Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae

Yarragudi, Arunadevi; Parfrey, Laura Wegener; Morse, Randall H.

doi:10.1093/nar/gkl1059

Cited by 111 publications

(121 citation statements)

References 43 publications

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“…Although the CDC19 promoter has a Rap1 binding site, little if any dependence on Rap1 was seen for Srb5 recruitment at this promoter, indicating that Mediator recruitment is independent of Rap1 at CDC19. Consistent with this result, expression of CDC19 was not altered at nonpermissive temperature in rap1 ts mutant yeast (37).…”

Section: Mediator Recruitment At Rp Gene Promoters Is Rap1 Dependentsupporting

confidence: 77%

Mediator complex association with constitutively transcribed genes in yeast

Ansari

Morse

2009

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

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Mediator is a large, multisubunit complex that is essential for transcription of mRNA by RNA Pol II in eukaryotes and is believed to bridge transcriptional activators and the general transcription machinery. However, several recent studies suggest that the requirement for Mediator during transcriptional activation is not universal, but rather activator dependent, and may be indirect for some genes. Here we have investigated Mediator association with several constitutively transcribed genes in yeast by comparing a yeast strain that harbors a temperature-sensitive mutation in an essential Mediator subunit, Srb4, with its wild-type (WT) counterpart. We find modest association of Mediator with constitutively active genes and show that this association is strongly decreased in srb4 ts yeast, whereas association with a nontranscribed region or repressed gene promoters is lower and unaffected in the mutant yeast. The tail module of Mediator remains associated with ribosomal protein (RP) gene promoters in srb4 ts yeast, while subunits from the head and middle modules are lost. Tail module association at Rap1-dependent gene promoters is lost in rap1 ts yeast, indicating that Rap1 is required for Mediator recruitment at these gene promoters and that its recruitment occurs via the tail module. Pol II association is also rapidly and severely affected in srb4 ts yeast, indicating that Mediator is directly required for pol II association at constitutively transcribed genes. Our results are consistent with Mediator functioning as a general transcription factor in yeast. Rap1 ͉ transcription

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Section: Mediator Recruitment At Rp Gene Promoters Is Rap1 Dependentsupporting

confidence: 77%

Mediator complex association with constitutively transcribed genes in yeast

Ansari

Morse

2009

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

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“…1B), suggesting that they are binding sites for trans-acting regulators. Previous studies in S. cerevisiae (Yarragudi et al 2007;Kaplan et al 2008;Clapier and Cairns 2009) and our own analysis across 12 species (Tsankov et al 2010) have confirmed that such sequences can correspond to binding sites for known general regulatory factors (GRFs), such as Reb1 (Fig. 1B, orange; Badis et al 2008;Zhu et al 2009) and the Rsc3/30 components of the RSC chromatin remodeling complex ( Fig.…”

Section: Identifying Motifs For Trans-acting Chromatin Regulatorssupporting

confidence: 58%

Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization

Tsankov¹,

Yanagisawa²,

Rhind³

et al. 2011

Genome Res.

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The packaging of eukaryotic genomes into nuclesomes plays critical roles in chromatin organization and gene regulation. Studies in Saccharomyces cerevisiae indicate that nucleosome occupancy is partially encoded by intrinsic antinucleosomal DNA sequences, such as poly(A) sequences, as well as by binding sites for trans-acting factors that can evict nucleosomes, such as Reb1 and the Rsc3/30 complex. Here, we use genome-wide nucleosome occupancy maps in 13 Ascomycota fungi to discover large-scale evolutionary reprogramming of both intrinsic and trans determinants of chromatin structure. We find that poly(G)s act as intrinsic antinucleosomal sequences, comparable to the known function of poly(A)s, but that the abundance of poly(G)s has diverged greatly between species, obscuring their antinucleosomal effect in low-poly(G) species such as S. cerevisiae. We also develop a computational method that uses nucleosome occupancy maps for discovering transacting general regulatory factor (GRF) binding sites. Our approach reveals that the specific sequences bound by GRFs have diverged substantially across evolution, corresponding to a number of major evolutionary transitions in the repertoire of GRFs. We experimentally validate a proposed evolutionary transition from Cbf1 as a major GRF in pre-whole-genome duplication (WGD) yeasts to Reb1 in post-WGD yeasts. We further show that the mating type switch-activating protein Sap1 is a GRF in S. pombe, demonstrating the general applicability of our approach. Our results reveal that the underlying mechanisms that determine in vivo chromatin organization have diverged and that comparative genomics can help discover new determinants of chromatin organization.

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“…Early studies identified the GRFs Abf1 and Rap1 as important in the chromatin structure of the HIS4 promoter (Arndt and Fink 1986;Devlin et al 1991;Yu and Morse 1999;Yarragudi et al 2004), More recently, analysis of genome-wide in vivo nucleosome maps revealed that, in addition to poly(dA:dT), other sequence motifs are associated with nucleosome depletion in vivo, and these correspond to the DNA-binding sites for GRFs such as Abf1, Reb1, and Rap1 (Lee et al 2007b;Yarragudi et al (2007); Badis et al 2008;Kaplan et al 2009;Tsankov et al 2010). These sequences are not nucleosome-depleted in in vitro nucleosome reconstitutions , and this fact has allowed automated determination of GRFs in multiple species by identification of short sequence motifs that are highly nucleosome-depleted in vivo but not in vitro (Tsankov et al 2010).…”

Section: Trans-determinants Of Nucleosome Positioning: General Regulamentioning

confidence: 99%

Chromatin and Transcription in Yeast

2012

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Understanding the mechanisms by which chromatin structure controls eukaryotic transcription has been an intense area of investigation for the past 25 years. Many of the key discoveries that created the foundation for this field came from studies of Saccharomyces cerevisiae, including the discovery of the role of chromatin in transcriptional silencing, as well as the discovery of chromatin-remodeling factors and histone modification activities. Since that time, studies in yeast have continued to contribute in leading ways. This review article summarizes the large body of yeast studies in this field.

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Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae

Cited by 111 publications

References 43 publications

Mediator complex association with constitutively transcribed genes in yeast

Mediator complex association with constitutively transcribed genes in yeast

Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization

Chromatin and Transcription in Yeast

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