Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast

Castro, E. de; Soriano, Ignacio; Marín, Laura; Serrano, Rebeca; Quintales, Luis; Antequera, Francisco

doi:10.1038/emboj.2011.350

Cited by 44 publications

(69 citation statements)

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“…They are enriched in poly dA:dT elements in S. cerevisiae (Iyer and Struhl 1995;Zhang et al 2011b), whereas they are not in S. pombe (Lantermann et al 2010). In fact, the A + T content of these regions is lower than the intergenic average in S. pombe (de Castro et al 2012). Chromatin assembly experiments have shown that the in vivo positioning pattern at the 5 ′ end of genes of S. cerevisiae can be reconstituted in the presence of ATP-dependent trans-acting factors, suggesting that the DNA sequence would play a minor role in nucleosome positioning (Zhang et al 2011b).…”

Section: Wwwgenomeorgmentioning

confidence: 93%

“…This precise positioning is essential to modulate the access of proteins to specific sites in the chromosomes to regulate transcription (Bai et al 2010;Koster et al 2015), replication initiation (Lipford and Bell 2001;Eaton et al 2010;Soriano et al 2014), and recombination (Pan et al 2011;de Castro et al 2012).…”

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

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Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome

et al. 2016

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In the yeast genome, a large proportion of nucleosomes occupy well-defined and stable positions. While the contribution of chromatin remodelers and DNA binding proteins to maintain this organization is well established, the relevance of the DNA sequence to nucleosome positioning in the genome remains controversial. Through quantitative analysis of nucleosome positioning, we show that sequence changes distort the nucleosomal pattern at the level of individual nucleosomes in three species of Schizosaccharomyces and in Saccharomyces cerevisiae. This effect is equally detected in transcribed and nontranscribed regions, suggesting the existence of sequence elements that contribute to positioning. To identify such elements, we incorporated information from nucleosomal signatures into artificial synthetic DNA molecules and found that they generated regular nucleosomal arrays indistinguishable from those of endogenous sequences. Strikingly, this information is speciesspecific and can be combined with coding information through the use of synonymous codons such that genes from one species can be engineered to adopt the nucleosomal organization of another. These findings open the possibility of designing coding and noncoding DNA molecules capable of directing their own nucleosomal organization.

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Section: Wwwgenomeorgmentioning

confidence: 93%

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome

et al. 2016

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“…In addition, most replication origins in Saccharomyces cerevisiae are also associated with NDRs (42), although some efficient origins lack NDRs (43). However, a recent study in Schizosaccharomyces pombe found that ORC binding and origins do not overlap with NDR (44). Interestingly, recent proteomic analyses in human cells have suggested that ORC preferentially binds nucleosomes with H3K9m3 or H3K27m3, and that this binding is even more effective in the presence of CpG methylation (45).…”

Section: -G)mentioning

confidence: 99%

Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana

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et al. 2012

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

211

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Nucleosomes package eukaryotic DNA and are composed of four different histone proteins, designated H3, H4, H2A, and H2B. Histone H3 has two main variants, H3.1 and H3.3, which show different genomic localization patterns in animals. We profiled H3.1 and H3.3 variants in the genome of the plant Arabidopsis thaliana and found that the localization of these variants shows broad similarity in plants and animals, along with some unique features. H3.1 was enriched in silent areas of the genome, including regions containing the repressive chromatin modifications H3 lysine 27 methylation, H3 lysine 9 methylation, and DNA methylation. In contrast, H3.3 was enriched in actively transcribed genes, especially peaking at the 3′ end of genes, and correlated with histone modifications associated with gene activation, such as histone H3 lysine 4 methylation and H2B ubiquitylation, as well as RNA Pol II occupancy. Surprisingly, both H3.1 and H3.3 were enriched on defined origins of replication, as was overall nucleosome density, suggesting a novel characteristic of plant origins. Our results are broadly consistent with the hypothesis that H3.1 acts as the canonical histone that is incorporated during DNA replication, whereas H3.3 acts as the replacement histone that can be incorporated outside of S-phase during chromatin-disrupting processes like transcription. N ucleosomes, the basic units of chromatin, consist of DNA wrapped around a core of eight histone proteins composed of two dimers of histones H2A and H2B and a tetramer of histones H3 and H4. In multicellular organisms, multiple variants of each histone protein coexist in the same nucleus. In the case of histone H3, three variants are found in both plants and animals: the canonical H3

