5-Bromouracil disrupts nucleosome positioning by inducing A-form-like DNA conformation in yeast cells

Miki, Kensuke; Shimizu, Mitsuhiro; Fujii, Michihiko; Hossain, Mohammad Nazir; Ayusawa, Dai

doi:10.1016/j.bbrc.2008.01.149

Cited by 18 publications

(21 citation statements)

References 41 publications

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“…In addition, the study by Oh and Fraser examined the proportion of progeny DNA associating with histone H3 by performing consecutive ChIPs for histone H3 and bromodeoxyuridine. However, it is possible that the incorporation of bromodeoxyuridine into replicating DNA altered the chromatin structure, as observed previously (52,73).…”

Section: Discussionmentioning

confidence: 69%

Herpes Simplex Virus ICP0 Promotes both Histone Removal and Acetylation on Viral DNA during Lytic Infection

Cliffe

Knipe

2008

J Virol

176

240

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During lytic infection, the genome of herpes simplex virus 1 (HSV-1) is associated with limited levels of histones but does not form a regular repeating nucleosomal structure. However, the previous observation that chromatin remodeling factors are recruited into viral replication compartments indicates that chromatin remodeling plays a role in HSV-1 gene expression and DNA replication. In this study we demonstrate the presence of histone H3 on HSV-1 DNA early in infection at levels equivalent to those found on a cellular gene. The proportion of viral DNA associated with histone H3 decreases at later times postinfection, independently of either viral DNA replication or transcription. We demonstrate that an immediate-early protein, infected cell protein 0 (ICP0), is required for both a reduction in the proportion of HSV-1 DNA associating with histone H3 and an increase in histone acetylation. This study provides evidence that ICP0 directly alters the chromatin structure of the HSV-1 genome during lytic infection, and this system will serve as a useful model for the reduction of histone load in higher eukaryotes.Eukaryotic DNA is packaged into a protein-DNA complex known as chromatin. The basic structure of chromatin is the nucleosome, which consists of core histone proteins (H2A, H2B, H3, and H4) around which 147 bp of DNA is wrapped. Modification of the chromatin structure to allow access to proteins involved in DNA replication, recombination and repair, and gene expression is a key mechanism utilized by the cell to regulate these processes. Chromatin structure can be modified by covalent modification of histones and DNA, as well as noncovalent chromatin remodeling. Chromatin remodeling, carried out by ATPase-dependent chromatin remodeling complexes, results in the sliding of nucleosomes along the DNA, unwinding of nucleosomes, and/or complete removal of nucleosomes (65). Histone acetylation is one of the best-characterized covalent histone modifications and is a hallmark of transcriptionally active chromatin. Histone acetylation is thought to result in relaxation of the basic chromatin structure through both increased charge repulsion (20) and by serving as a binding site for chromatin-remodeling complexes (1,29,38).Like cellular DNA, the genomes of DNA viruses that replicate within the nucleus also associate with chromatin, albeit to varied degrees (48). The genome of herpes simplex virus 1 (HSV-1) has been shown to associate with histones during both lytic infection of epithelial cells and latent infection of neurons (13,32,39). During latent infection, the viral genome is packaged into nucleosomes and forms a classical laddering pattern following digestion with micrococcal nuclease (13). Consistent with the silencing of lytic genes during a latent infection, lytic gene promoters show markers of heterochromatin, such as H3K9me2, and low levels of histone acetylation (43,78). In contrast, during lytic infection, regular repeating nucleosome arrays of HSV-1 DNA have not been detected (39,45,47). However, at leas...

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Section: Discussionmentioning

confidence: 69%

Herpes Simplex Virus ICP0 Promotes both Histone Removal and Acetylation on Viral DNA during Lytic Infection

Cliffe

Knipe

2008

J Virol

176

240

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“…This strategy avoids local heating (15), and differs from approaches that use higher energy UV (337 nm) light, which produce damage not confined to the nuclear interior. We deliberately avoided presensitizing analogues such as BrdU, which can disrupt chromatin (16). After laser targeting along a 0.4 m-wide line (Fig.…”

Section: Resultsmentioning

confidence: 99%

Double-strand DNA breaks recruit the centromeric histone CENP-A

Zeitlin¹,

Baker²,

Chapados

et al. 2009

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

133

129

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The histone H3 variant CENP-A is required for epigenetic specification of centromere identity through a loading mechanism independent of DNA sequence. Using multiphoton absorption and DNA cleavage at unique sites by I-SceI endonuclease, we demonstrate that CENP-A is rapidly recruited to double-strand breaks in DNA, along with three components (CENP-N, CENP-T, and CENP-U) associated with CENP-A at centromeres. The centromere-targeting domain of CENP-A is both necessary and sufficient for recruitment to double-strand breaks. CENP-A accumulation at DNA breaks is enhanced by active non-homologous end-joining but does not require DNA-PKcs or Ligase IV, and is independent of H2AX. Thus, induction of a double-strand break is sufficient to recruit CENP-A in human and mouse cells. Finally, since cell survival after radiation-induced DNA damage correlates with CENP-A expression level, we propose that CENP-A may have a function in DNA repair.

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“…Further, distamycin A and the AT-hook protein HMG-I, which bind to the minor grooves of AT-tracts, potentiate the eVects of BrdU in human cells Satou et al 2004). Recently, we have also shown that BrdU disrupts nucleosome positioning through certain types of sequence in the yeast Saccharomyces cerevisiae (Miki et al 2008). These results suggest that BrdU targets certain types of sequence to change chromatin structure and gene expression.…”

Section: Introductionmentioning

confidence: 93%

Identification of genes that affect sensitivity to 5-bromodeoxyuridine in the yeast Saccharomyces cerevisiae

et al. 2010

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Small molecules that exhibit biological effects have been successfully used to study various biological phenomena. 5-Bromodeoxyuridine (BrdU) is a thymidine analog that affects various biological processes, such as cellular differentiation and cellular senescence in cultured mammalian cells. Although BrdU is thought to modulate these phenomena by changing chromatin structure and gene expression, the molecular mechanisms for the action of BrdU are not understood well. To analyze the molecular mechanisms of BrdU with genetic methods, we used the yeast Saccharomyces cerevisiae as a model. Our genetic screening has revealed that a defect in MPT5/HTR1/UTH4/PUF5 led to an increased sensitivity to BrdU, and that overexpression of VHT1 or SDT1 led to resistance to BrdU. The increased sensitivity to BrdU caused by a defect in MPT5 was suppressed by a mutation in SIR2, SIR3, or SIR4, which is involved in chromatin silencing and transcriptional repression. These findings suggest that chromatin silencing proteins are involved in the modulation of the cellular phenomena by BrdU, and would provide clues to answer the old question of how BrdU affects various biological phenomena.

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5-Bromouracil disrupts nucleosome positioning by inducing A-form-like DNA conformation in yeast cells

Cited by 18 publications

References 41 publications

Herpes Simplex Virus ICP0 Promotes both Histone Removal and Acetylation on Viral DNA during Lytic Infection

Herpes Simplex Virus ICP0 Promotes both Histone Removal and Acetylation on Viral DNA during Lytic Infection

Double-strand DNA breaks recruit the centromeric histone CENP-A

Identification of genes that affect sensitivity to 5-bromodeoxyuridine in the yeast Saccharomyces cerevisiae

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