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Cell type-specific regulation by intragenic CpG islands [WGBS]

ABSTRACT: We wanted to emphisize the role of intragenic CpG island in various cell differentiation. We especially examined the effect of DNA methyltransferase (DNMT) in the neural differentiation from mouse ES cell. Therefore, we performed the Whole-Genome Bisulfite Sequencing (WGBS) analysis of mouse ES cell, ESC-derived NPC, and also in DNMT double knockout (DKO) conditions. By utilizing these result, we confirmed the genes regulated by intragenic CpG island methylation have effect in NPC differentation.

ORGANISM(S): Mus musculus

PROVIDER: GSE82125 | GEO | 2017/12/30

REPOSITORIES: GEO

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Cell type-specific regulation by intragenic CpG islands [RNA-seq]

Project description:We wanted to emphisize the role of intragenic CpG island in various cell differentiation. We especially examined the effect of DNA methyltransferase (DNMT) in the neural differentiation from mouse ES cell. Therefore, we performed the transcriptome analysis of mouse ES cell, ESC-derived NPC, and also in DNMT double knockout (DKO) conditions. By utilizing these result, we confirmed the genes regulated by intragenic CpG island methylation have effect in NPC differentation.

2017-12-30 | GSE81925 | GEO

DNA methyation of intragenic CpG islands are required for differentiation from iPSC to NPC

Project description:We generated whole genome bisulfite sequencing (WGBS) data with high sequencing depth in induced pluripotent stem cell (iPSC), neuronal progentior cell (NPC) and Early Neuron (EN), and investigated the relationship between DNA methylation changes in CpG islands (CGIs) and corresponding gene expression during NPC differentiation

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Cell type-specific regulation by intragenic CpG islands

Project description:Cell type-specific regulation by intragenic CpG islands

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DNA methyation of intragenic CpG islands are required for differentiation from iPSC to NPC

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Cell Type-Specific DNA Methylation at Intragenic CpG Islands in the Immune System (gene expression data)

Project description:Human and mouse genomes contain a similar number of CpG islands (CGIs), which are discrete CpG-rich DNA sequences associated with transcription start sites. In both species, about 50% of all CGIs are remote from annotated promoters, but nevertheless often have promoter-like features. To document the role of CGI methylation in cell differentiation, we analysed DNA methylation at a comprehensive CGI set in cells of the mouse hematopoietic lineage. Using a method that potentially detects ~33% of genomic CpGs in the methylated state (>7 million) we found that large differences in gene expression were accompanied by surprisingly few DNA methylation changes. There were, however, many DNA methylation differences between hematopoietic cells and a distantly related tissue, brain. Altered DNA methylation occurred predominantly at CGIs within gene bodies, which have the properties of cell type-restricted promoters, but infrequently at annotated gene promoters or CGI flanking sequences. Elevated intragenic CGI methylation correlated with silencing of the associated gene. Differentially methylated intragenic CGIs tended to lack H3K4me3 and associate with a transcriptionally repressive environment regardless of methylation state. Our results indicate that DNA methylation changes play a relatively minor role in the late stages of differentiation, but point to a distinct role for intragenic CGIs.

2011-05-23 | GSE25578 | GEO

Cell Type-Specific DNA Methylation at Intragenic CpG Islands in the Immune System (gene expression data)

2011-05-23 | E-GEOD-25578 | biostudies-arrayexpress

Cell Type-Specific DNA Methylation at Intragenic CpG Islands in the Immune System (MAP-Seq and ChIP-Seq data)

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Fbxl19 recruits Rnf20 to CpG Islands and promotes H2B mono-ubiquitination [Affymetrix]

Project description:Rnf20 catalyzes lysine 120 mono-ubiquitination of histone H2B (H2Bub1) that has been previously involved in normal differentiation of embryonic stem (ES) and adult stem cells. However, the mechanisms underlying by which Rnf20 is recruited to its target chromosomal loci to generate H2Bub1 are still elusive. Here, we reveal that Fbxl19, a CxxC domain-containing protein, physically interacts with Rnf20, guides it preferentially to CpG island-containing target promoters, and thereby promotes mono-ubiqutination of H2B. We first show that up-regulation of Fbxl19 induces the level of global H2Bub1, while down-regulation of Fbxl19 reduces the level of H2Bub1 in mouse ES cells. Our genome-wide target mapping unveils the preferential occupancy of Fbxl19 on CpG island-containing promoters, and we further show that the binding of Fbxl19 is essential for the recruitment of Rnf20 to its target genes and subsequent H2Bub1. Altogether, our results demonstrate that Fbxl19 plays critical roles in the H2Bub1 pathway by recruiting Rnf20 to CGI target genes specifically and selectively.

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Functional characterisation of CpG islands in mouse tissues

Project description:Tissue-specific methylation patterns suggest a role for CpG island (CGI) methylation in differentiation and cell-type-specific gene regulation. We have applied CXXC affinity purification (CAP), MBD affinity purification (MAP) and chromatin immunoprecipitation (ChIP) in combination with solexa sequencing to investigate the extent and functional significance of CGI methylation in mouse sperm, blood, cerebellum and ES cells.

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Cell Type-Specific DNA Methylation at Intragenic CpG Islands in the Immune System (MAP-Seq and ChIP-Seq data)

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