Cfp1 integrates both CpG content and gene activity for accurate H3K4me3 deposition in embryonic stem cells. Genes Dev

Wellcome Trust Centre for Cell Biology, University of Edinburgh, United Kingdom.
Genes & development (Impact Factor: 10.8). 08/2012; 26(15):1714-28. DOI: 10.1101/gad.194209.112
Source: PubMed


Trimethylation of histone H3 Lys 4 (H3K4me3) is a mark of active and poised promoters. The Set1 complex is responsible for most somatic H3K4me3 and contains the conserved subunit CxxC finger protein 1 (Cfp1), which binds to unmethylated CpGs and links H3K4me3 with CpG islands (CGIs). Here we report that Cfp1 plays unanticipated roles in organizing genome-wide H3K4me3 in embryonic stem cells. Cfp1 deficiency caused two contrasting phenotypes: drastic loss of H3K4me3 at expressed CGI-associated genes, with minimal consequences for transcription, and creation of "ectopic" H3K4me3 peaks at numerous regulatory regions. DNA binding by Cfp1 was dispensable for targeting H3K4me3 to active genes but was required to prevent ectopic H3K4me3 peaks. The presence of ectopic peaks at enhancers often coincided with increased expression of nearby genes. This suggests that CpG targeting prevents "leakage" of H3K4me3 to inappropriate chromatin compartments. Our results demonstrate that Cfp1 is a specificity factor that integrates multiple signals, including promoter CpG content and gene activity, to regulate genome-wide patterns of H3K4me3.

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Available from: Thomas Clouaire, Oct 05, 2015
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    • "It has been postulated that dedicated proteins might bind selectively, and with high affinity to methylated CpG-rich sequences, and participate in the recruitment of chromatin remodeling repressor complexes to silence target genes (Bartke et al., 2010; Joulie et al., 2010; Fournier et al., 2012; Spruijt et al., 2013). Conversely, active promoters and enhancers acquired chromatin marks, such as histone H3 lysine 4 monomethylation (at enhancers) or trimethylation (at promoters) that prevent the activity of DNMTs (Thomson et al., 2010; Clouaire et al., 2012; Zhou et al., 2012), hence the unmethylated status of most HCP and ICP promoters in the genome (Fig. 2). The recent advances in the field had a significant impact on our understanding of the role of DNA methylation in mammals, the enzymatic machineries involved in its regulation and its impact on gene expression in normal and pathological contexts. "
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    ABSTRACT: DNA methylation in mammals is a key epigenetic modification essential to normal genome regulation and development. DNA methylation patterns are established during early embryonic development, and subsequently maintained during cell divisions. Yet, discrete site-specific de novo DNA methylation or DNA demethylation events play a fundamental role in a number of physiological and pathological contexts, leading to critical changes in the transcriptional status of genes such as differentiation, tumor suppressor or imprinted genes. How the DNA methylation machinery targets specific regions of the genome during early embryogenesis and in adult tissues remains poorly understood. Here, we report advances being made in the field with a particular emphasis on the implication of transcription factors in establishing and in editing DNA methylation profiles. J. Cell. Physiol. © 2014 Wiley Periodicals, Inc.
    Journal of Cellular Physiology 04/2015; 230(4). DOI:10.1002/jcp.24836 · 3.84 Impact Factor
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    • "Data analysis was performed as described in the materials and methods section. Alterations in H3K4me3 and H3K27ac were investigated, which are markers associated with promoter activation (transcription start site (TSS), H3K4me3 and H3K27ac) and enhancer activation (primarily H3K27ac) [44], [45]. In addition to the analysis of (differential) modification patterns, motif enrichment of the modified regions was investigated and compared between the cell lines. "
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    ABSTRACT: Background Originating from Primordial Germ Cells/gonocytes and developing via a precursor lesion called Carcinoma In Situ (CIS), Germ Cell Cancers (GCC) are the most common cancer in young men, subdivided in seminoma (SE) and non-seminoma (NS). During physiological germ cell formation/maturation, epigenetic processes guard homeostasis by regulating the accessibility of the DNA to facilitate transcription. Epigenetic deregulation through genetic and environmental parameters (i.e. genvironment) could disrupt embryonic germ cell development, resulting in delayed or blocked maturation. This potentially facilitates the formation of CIS and progression to invasive GCC. Therefore, determining the epigenetic and functional genomic landscape in GCC cell lines could provide insight into the pathophysiology and etiology of GCC and provide guidance for targeted functional experiments. Results This study aims at identifying epigenetic footprints in SE and EC cell lines in genome-wide profiles by studying the interaction between gene expression, DNA CpG methylation and histone modifications, and their function in the pathophysiology and etiology of GCC. Two well characterized GCC-derived cell lines were compared, one representative for SE (TCam-2) and the other for EC (NCCIT). Data were acquired using the Illumina HumanHT-12-v4 (gene expression) and HumanMethylation450 BeadChip (methylation) microarrays as well as ChIP-sequencing (activating histone modifications (H3K4me3, H3K27ac)). Results indicate known germ cell markers not only to be differentiating between SE and NS at the expression level, but also in the epigenetic landscape. Conclusion The overall similarity between TCam-2/NCCIT support an erased embryonic germ cell arrested in early gonadal development as common cell of origin although the exact developmental stage from which the tumor cells are derived might differ. Indeed, subtle difference in the (integrated) epigenetic and expression profiles indicate TCam-2 to exhibit a more germ cell-like profile, whereas NCCIT shows a more pluripotent phenotype. The results provide insight into the functional genome in GCC cell lines.
    PLoS ONE 06/2014; 9(6):e98330. DOI:10.1371/journal.pone.0098330 · 3.23 Impact Factor
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    • "H2A.Z and H3.3 were enriched in regulatory elements (i.e., enhancers, insulators, and CGIs; Figure 3, 4, 5). Various chromatin proteins bind to these regions, including the transcription factors, CTCF and Cfp1, which recruit histone modification enzymes [61], [62]. Therefore, H2A.Z and H3.3 might be recruited to these regions to form nucleosomes that are readily accessible to chromatin proteins. "
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    ABSTRACT: Genome-wide distribution of the majority of H2A and H3 variants (H2A, H2AX, H2AZ, macroH2A, H3.1, H3.2 and H3.3) was simultaneously investigated in mouse embryonic stem cells by chromatin immunoprecipitation sequencing. Around the transcription start site, histone variant distribution differed between genes possessing promoters of high and low CpG density, regardless of their expression levels. In the intergenic regions, regulatory elements were enriched in H2A.Z and H3.3, whereas repeat elements were abundant in H2A and macroH2A, and H3.1, respectively. Analysis of H2A and H3 variant combinations composing nucleosomes revealed that the H2A.Z and H3.3 combinations were present at a higher frequency throughout the genome than the other combinations, suggesting that H2A.Z and H3.3 associate preferentially with each other to comprise the nucleosomes independently of genome region. Finally, we found that chromatin was unstable only in regions where it was enriched in both H2A.Z and H3.3, but strongly quantified stable in regions in which only H3.3 was abundant. Therefore, histone variant composition is an important determinant of chromatin structure, which is associated with specific genomic functions.
    PLoS ONE 03/2014; 9(3):e92689. DOI:10.1371/journal.pone.0092689 · 3.23 Impact Factor
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