Reduced Genomic Cytosine Methylation and Defective Cellular Differentiation in Embryonic Stem Cells Lacking CpG Binding Protein

Department of Biochemistry and Molecular Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, United States
Molecular and Cellular Biology (Impact Factor: 4.78). 07/2005; 25(12):4881-91. DOI: 10.1128/MCB.25.12.4881-4891.2005
Source: PubMed


Cytosine methylation at CpG dinucleotides is a critical epigenetic modification of mammalian genomes. CpG binding protein
(CGBP) exhibits a unique DNA-binding specificity for unmethylated CpG motifs and is essential for early murine development.
Embryonic stem cell lines deficient for CGBP were generated to further examine CGBP function. CGBP−/− cells are viable but show an increased rate of apoptosis and are unable to achieve in vitro differentiation following removal
of leukemia inhibitory factor from the growth media. Instead, CGBP−/− embryonic stem cells remain undifferentiated as revealed by persistent expression of the pluripotent markers Oct4 and alkaline
phosphatase. CGBP−/− cells exhibit a 60 to 80% decrease in global cytosine methylation, including hypo-methylation of repetitive elements, single-copy
genes, and imprinted genes. Total DNA methyltransferase activity is reduced by 30 to 60% in CGBP−/− cells, and expression of the maintenance DNA methyltransferase 1 protein is similarly reduced. However, de novo DNA methyltransferase
activity is normal. Nearly all aspects of the pleiotropic CGBP−/− phenotype are rescued by introduction of a CGBP expression vector. Hence, CGBP is essential for normal epigenetic modification
of the genome by cytosine methylation and for cellular differentiation, consistent with the requirement for CGBP during early
mammalian development.

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Available from: Diana Carlone, Jun 25, 2014
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    • "This study particularly focused on the question of how profiles of this mark are shaped by Cfp1, which is known to be a conserved DNA-binding subunit of the H3K4 histone methyltransferase (HMT) Set1 complex. The experiment presented consists of ChIP-Seq measurements from three different cell lines: (1) a wild-type mouse ES cell line (WT), (2) a mutant ES line lacking Cfp1 (Cfp1-/-) [30,31], and (3) a rescue cell line obtained by stable transfection of a human Cfp1 cDNA into Cfp1-/- ES cells (Resc) [32,33]. We expected that H3K4me3 is reduced in the Cfp1-/- cells. "
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    ABSTRACT: Cell-specific gene expression is controlled by epigenetic modifications and transcription factor binding.While genome-wide maps for these protein-DNA interactions have become widely available,quantitative comparison of the resulting ChIP-Seq data sets remains challenging. Current approachesto detect differentially bound or modified regions are mainly borrowed from RNA-Seq data analysis,thus focusing on total counts of fragments mapped to a region, ignoring any information encoded inthe shape of the peaks. Here, we present MMDiff, a robust, broadly applicable method for detecting differences between sequencecount data sets. Based on quantifying shape changes in signal profiles, it overcomes challengesimposed by the highly structured nature of the data and the paucity of replicates.We first use a simulated data set to compare the performance of MMDiff with results obtained byfour alternative methods. We demonstrate that MMDiff excels when peak profiles change betweensamples. We next use MMDiff to re-analyse a recent data set of the histone modification H3K4me3elucidating the establishment of this prominent epigenomic marker. Our empirical analysis showsthat the method yields reproducible results across experiments, and is able to detect functional importantchanges in histone modifications. To further explore the broader applicability of MMDiff,we apply it to two ENCODE data sets: one investigating the histone modification H3K27ac and onemeasuring the genome-wide binding of the transcription factor CTCF. In both cases, MMDiff provesto be complementary to count-based methods. In addition, we can show that MMDiff is capable ofdirectly detecting changes of homotypic binding events at neighbouring binding sites. MMDiff isreadily available as a Bioconductor package. Our results demonstrate that higher order features of ChIP-Seq peaks carry relevant and often complementaryinformation to total counts, and hence are important in assessing differential histone modificationsand transcription factor binding. We have developed a new computational method, MMDiff,that is capable of exploring these features and therefore closes an existing gap in the analysis of ChIPSeqdata sets.
    Full-text · Article · Nov 2013 · BMC Genomics
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    • "The SET1A complex was purified as a multi-protein complex that associates with CFP1 [19]. CFP1 is required for stem cell differentiation and interacts with unmethylated CpGs via its zinc finger domain CXXC [97]. Interestingly, Cfp1−/− ES cells displayed aberrant H3K4me3 peaks at numerous ectopic sites (i.e., distinct regions outside annotated CpG islands), suggesting that CFP1 recruits the SET1 complex to CpG island-containing promoters and consequently prevents it from generating H3K4me3 to inappropriate chromatin locations [19,98,99]. "
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    ABSTRACT: Epigenetic mechanisms are fundamental to understanding the regulatory networks of gene expression that govern stem cell maintenance and differentiation. Methylated histone H3 lysine 4 (H3K4) has emerged as a key epigenetic signal for gene transcription; it is dynamically modulated by several specific H3K4 methyltransferases and demethylases. Recent studies have described new epigenetic mechanisms by which H3K4 methylation modifiers control self-renewal and lineage commitments of stem cells. Such advances in stem cell biology would have a high impact on the research fields of cancer stem cell and regenerative medicine. In this review, we discuss the recent progress in understanding the roles of H3K4 methylation modifiers in regulating embryonic and adult stem cells’ fates.
    Full-text · Article · Oct 2013 · Cell and Bioscience
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    • "A similar composite profile for the 20% most affected promoters showed a more drastic depletion of H3K4me3 both upstream of and downstream from the TSS (Fig. 1D,E). To confirm that the absence of Cfp1 was primarily responsible for the observed decrease, we performed H3K4me3 ChIP-seq in a rescue cell line obtained by stable transfection of a human Cfp1 cDNA into Cfp1 À/À ES cells (Carlone et al. 2005; Tate et al. 2009a). These wild-type rescue cells, which express Cfp1 at near endogenous levels "
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