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“…The media used in this study included yeast extract medium with supplements (YES) and essential minimal medium (EMM), which were prepared as described previously (Forsburg and Rhind 2006) with the following modifications: YES was supplemented with 2 g complete dropout powder, while EMM was supplemented with 2 g dropout powder lacking leucine and uracil. Dropout stock powder was prepared by mixing 5 g adenine SO 4 with 2 g each of the remaining 19 amino acids and uracil.…”

Section: Methodsmentioning

confidence: 99%

Single-Nucleotide-Specific Targeting of the Tf1 Retrotransposon Promoted by the DNA-Binding Protein Sap1 of Schizosaccharomyces pombe

et al. 2015

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Transposable elements (TEs) constitute a substantial fraction of the eukaryotic genome and, as a result, have a complex relationship with their host that is both adversarial and dependent. To minimize damage to cellular genes, TEs possess mechanisms that target integration to sequences of low importance. However, the retrotransposon Tf1 of Schizosaccharomyces pombe integrates with a surprising bias for promoter sequences of stress-response genes. The clustering of integration in specific promoters suggests that Tf1 possesses a targeting mechanism that is important for evolutionary adaptation to changes in environment. We report here that Sap1, an essential DNA-binding protein, plays an important role in Tf1 integration. A mutation in Sap1 resulted in a 10-fold drop in Tf1 transposition, and measures of transposon intermediates support the argument that the defect occurred in the process of integration. Published ChIP-Seq data on Sap1 binding combined with high-density maps of Tf1 integration that measure independent insertions at single-nucleotide positions show that 73.4% of all integration occurs at genomic sequences bound by Sap1. This represents high selectivity because Sap1 binds just 6.8% of the genome. A genome-wide analysis of promoter sequences revealed that Sap1 binding and amounts of integration correlate strongly. More important, an alignment of the DNA-binding motif of Sap1 revealed integration clustered on both sides of the motif and showed high levels specifically at positions +19 and 29. These data indicate that Sap1 contributes to the efficiency and position of Tf1 integration. KEYWORDS Sap1; Tf1; integration; transposition; Schizosaccharomyces pombe R ETROTRANSPOSONS are pervasive among eukaryotes and, in many cases, account for a substantial portion of the host genome (Moore et al. 2004;Scheifele et al. 2009;Levin and Moran 2011). The ability of these elements to selectively integrate into specific target sequences has been paramount to their success because the employment of specific targeting mechanisms has allowed these retrotransposons to propagate within host genomes without disrupting genes and compromising the host's survival (Levin and Moran 2011). The long terminal repeat (LTR) retrotransposons Ty1, Ty3, and Ty5 of Saccharomyces cerevisiae avoid causing damage to the host by targeting noncoding genomic regions; Ty1 and Ty3 integrate upstream of RNA polemerase III-transcribed genes, while Ty5 integrates into heterochromatin (Chalker and Sandmeyer 1990;1992;Ji et al. 1993;Kirchner et al. 1995;Devine and Boeke 1996;Zou et al. 1996;Zou and Voytas 1997;Yieh et al. 2000;Sandmeyer 2003;Lesage and Todeschini 2005).In Schizosaccharomyces pombe, the LTR retrotransposon Tf1 has a unique targeting mechanism that directs integration to promoters of RNA polymerase II-transcribed genes with a bias for the promoters of stress-response genes (Behrens et al. 2000;Singleton and Levin 2002;Bowen et al. 2003;Leem et al. 2008;Guo and Levin 2010). Surprisingly, insertion of Tf1 into promoters rarel...

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Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast

Cited by 44 publications

References 64 publications

Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome

Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome

Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana

Single-Nucleotide-Specific Targeting of the Tf1 Retrotransposon Promoted by the DNA-Binding Protein Sap1 of Schizosaccharomyces pombe

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