description:MicroRNAs (miRNAs) are a class of small non-coding RNAs that function as post-transcriptional regulators of gene expression. Many miRNAs are expressed in the developing brain and regulate multiple aspects of neural development including neurogenesis, dendritogenesis and synapse formation. Rett syndrome (RTT) is a progressive neurodevelopmental disorder caused by mutations in the gene encoding Methyl-CpG binding protein 2 (MECP2). While Mecp2 is known to act as a global transcriptional regulator, miRNAs that are directly regulated by Mecp2 in the brain are not known. Using massively parallel sequencing methods, we have identified miRNAs whose expression is altered in cerebella of Mecp2-null mice before and after the onset of severe neurological symptoms. In vivo genome-wide analyses indicate that promoter regions of a significant fraction of dys-regulated miRNA transcripts, including a large polycistronic cluster of brain-specific miRNAs, are DNA methylated and directly bound by Mecp2. Functional analysis demonstrates that the 3’ untranslated region (UTR) of messenger RNA encoding Brain-derived neurotrophic factor (Bdnf) can be targeted by multiple miRNAs aberrantly up-regulated in absence of Mecp2. Taken together, these results suggest that dys-regulation of miRNAs may contribute to RTT pathoetiology, and also provide a valuable resource to further investigate the role of miRNAs in RTT. Chromatin extracted from postnatal 6-8 week old cerebellar (CB) tissues of wild-type (WT) or Mecp2-null (KO) male mice was immunoprecipitated with indicated antibodies and analyzed by a NimbleGen mouse 385K genomic tiling microarray (the array set26 of a 37-array set, which covers the mouse chromosome 12 that includes the entire Dlk1-Gtl2 imprinting domain). Whole cell extract (WCE) was used as input controls for ChIP or MeDIP/WCE experiments. For ChIP/ChIP experiments, immunoprecipitated DNA from WT and KO CB was directly compared on the same microarrays. DNA methylation profiles in WT CB were also analyzed by methylated DNA immunoprecipitation (MeDIP) followed by hybridization to the same genomic tiling microarrays (MeDIP-chip).

Dataset Information

DNA methylation in B cells

Publications

A human B cell methylome at 100-base pair resolution.

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