Differential regulation of repeated histone genes during the fission yeast cell cycle

Takayama, Yuko; Takahashi, Kohske

doi:10.1093/nar/gkm213

Cited by 48 publications

(105 citation statements)

References 47 publications

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“…www.genome.org acts with Cnp1p (Chen et al 2003a,b;Takahashi et al 2005;Takayama and Takahashi 2007). In either case, our work shows that the activity of Ams2 may influence the composition but not the locations of centromeric nucleosomes and thus argues against the nucleosome eviction hypothesis for functional centromeres (see Supplemental Fig.…”

Section: Genome Research 1069mentioning

confidence: 55%

“…Ams2p, a GATA-like transcription factor, has been shown to bind to the centromere core regions and plays an important role in localizing Cnp1p to centromeres during S phase (Chen et al 2003a,b;Takahashi et al 2005;Takayama and Takahashi 2007). The precise mechanism for how Ams2p facilitates Cnp1p loading is not known.…”

Section: Ams2-binding Sitesmentioning

confidence: 99%

“…The preferential location of GATA motifs in troughs further supports the idea that Ams2p binds the centromeric core DNA. Ams2p also functions as an authentic transcription factor by binding to the promoters of histone genes and is required for their S-phase-specific transcription (Takayama and Takahashi 2007). Among the histone genes, only H2A.2, H3.3, and H4.3 had a GATA motif in the promoter (see Supplemental Fig.…”

Section: Genome Research 1069mentioning

confidence: 99%

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A high-resolution map of nucleosome positioning on a fission yeast centromere

Song¹,

Liu²,

Liu³

et al. 2008

Genome Res.

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A key element for defining the centromere identity is the incorporation of a specific histone H3, CENPA, known as Cnp1p in Schizosaccharomyces pombe. Previous studies have suggested that functional S. pombe centromeres lack regularly positioned nucleosomes and may involve chromatin remodeling as a key step of kinetochore assembly. We used tiling microarrays to show that nucleosomes are, in fact, positioned in regular intervals in the core of centromere 2, providing the first high-resolution map of regional centromere chromatin. Nucleosome locations are not disrupted by mutations in kinetochore protein genes cnp1, mis18, mis12, nuf2, mal2; overexpression of cnp1; or the deletion of ams2, which encodes a GATA-like factor participating in CENPA incorporation. Bioinformatics analysis of the centromere sequence indicates certain enriched motifs in linker regions between nucleosomes and reveals a sequence bias in nucleosome positioning. In addition, sequence analysis of nucleosome-free regions identifies novel binding sites of Ams2p. We conclude that centromeric nucleosome positions are stable and may be derived from the underlying DNA sequence.

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Section: Genome Research 1069mentioning

confidence: 55%

Section: Ams2-binding Sitesmentioning

confidence: 99%

Section: Genome Research 1069mentioning

confidence: 99%

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A high-resolution map of nucleosome positioning on a fission yeast centromere

Song¹,

Liu²,

Liu³

et al. 2008

Genome Res.

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“…The GATA-type transcription factor Ams2 is required for S-phase activation of H3 and H4 genes in fission yeast (Takayama and Takahashi 2007). Thus, it was no surprise that we observed upregulation of Tf2 transcription in ams2D, too (Fig.…”

Section: Rad52 Enrichment Patterns In Pfh1 Helicase Mutantsmentioning

confidence: 61%

Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method

Zhou

Zhang

et al. 2012

Genome Res.

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Spontaneous DNA damage may occur nonrandomly in the genome, especially when genome maintenance mechanisms are undermined. We developed single-strand DNA (ssDNA)-associated protein immunoprecipitation followed by sequencing (SPI-seq) to map genomic hotspots of DNA damage. We demonstrated this method with Rad52, a homologous recombination repair protein, which binds to ssDNA formed at DNA lesions. SPI-seq faithfully detected, in fission yeast, Rad52 enrichment at artificially induced double-strand breaks (DSBs) as well as endogenously programmed DSBs for mating-type switching. Applying Rad52 SPI-seq to fission yeast mutants defective in DNA helicase Pfh1 or histone H3K56 deacetylase Hst4, led to global views of DNA lesion hotspots emerging in these mutants. We also found serendipitously that histone dosage aberration can activate retrotransposon Tf2 and cause the accumulation of a Tf2 cDNA species bound by Rad52. SPI-seq should be widely applicable for mapping sites of DNA damage and uncovering the causes of genome instability.

