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53
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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Cited by 269 (2 self)
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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.
A profile of histone lysine methylation across transcribed mammalian chromatin
- Mol. Cell Biol
, 2006
"... This article cites 79 articles, 31 of which can be accessed free ..."
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Cited by 26 (1 self)
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This article cites 79 articles, 31 of which can be accessed free
Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution
"... We show that the nuclear architecture of rod photoreceptor cells differs fundamentally in nocturnal and diurnal mammals. The rods of diurnal retinas possess the conventional architecture found in nearly all eukaryotic cells, with most heterochromatin situated at the nuclear periphery and euchromatin ..."
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Cited by 21 (1 self)
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We show that the nuclear architecture of rod photoreceptor cells differs fundamentally in nocturnal and diurnal mammals. The rods of diurnal retinas possess the conventional architecture found in nearly all eukaryotic cells, with most heterochromatin situated at the nuclear periphery and euchromatin residing toward the nuclear interior. The rods of nocturnal retinas have a unique inverted pattern, where heterochromatin localizes in the nuclear center, whereas euchromatin, as well as nascent transcripts and splicing machinery, line the nuclear border. The inverted pattern forms by remodeling of the conventional one during terminal differentiation of rods. The inverted rod nuclei act as collecting lenses, and computer simulations indicate that columns of such nuclei channel light efficiently toward the lightsensing rod outer segments. Comparison of the two patterns suggests that the conventional architecture prevails in eukaryotic nuclei because it results in more flexible chromosome arrangements, facilitating positional regulation of nuclear functions.
Non-coding murine centromeric transcripts associate with and potentiate Aurora B kinase. Nucleic Acids Res
- 2009
"... associate with and potentiate Aurora B kinase ..."
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p38 MAPK signaling regulates recruitment of Ash2L-containing methyltransferase complexes to specific genes during differentiation. Nat Struct Mol Biol 14
, 2007
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Tsukamoto T: The assembly and maintenance of heterochromatin initiated by transgene repeats are independent of the RNA interference pathway in mammalian cells
- Mol Cell Biol
"... This article cites 52 articles, 29 of which can be accessed free ..."
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Cited by 9 (0 self)
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This article cites 52 articles, 29 of which can be accessed free
Targeted recruitment of histone modifications in humans predicted by genomic sequences
- J. Comput. Biol
, 2009
"... Histone modifications are important epigenetic regulators and play a critical role in develop-ment. The targeting mechanism for histone modifications is complex and still incompletely understood. Here we applied a computational approach to predict genome-scale histone modification targets in humans ..."
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Cited by 4 (2 self)
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Histone modifications are important epigenetic regulators and play a critical role in develop-ment. The targeting mechanism for histone modifications is complex and still incompletely understood. Here we applied a computational approach to predict genome-scale histone modification targets in humans by the genomic DNA sequences using a set of recent ChIP-seq data. We found that a number of histone modification marks could be predicted with high accuracy. On the other hand, the impact of DNA sequences for each mark is intrinsically different dependent upon the target- and tissue-specificity. Diverse patterns are associated with different repetitive elements. Unexpectedly, we found that non-overlapping, functionally opposite histone modification marks could share similar sequence features. We propose that these marks may target a common set of loci but are mutually exclusive and that the competition may be important for developmental control. Taken together, we show that our computational approach has provided new insights into the targeting mechanism of histone modifications.
Supplemental Material
, 2008
"... H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome ..."
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Cited by 1 (0 self)
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H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome
JCB Article
"... Simple epithelium keratins 8 and 18 provide resistance to Fas-mediated apoptosis. The protection occurs through a receptor-targeting modulation ..."
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Simple epithelium keratins 8 and 18 provide resistance to Fas-mediated apoptosis. The protection occurs through a receptor-targeting modulation
