Review: Chromatin Structural Features and Targets That Regulate Transcription

Wolffe, Alan P.; Guschin, Dmitry

doi:10.1006/jsbi.2000.4217

Cited by 325 publications

(215 citation statements)

References 195 publications

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“…Local or extended structural changes in chromatin play an important role in the control of gene expression and are governed by complexes that remodel chromatin and by enzymes that posttranslationally modify histones (reviewed in Ref. [1]). …”

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confidence: 99%

Class II histone deacetylases: versatile regulators

2003

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Histone acetylation and deacetylation play essential roles in modifying chromatin structure and regulating gene expression in eukaryotes. Histone deacetylases (HDACs) catalyze the deacetylation of lysine residues in the histone N-terminal tails and are found in large multiprotein complexes with transcriptional co-repressors. Human HDACs are grouped into three classes based on their similarity to known yeast factors: class I HDACs are similar to the yeast transcriptional repressor yRPD3, class II HDACs to yHDA1 and class III HDACs to ySIR2. In this review, we focus on the biology of class II HDACs. These newly discovered enzymes have been implicated as global regulators of gene expression during cell differentiation and development. We discuss their emerging biological functions and the molecular mechanisms by which they are regulated.

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confidence: 99%

Class II histone deacetylases: versatile regulators

2003

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“…Specialized chromatin-modifying enzymes can phosphorylate, acetylate, ubiquitylate, or methylate specific amino acids within certain histones, and each of these modifications are associated with distinct biological events (1). One of the first histone modifications to be identified nearly forty-five years ago was the methylation of histone H4 lysine 20 (H4K20) 4 (2).…”

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Catalytic Function of the PR-Set7 Histone H4 Lysine 20 Monomethyltransferase Is Essential for Mitotic Entry and Genomic Stability

Houston

McManus

Adams

et al. 2008

Journal of Biological Chemistry

142

169

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Histone-modifying enzymes play a critical role in modulating chromatin dynamics. In this report we demonstrate that one of these enzymes, PR-Set7, and its corresponding histone modification, the monomethylation of histone H4 lysine 20 (H4K20), display a distinct cell cycle profile in mammalian cells: low at G 1 , increased during late S phase and G 2 , and maximal from prometaphase to anaphase. The lack of PR-Set7 and monomethylated H4K20 resulted in a number of aberrant phenotypes in several different mammalian cell types. These include the inability of cells to progress past G 2 , global chromosome condensation failure, aberrant centrosome amplification, and substantial DNA damage. By employing a catalytically dead dominant negative PR-Set7 mutant, we discovered that its mono-methyltransferase activity was required to prevent these phenotypes. Importantly, we demonstrate that all of the aberrant phenotypes associated with the loss of PR-Set7 enzymatic function occur independently of p53. Collectively, our findings demonstrate that PR-Set7 enzymatic activity is essential for mammalian cell cycle progression and for the maintenance of genomic stability, most likely by monomethylating histone H4K20. Our results predict that alterations of this pathway could result in gross chromosomal aberrations and aneuploidy.Dynamic alterations in chromatin structure are modulated, in part, by the post-translational modifications of the DNAassociated histone proteins. Specialized chromatin-modifying enzymes can phosphorylate, acetylate, ubiquitylate, or methylate specific amino acids within certain histones, and each of these modifications are associated with distinct biological events (1). One of the first histone modifications to be identified nearly forty-five years ago was the methylation of histone H4 lysine 20 (H4K20) 4 (2). Earlier biochemical studies linked H4K20 methylation to diverse biological events including transcriptional regulation, chromatin compaction, cell division, and the formation of heterochromatin (3-9). Importantly, it was also found that H4K20 is differentially methylated in vivo and therefore can be either mono-, di-, or trimethylated (10). Together, these findings strongly suggest that different methylated states of H4K20 may be involved in distinct biological processes, similar to what is observed for the various methylated states of histone H3 lysine 4 and 9 methylation (11, 12).Increasing evidence indicates that certain enzymes are responsible for the specific degree of histone lysine methylation (13). For example, the mono-and dimethylation of histone H3 lysine 9 in humans is mediated by the G9a enzyme, whereas trimethylation is mediated by the SUV39H1 enzyme (14,15). Similarly, the Suv4 -20 enzymes are responsible for di-and trimethylation in mammals (16,17). Trimethylated H4K20 is associated with repressed chromatin because it is targeted to constitutive heterochromatin, various repetitive elements, and imprinting control regions (16,18,19). Dimethylated H4K40 is more widely distributed within...

