Genome-wide mapping of nucleosome positions in Schizosaccharomyces pombe

Lantermann, Alexandra B.; Strålfors, Annelie; Fagerström‐Billai, Fredrik; Korber, Philipp; Ekwall, Karl

doi:10.1016/j.ymeth.2009.02.004

Cited by 37 publications

(53 citation statements)

References 25 publications

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“…Briefly, we treated chromatin from wild-type and Δ atf1 strains (Figure 1A) with MNase, isolated mononucleosomes and PCR-amplified them with pairs of overlapping primers covering promoters and 5′-end of coding sequences of the gpd1 and ctt1 genes, as described elsewhere (1). We confirmed the presence of wide NDRs upstream of the TSS of both genes, as previously described (1,19). However, Δ atf1 cells displayed higher relative nucleosome occupancy exactly where the CRE sites are (Figure 1B and C).…”

Section: Resultssupporting

confidence: 88%

“…Mononucleosomes were obtained as described before (1,11,19), and the resulting DNA was analysed by qPCR as described previously (1,20). Briefly, strains were cultured in 250 ml of YE5S medium to an OD 600 of 0.5 and then cross-linked with formaldehyde (final concentration of 0.5% (v/v)) for 20 min at 25°C.…”

Section: Methodsmentioning

confidence: 99%

“…Fixed cells were subjected to chromatin isolation and MNase digestion as described above for nucleosome-scanning analysis (1,19). Again, the MNase concentration has to be carefully optimized to discard samples with underdigested or overdigested chromatin (we only purified mononucleosomes from samples with 80–90% of mononucleosomal fraction), since the extent of the digestion has to be very similar to compare nucleosome maps for different strains or experiments (21).…”

Section: Methodsmentioning

confidence: 99%

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Binding of the transcription factor Atf1 to promoters serves as a barrier to phase nucleosome arrays and avoid cryptic transcription

Garcia

Paulo

Gao

et al. 2014

Nucleic Acids Research

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Schizosaccharomyces pombe displays a large transcriptional response common to several stress conditions, regulated primarily by the transcription factor Atf1. Atf1-dependent promoters contain especially broad nucleosome depleted regions (NDRs) prior to stress imposition. We show here that basal binding of Atf1 to these promoters competes with histones to create wider NDRs at stress genes. Moreover, deletion of atf1 results in nucleosome disorganization specifically at stress coding regions and derepresses antisense transcription. Our data indicate that the transcription factor binding to promoters acts as an effective barrier to fix the +1 nucleosome and phase downstream nucleosome arrays to prevent cryptic transcription.

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Section: Resultssupporting

confidence: 88%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Binding of the transcription factor Atf1 to promoters serves as a barrier to phase nucleosome arrays and avoid cryptic transcription

Garcia

Paulo

Gao

et al. 2014

Nucleic Acids Research

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“…The pattern observed at the ade6 gene (Fig. 1B) was in good agreement with previous high-resolution studies of this gene (Song et al 2008;Lantermann et al 2009). In agreement with studies in S. cerevisiae and other organisms, we found NFRs in the promoters of both active and repressed genes.…”

Section: Chromatin Features Of Euchromatic Locisupporting

confidence: 91%

“…In agreement with studies in S. cerevisiae and other organisms, we found NFRs in the promoters of both active and repressed genes. In S. pombe, the meiosis-specific gene mek1 has been shown to display a small NFR in its repressed state (Wilhelm et al 2008;Lantermann et al 2009), and we recapitulated this observation using our methods (Supplemental Fig. S3D).…”

Section: Chromatin Features Of Euchromatic Locisupporting

confidence: 57%

Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions

Garcia¹,

Dumesic²,

Hartley³

et al. 2010

Genes Dev.

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High-resolution nucleosome occupancy maps of heterochromatic regions of wild-type and silencing-defective mutants of the fission yeast Schizosaccharomyces pombe revealed that heterochromatin induces the elimination of nucleosome-free regions (NFRs). NFRs associated with transcription initiation sites as well as those not associated with promoters are affected. We dissected the roles of the histone H3K9 methyltransferase Clr4 and the HP1 proteins Swi6 and Chp2, as well as the two catalytic activities of the SHREC histone deacetylase (HDAC)/ ATPase effector complex. Strikingly, different DNA sites have distinct combinatorial requirements for these factors: Five classes of NFRs were identified that are eliminated by silencing factors through a mechanistic hierarchy governed by Clr4. The SHREC HDAC activity plays a major role in the elimination of class I-IV NFRs by antagonizing the action of RSC, a remodeling complex implicated in NFR formation. We propose that heterochromatin formation involves the deployment in several sequence-specific mechanisms to eliminate gaps between nucleosomes, thereby blocking access to the DNA.[Keywords: Schizosaccharomyces pombe; heterochromatin; nucleosome-free regions; silencing] Supplemental material is available at http://www.genesdev.org.

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Current awareness on yeast

2009

Yeast

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In order to keep subscribers up‐to‐date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly‐published material on yeasts. Each bibliography is divided into 10 sections. 1 Reviews; 2 General; 3 Biochemistry; 4 Biotechnology; 5 Cell Biology; 6 Gene Expression; 7 Genetics; 8 Physiology; 9 Medical Mycology; 10 Recombinant DNA Technology. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. (5 weeks journals ‐ search completed 4th. Nov. 2009)

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Genome-wide mapping of nucleosome positions in Schizosaccharomyces pombe

Cited by 37 publications

References 25 publications

Binding of the transcription factor Atf1 to promoters serves as a barrier to phase nucleosome arrays and avoid cryptic transcription

Binding of the transcription factor Atf1 to promoters serves as a barrier to phase nucleosome arrays and avoid cryptic transcription

Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions

Current awareness on yeast

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