The <i>ade6</i> gene of the fission yeast <i>Schizosaccharomyces pombe</i> has the same chromatin structure in the chromosome and in plasmids

Bernardi, Fabio; Koller, Th.; Thoma, Fritz

doi:10.1002/yea.320070603

Cited by 34 publications

(48 citation statements)

References 29 publications

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“…9a and b). The repeat lengths were about 160 bp, well within the range of previous observations (7,30,59). The differences in repeat lengths indicated in the legend to Fig.…”

supporting

confidence: 88%

“…S. cerevisiae has no endogenous histone Hi. While the composition and structure of the yeast nucleosome core are very similar to those of higher eukaryotes (6), the nucleosomal repeat is only about 160 bp long (7,30,59) and therefore is too small to represent an octamer of core histones plus histone Hi. However, mapping of nucleosome positions showed that individual nucleosomes can be tightly packed while others can be well spaced and accommodate more than 170 bp (52,54). We showed that a sea urchin Hi could be expressed at low and high levels (in amounts similar to those of core histones) and that it copurified with nuclei and bound to chromatin.…”

mentioning

confidence: 99%

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Histone H1 expressed in Saccharomyces cerevisiae binds to chromatin and affects survival, growth, transcription, and plasmid stability but does not change nucleosomal spacing.

Linder¹,

Thoma²

1994

Mol. Cell. Biol.

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Histone HI is proposed to serve a structural role in nucleosomes and chromatin fibers, to affect the spacing of nucleosomes, and to act as a general repressor of transcription. To test these hypotheses, a gene coding for a sea urchin histone Hi was expressed from the inducible GAL] promoter in Saccharomyces cerevisiae by use of a YEp vector for high expression levels (strain YCL7) and a centromere vector for low expression levels (strain YCL1). The Hi protein was identified by its inducibility in galactose, its apparent molecular weight, and its solubility in 5% perchloric acid. When YCL7 was shifted from glucose to galactose for more than 40 h to achieve maximal levels of HI, Hi could be copurified in approximately stoichiometric amounts with core histones of Nonidet P-40-washed nuclei and with soluble chromatin fractionated on sucrose gradients. While S. cerevisiae tolerated the expression of low levels of Hi in YCLI without an obvious phenotype, the expression of high levels of HI correlated with greatly reduced survival, inhibition of growth, and increased plasmid loss but no obvious change in the nucleosomal repeat length. After an initial induction, RNA levels for GALi and Hi were drastically reduced, suggesting that Hi acts by the repression of galactose-induced genes. Similar effects, but to a lower extent, were observed when the C-terminal tail of HI was expressed.Most of the eukaryotic genome is packaged by histone proteins into nucleosomes, 30-nm chromatin fibers, and higher-order structures. The Hi class of histones includes a variety of subtypes or variants of lysine-rich proteins with a short N-terminal tail, a central globular domain, and a long, highly charged C-terminal tail. Hi is proposed to serve different roles (for a review, see reference 62). (i) At the nucleosome level, DNA is wrapped in two superhelical turns around an octamer of core histones (two each of H2A, H2B, H3, and H4). Our current view is that on the average, one histone HI molecule binds from the outside at the entry and exit site of the linker DNA and stabilizes two turns of DNA in the nucleosome. This view is supported by electron microscopy (16, 57), proteinprotein cross-linking (8) (4,37,58). The structural and functional roles of the individual domains of Hi are less clear. The globular region appears to be sufficient for sealing the nucleosome in vitro (1) and was suggested to organize the 30-nm fibers (33,58). The Nterminal tail and, in particular, the positively charged Cterminal tail might bind to linker DNA or adjacent nucleosomes and thereby contribute to the condensation of chromatin fibers (27,58

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“…9a and b). The repeat lengths were about 160 bp, well within the range of previous observations (7,30,59). The differences in repeat lengths indicated in the legend to Fig.…”

supporting

confidence: 88%

mentioning

confidence: 99%

Histone H1 expressed in Saccharomyces cerevisiae binds to chromatin and affects survival, growth, transcription, and plasmid stability but does not change nucleosomal spacing.

Linder¹,

Thoma²

1994

Mol. Cell. Biol.

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“…We used the program from Segal et al For comparison, the average number of positioned nucleosomes is 3.3/kb in the S. cerevisiae genome (Lee et al 2007) and ∼2/kb in human promoters (Ozsolak et al 2007). (Bernardi et al 1991). Positioned nucleosomes detected by our method are shown as histone octamers and agree very well with Bernardi et al (1991).…”

Section: Altering Cnp1p Loading Does Not Affect the Centromere Nucleosupporting

confidence: 66%

“…(Bernardi et al 1991). Positioned nucleosomes detected by our method are shown as histone octamers and agree very well with Bernardi et al (1991). (B) The median nucleosome signal of three biological replicates, each with (bold black) two technical replicates; (colored lines) individual replicates.…”

Section: Altering Cnp1p Loading Does Not Affect the Centromere Nucleomentioning

confidence: 54%

“…1B). To validate our experimental and computational procedures, we compared the nucleosome positions determined by our method with the known locations of eight positioned nucleosomes in the ade6 gene (Bernardi et al 1991). As shown in Figure 2A, all eight nucleosomes were detected, confirming the accuracy and sensitivity of our approach.…”

Section: Agreement With Known Nucleosome Locations In Ade6mentioning

confidence: 58%

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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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Species specific protein--DNA interactions may determine the chromatin units of genes in S.cerevisiae and in S.pombe.

1992

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Yeast genes, such as URA3, are chromatin units characterized by positioned nucleosomes and flanking nuclease sensitive regions (NSRs). To investigate the structural determinants at the chromatin level in vivo, the URA3 gene was dissected into three parts (U5′, Umid and U3′), and the chromatin structures of the individual parts were analysed after insertion into minichromosomes and after chromatin assembly in vivo in Saccharomyces cerevisiae. While nucleosome positions were altered on Umid, the 5′‐end and the 3′‐end of URA3 maintained their native structures (a positioned nucleosome and a NSR each) independent of the site or orientation of insertion. This suggests that the chromatin unit of the native URA3 gene is dominated by strong protein boundaries at the 5′‐ and 3′‐ends. In an alternative approach, we investigated whether nucleosome positions or NSRs were maintained when the whole URA3 gene was placed on a shuttle vector and assembled into chromatin by Schizosaccharomyces pombe providing different proteins, but the same nucleosomal spacing. In a complementary exchange experiment, the ade6 gene of S.pombe was shuttled to S.cerevisiae. In spite of a general conservation of histone proteins and nucleosome core structures, neither nucleosome positions nor NSRs were maintained in the heterologous background. The results demonstrate that chromatin structures are species specific and that the structural boundaries of yeast genes may be dominated by strong species specific protein‐DNA interactions.

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The ade6 gene of the fission yeast Schizosaccharomyces pombe has the same chromatin structure in the chromosome and in plasmids

Cited by 34 publications

References 29 publications

Histone H1 expressed in Saccharomyces cerevisiae binds to chromatin and affects survival, growth, transcription, and plasmid stability but does not change nucleosomal spacing.

Histone H1 expressed in Saccharomyces cerevisiae binds to chromatin and affects survival, growth, transcription, and plasmid stability but does not change nucleosomal spacing.

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

Species specific protein--DNA interactions may determine the chromatin units of genes in S.cerevisiae and in S.pombe.

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