Chromatin architectures at fission yeast transcriptional promoters and replication origins

Givens, Robert M.; Lai, William; Rizzo, Jason M.; Bard, Jonathan; Mieczkowski, Piotr A.; Leatherwood, Janet; Huberman, Joel A.; Buck, Michael

doi:10.1093/nar/gks351

Cited by 40 publications

(52 citation statements)

References 59 publications

(166 reference statements)

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“…This is in contrast to two strong nucleosome positions in the cnt region observed in S. cerevisiae (33). The fuzziness is also reflected in the noisiness and breadth of the occupancy peaks from the published MNase maps (16,29) (Fig. 4B).…”

Section: Significancementioning

confidence: 72%

“…pombe Has a Linker Length Distribution of 10n + 4/5 bp. The S. pombe genome is known to have a shorter nucleosome repeat length than S. cerevisiae (28,29,35). The chemical map displays additional fine details.…”

Section: Significancementioning

confidence: 99%

“…Although similar in size, S. pombe is distinguished from S. cerevisiae by sharing important characteristics of chromosome structure with metazoans, including relatively large chromosomes, numerous introns, large repetitive centromeres, low-complexity replication origins, the composition of chromatin remodeling complexes, and siRNA-regulated heterochromatin (24-27). Recent micrococcal nuclease (MNase) mapping studies (16,28,29) revealed substantial differences between the two species in nucleosomal DNA sequence features and chromatin organization, including how histone-DNA sequence preferences affect nucleosome positioning and nucleosome occupancy patterns around transcription start sites (TSSs) and DNA replication origins. To address these questions at higher resolution and to control for potential sequence-specificity bias due to different MNase digestion extent (30-32), the in vivo chemical mapping approach of Brogaard et al (33) was used to map nucleosome centers directly in S. pombe in this study.…”

mentioning

confidence: 99%

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Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning

Moyle-Heyrman¹,

Zaichuk²,

et al. 2013

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

115

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Using a recently developed chemical approach, we have generated a genome-wide map of nucleosomes in vivo in Schizosaccharomyces pombe (S. pombe) at base pair resolution. The shorter linker length previously identified in S. pombe is due to a preponderance of nucleosomes separated by ∼4/5 bp, placing nucleosomes on opposite faces of the DNA. The periodic dinucleotide feature thought to position nucleosomes is equally strong in exons as in introns, demonstrating that nucleosome positioning information can be superimposed on coding information. Unlike the case in Saccharomyces cerevisiae, A/T-rich sequences are enriched in S. pombe nucleosomes, particularly at ±20 bp around the dyad. This difference in nucleosome binding preference gives rise to a major distinction downstream of the transcription start site, where nucleosome phasing is highly predictable by A/T frequency in S. pombe but not in S. cerevisiae, suggesting that the genomes and DNA binding preferences of nucleosomes have coevolved in different species. The poly (dA-dT) tracts affect but do not deplete nucleosomes in S. pombe, and they prefer special rotational positions within the nucleosome, with longer tracts enriched in the 10-to 30-bp region from the dyad. S. pombe does not have a welldefined nucleosome-depleted region immediately upstream of most transcription start sites; instead, the −1 nucleosome is positioned with the expected spacing relative to the +1 nucleosome, and its occupancy is negatively correlated with gene expression. Although there is generally very good agreement between nucleosome maps generated by chemical cleavage and micrococcal nuclease digestion, the chemical map shows consistently higher nucleosome occupancy on DNA with high A/T content.chromatin structure | heterochromatin | gene regulation E ukaryotic DNA is organized into nucleosome arrays that facilitate proper genome compaction and regulation of the genetic information. Genome-wide nucleosome maps from different organisms have provided important insights into how nucleosome positioning regulates chromosome functions (1-6). It is commonly accepted that the DNA sequence itself plays a major role in the exact positions where histone octamers bind DNA to form nucleosomes (7-9). Most remarkably, nucleosomes prefer special dinucleotide motifs at specific rotational angles within the nucleosome core (10, 11) and disfavor poly (dA-dT) tracts (12-15). Although the ability of DNA to interact with the histone core is important, nucleosome occupancy is influenced by additional extrinsic factors, including species-specific DNA binding proteins (16), ATP-dependent remodeling complexes (17,18), and the transcription machinery (19)(20)(21)(22).The underlying mechanisms for the species-or cell typespecific nucleosome positioning features have not been well understood. The fission yeast Schizosaccharomyces pombe and the budding yeast Saccharomyces cerevisiae are two highly diverged model organisms widely used to study basic biological processes in eukaryotes (23). Although similar in siz...

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Section: Significancementioning

confidence: 72%

Section: Significancementioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning

Moyle-Heyrman¹,

Zaichuk²,

et al. 2013

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

115

View full text Add to dashboard Cite

show abstract

“…To assess the distribution of elongating polymerases around nucleosomes in S. pombe, we displayed average PRO-seq density relative to previously identified nucleosome centers (Givens et al 2012). For both paused and not paused genes, we parsed nucleosomes within gene boundaries based on their relative positions to the TSS.…”

Section: Budding and Fission Yeast Exhibit Vastly Different Polymerasmentioning

confidence: 99%

Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast

Booth¹,

Wang²,

Cheung³

et al. 2016

Genome Res.

146

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Complex regulation of gene expression in mammals has evolved from simpler eukaryotic systems, yet the mechanistic features of this evolution remain elusive. Here, we compared the transcriptional landscapes of the distantly related budding and fission yeast. We adapted the Precision Run-On sequencing (PRO-seq) approach to map the positions of RNA polymerase active sites genome-wide in Schizosaccharomyces pombe and Saccharomyces cerevisiae. Additionally, we mapped preferred sites of transcription initiation in each organism using PRO-cap. Unexpectedly, we identify a pause in early elongation, specific to S. pombe, that requires the conserved elongation factor subunit Spt4 and resembles promoter-proximal pausing in metazoans. PRO-seq profiles in strains lacking Spt4 reveal globally elevated levels of transcribing RNA Polymerase II (Pol II) within genes in both species. Messenger RNA abundance, however, does not reflect the increases in Pol II density, indicating a global reduction in elongation rate. Together, our results provide the first base-pair resolution map of transcription elongation in S. pombe and identify divergent roles for Spt4 in controlling elongation in budding and fission yeast.

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“…Thus, the positioned nucleosomes first observed at ARS1 on a plasmid appear to be a defining feature of S. cerevisiae origins of DNA replication. Furthermore, decreased nucleosome occupancy at origins of replication has also been observed in a variety of different eukaryotic organisms outside of S. cerevisiae, including Drosophila (MacAlpine et al 2010), mammalian cells (Lubelsky et al 2011), and Schizosaccharomyces pombe (Givens et al 2012). …”

Section: Nucleosome Positioning and Origin Selectionmentioning

confidence: 95%

Chromatin and DNA Replication

MacAlpine

Almouzni

2013

Cold Spring Harbor Perspectives in Biology

175

141

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Chromatin architectures at fission yeast transcriptional promoters and replication origins

Cited by 40 publications

References 59 publications

Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning

Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning

Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast

Chromatin and DNA Replication

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