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“…It acts like an animal H3.3 in that it is used by HIRA (4). In Schizosaccharomyces pombe, a single H3 protein is produced, partly from two RC H3 genes and partly from two constitutive ones (5). Neither model organism can be used to study the contribution of histone H3 variants in replicative and replacement nucleosome assembly.…”

mentioning

confidence: 99%

Identification of a Replication-independent Replacement Histone H3 in the Basidiomycete Ustilago maydis

Verma

Kapros

Waterborg

2011

Journal of Biological Chemistry

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Ustilago maydis is a haploid basidiomycete with single genes for two distinct histone H3 variants. The solitary U1 gene codes for H3.1, predicted to be a replication-independent replacement histone. The U2 gene is paired with histone H4 and produces a putative replication-coupled H3.2 variant. These predictions were evaluated experimentally. U2 was confirmed to be highly expressed in the S phase and had reduced expression in hydroxyurea, and H3.2 protein was not incorporated into transcribed chromatin of stationary phase cells. Constitutive expression of U1 during growth produced ϳ25% of H3 as H3.1 protein, more highly acetylated than H3.2. The level of H3.1 increased when cell proliferation slowed, a hallmark of replacement histones. Half of new H3.1 incorporated into highly acetylated chromatin was lost with a half-life of 2.5 h, the fastest rate of replacement H3 turnover reported to date. This response reflects the characteristic incorporation of replacement H3 into transcribed chromatin, subject to continued nucleosome displacement and a loss of H3 as in animals and plants. Although the two H3 variants are functionally distinct, neither appears to be essential for vegetative growth. KO gene disruption transformants of the U1 and U2 loci produced viable cell lines. The structural and functional similarities of the Ustilago replication-coupled and replication-independent H3 variants with those in animals, in plants, and in ciliates are remarkable because these distinct histone H3 pairs of variants arose independently in each of these clades and in basidiomycetes.Core histones provide the packaging proteins for DNA in eukaryotic cells. During the S phase when genomic DNA is duplicated, replication-coupled expression of histone genes provides new protein to assemble newly replicated DNA. Histone chaperones assist in the creation of new nucleosomes to maintain a stable, compacted, repressed state of chromatin. Within this context, regulatory proteins modulate chromatin environments to facilitate access to the DNA for gene transcription. The components and processes that allow RNA polymerases to transcribe a chromatin template, such as epigenetic modifications of DNA and histones, are being identified and intensely studied. The processes of nucleosome displacement from DNA by transcribing RNA polymerases and of nucleosome reassembly from available histones remain poorly understood.In research going back decades, it was observed that the composition of nucleosomes across transcribed gene regions, identified in part by high levels of histone acetylation, changed over time. Replication-coupled (RC) 2 histone H3 variants like H3.2 in birds were replaced by histone H3.3, a constitutively expressed form of animal histone H3. This histone is now known as a replacement histone or as a replication-independent (RI) H3 variant (1, 2). Specialized chaperones such as HIRA and Daxx selectively bind these RI H3 proteins at a small region, residues 87-90, which is uniquely different between RI and RC forms (3, 4). In the S phase...

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Differential regulation of repeated histone genes during the fission yeast cell cycle

Cited by 48 publications

References 47 publications

A high-resolution map of nucleosome positioning on a fission yeast centromere

A high-resolution map of nucleosome positioning on a fission yeast centromere

Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method

Identification of a Replication-independent Replacement Histone H3 in the Basidiomycete Ustilago maydis

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