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“…C hromatin folding and the dynamic interplay between chromatin structures and various cellular factors directly regulate fundamental gene expression and silencing processes (1)(2)(3)(4). Extensive studies have probed the structural and dynamic properties of chromatin and the molecular mechanisms that determine these properties (5)(6)(7)(8).…”

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confidence: 99%

Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

Sun

Zhang

Schlick

2005

Proc. Natl. Acad. Sci. U.S.A.

109

113

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Although numerous experiments indicate that the chromatin fiber displays salt-dependent conformations, the associated molecular mechanism remains unclear. Here, we apply an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome with all histone tails incorporated to describe by Monte Carlo simulations salt-dependent rearrangements of a nucleosomal array with 12 nucleosomes. The ensemble of nucleosomal array conformations display salt-dependent condensation in good agreement with hydrodynamic measurements and suggest that the array adopts highly irregular 3D zig-zag conformations at high (physiological) salt concentrations and transitions into the extended ''beads-on-a-string'' conformation at low salt. Energy analyses indicate that the repulsion among linker DNA leads to this extended form, whereas internucleosome attraction drives the folding at high salt. The balance between these two contributions determines the salt-dependent condensation. Importantly, the internucleosome and linker DNA-nucleosome attractions require histone tails; we find that the H3 tails, in particular, are crucial for stabilizing the moderately folded fiber at physiological monovalent salt.chromatin modeling ͉ irregular 3D zig-zag ͉ Discrete Surface Charge Optimization model C hromatin folding and the dynamic interplay between chromatin structures and various cellular factors directly regulate fundamental gene expression and silencing processes (1-4). Extensive studies have probed the structural and dynamic properties of chromatin and the molecular mechanisms that determine these properties (5-8). Nonetheless, questions remain concerning how a chain of nucleosomes connected by linker DNA folds into a condensed 30-nm chromatin fiber under physiological conditions (9) and what the exact arrangements of nucleosomes in the 30-nm fiber are (6). Two principal architectures of fiber arrangement proposed are the solenoid and zig-zag models. They differ significantly in how the linker DNA is arranged within the condensed chromatin fiber. In the solenoid model, the linker DNA is bent such that the consecutive nucleosomes interact with each other and form a helix (10-14); in the zig-zag model, the linker DNA remains straight and crosses the fiber axis so that the consecutive nucleosomes appear at the opposite side of the fiber axis (5, 15-18).The structure of chromatin strongly depends on the salt environment, both in terms of the valence of the ions and their concentration in solution (1). At low salt concentrations, chromatin adopts the extended ''beads-on-a-string'' conformation, whereas at high salt concentrations it folds into compact forms. In the presence of linker histones (H1 or H5) under physiological salt conditions, chromatin forms the folded 30-nm fiber. The histone tails are known to be crucial for the folding of chromatin fibers (19-21; reviewed in ref. 22). The tail domains, accounting for Ϸ50% of the positive charges of the histone octamer, are located at the N-terminal portions of H2A, H2B, H3, and H4, and ...

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Review: Chromatin Structural Features and Targets That Regulate Transcription

Cited by 325 publications

References 195 publications

Class II histone deacetylases: versatile regulators

Class II histone deacetylases: versatile regulators

Catalytic Function of the PR-Set7 Histone H4 Lysine 20 Monomethyltransferase Is Essential for Mitotic Entry and Genomic Stability

Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

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