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17
A bivalent chromatin structure marks key developmental genes in embryonic stem cells, Cell 125
, 2006
"... The most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster within regions enriched for genes encoding developmentally important transcription factors (TFs). This suggests that HCNE-rich regions may contain key regulatory controls involved in development. We explored this by ex ..."
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The most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster within regions enriched for genes encoding developmentally important transcription factors (TFs). This suggests that HCNE-rich regions may contain key regulatory controls involved in development. We explored this by examining histone methylation in mouse embryonic stem (ES) cells across 56 large HCNE-rich loci. We identified a specific modification pattern, termed ‘‘bivalent domains,’ ’ consisting of large regions of H3 lysine 27 methylation harboring smaller regions of H3 lysine 4 methylation. Bivalent domains tend to coincide with TF genes expressed at low levels. We propose that bivalent domains silence developmental genes in ES cells while keeping them poised for activation. We also found striking correspondences between genome sequence and histone methylation in ES cells, which become notably weaker in differentiated cells. These results highlight the importance of DNA sequence in defining the initial epigenetic landscape and suggest a novel chromatin-based mechanism for maintaining pluripotency.
The impact of intragenic CpG content on gene expression. Nucleic Acids Res
, 2010
"... The development of vaccine components or recom-binant therapeutics critically depends on sustained expression of the corresponding transgene. This study aimed to determine the contribution of intragenic CpG content to expression efficiency in transiently and stably transfected mammalian cells. Based ..."
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The development of vaccine components or recom-binant therapeutics critically depends on sustained expression of the corresponding transgene. This study aimed to determine the contribution of intragenic CpG content to expression efficiency in transiently and stably transfected mammalian cells. Based upon a humanized version of green fluorescent protein (GFP) containing 60 CpGs within its coding sequence, a CpG-depleted variant of the GFP reporter was established by carefully modulating the codon usage. Interestingly, GFP reporter activity and detectable protein amounts in stably transfected CHO and 293 cells were significantly decreased upon CpG depletion and independent from promoter usage (CMV, EF1a). The reduction in protein expression associated with CpG depletion was likewise observed for other unrelated reporter genes and was clearly reflected by a decline in mRNA copy numbers rather than translational efficiency. Moreover, decreased mRNA levels were neither due to nuclear export restrictions nor alternative splicing or mRNA instability. Rather, the intragenic CpG content influenced de novo transcriptional activity thus implying a common transcription-based mech-anism of gene regulation via CpGs. Increased high CpG transcription correlated with changed nucleosomal positions in vitro albeit histone density at the two genes did not change in vivo as monitored by ChIP.
A Lentiviral Functional Proteomics Approach Identifies Chromatin Remodeling Complexes
"... Protein complexes and protein-protein interactions are essential for almost all cellular processes. Here, we es-tablish a mammalian affinity purification and lentiviral ex-pression (MAPLE) system for characterizing the subunit compositions of protein complexes. The system is flexible (i.e. multiple ..."
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Protein complexes and protein-protein interactions are essential for almost all cellular processes. Here, we es-tablish a mammalian affinity purification and lentiviral ex-pression (MAPLE) system for characterizing the subunit compositions of protein complexes. The system is flexible (i.e. multiple N- and C-terminal tags and multiple promot-ers), is compatible with GatewayTM cloning, and incorpo-rates a reference peptide. Its major advantage is that it permits efficient and stable delivery of affinity-tagged open reading frames into most mammalian cell types. We benchmarked MAPLE with a number of human protein complexes involved in transcription, including the RNA polymerase II-associated factor, negative elongation fac-tor, positive transcription elongation factor b, SWI/SNF, and mixed lineage leukemia complexes. In addition,
The COMPASS Family of H3K4 Methylases in Drosophila
, 2011
"... Methylation of histone H3 lysine 4 (H3K4) in Saccharomyces cerevisiae is implemented by Set1/COMPASS, which was originally purified based on the similarity of yeast Set1 to human MLL1 and Drosophila melanogaster Trithorax (Trx). While humans have six COMPASS family members, Drosophila possesses a re ..."
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Methylation of histone H3 lysine 4 (H3K4) in Saccharomyces cerevisiae is implemented by Set1/COMPASS, which was originally purified based on the similarity of yeast Set1 to human MLL1 and Drosophila melanogaster Trithorax (Trx). While humans have six COMPASS family members, Drosophila possesses a representative of the three subclasses within COMPASS-like complexes: dSet1 (human SET1A/SET1B), Trx (human MLL1/2), and Trr (human MLL3/4). Here, we report the biochemical purification and molecular characterization of the Drosophila COMPASS family. We observed a one-to-one similarity in subunit composition with their mam-malian counterparts, with the exception of LPT (lost plant homeodomains [PHDs] of Trr), which copurifies with the Trr complex. LPT is a previously uncharacterized protein that is homologous to the multiple PHD fingers found in the N-terminal regions of mammalian MLL3/4 but not Drosophila Trr, indicating that Trr and LPT constitute a split gene of an MLL3/4 ancestor. Our study demonstrates that all three complexes in Drosophila are H3K4 methyltransferases; however, dSet1/COMPASS is the major monoubiquitination-depen-dent H3K4 di- and trimethylase in Drosophila. Taken together, this study provides a springboard for the functional dissection of the COMPASS family members and their role in the regulation of histone H3K4 methylation throughout development in Drosophila. Histone H3 lysine 4 methylation (H3K4me) is associated
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, 2009
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Histone Methylation, and Differentiation �
, 2009
"... These include: This article cites 65 articles, 26 of which can be accessed free at: ..."
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These include: This article cites 65 articles, 26 of which can be accessed free at:
REFERENCES CONTENT ALERTS Epigenetic Regulation of Tumor Necrosis Factor Alpha
, 2007
"... These include: This article cites 66 articles, 36 of which can be accessed free at: ..."
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These include: This article cites 66 articles, 36 of which can be accessed free at:
IN GENE REGULATION AND CELL CYCLE
, 2009
"... I would like taking this opportunity to express my deep gratitude to Dr ..."
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CONTENT
"... 1.1 DNA methylation in eukaryotes 3 1.1.1 Epigenetic gene regulation 3 1.1.2 Discovery of 5‐methylcytosine in DNA 4 ..."
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1.1 DNA methylation in eukaryotes 3 1.1.1 Epigenetic gene regulation 3 1.1.2 Discovery of 5‐methylcytosine in DNA 4
