Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA318371 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Mot1 is a conserved and essential Swi2/Snf2 ATPase that can remove TATA-binding protein (TBP) from DNA using ATP hydrolysis, and in so doing exerts global effects on transcription. Spt16 is also essential and functions globally in transcriptional regulation as a component of the FACT histone chaperone complex. Here we demonstrate that Mot1 and Spt16 regulate a largely overlapping set of genes in Saccharomyces cerevisiae. As expected, Mot1 was found to control TBP levels at co-regulated promoters. In contrast, Spt16 did not affect TBP recruitment. On a global scale, Spt16 was required for Mot1 promoter localization, and Mot1 also affected Spt16 localization to genes. Interestingly, we find that Mot1 has an unanticipated role in establishing or maintaining the occupancy and positioning of nucleosomes at the 5â ends of genes. Spt16 has a broad role in regulating chromatin organization in gene bodies, including those nucleosomes affected by Mot1. These results suggest that the large-scale overlap in Mot1 and Spt16 function arises from a combination of both their unique and shared functions in transcription complex assembly and chromatin structure regulation. ChIP was performed for Spt16-myc in WT cells and mot1-42 cells in duplicate with input DNA from WT as control. ChIP was performed for Mot1-myc in WT cells and spt16-197 cells in dublicate with input DNA from WT as control. Micrococcal nuclease digested chromatin from WT, mot1-42, spt16-197, and mot1-42 spt16-197 cells were immunoprecipitated with H3 antibody in duplicate. All samples were sequenced by Illumina MiSeq.
2016-05-16 | E-GEOD-80234 | biostudies-arrayexpress
Project description:Mot1 is a conserved and essential Swi2/Snf2 ATPase that can remove TATA-binding protein (TBP) from DNA using ATP hydrolysis, and in so doing exerts global effects on transcription. Spt16 is also essential and functions globally in transcriptional regulation as a component of the FACT histone chaperone complex. Here we demonstrate that Mot1 and Spt16 regulate a largely overlapping set of genes in Saccharomyces cerevisiae. As expected, Mot1 was found to control TBP levels at co-regulated promoters. In contrast, Spt16 did not affect TBP recruitment. On a global scale, Spt16 was required for Mot1 promoter localization, and Mot1 also affected Spt16 localization to genes. Interestingly, we find that Mot1 has an unanticipated role in establishing or maintaining the occupancy and positioning of nucleosomes at the 5’ ends of genes. Spt16 has a broad role in regulating chromatin organization in gene bodies, including those nucleosomes affected by Mot1. These results suggest that the large-scale overlap in Mot1 and Spt16 function arises from a combination of both their unique and shared functions in transcription complex assembly and chromatin structure regulation.
2016-05-16 | GSE80234 | GEO
Project description:Mot1 is a conserved and essential Swi2/Snf2 ATPase that can remove TATA-binding protein (TBP) from DNA using ATP hydrolysis, and in so doing exerts global effects on transcription. Spt16 is also essential and functions globally in transcriptional regulation as a component of the FACT histone chaperone complex. Here we demonstrate that Mot1 and Spt16 regulate a largely overlapping set of genes in Saccharomyces cerevisiae. As expected, Mot1 was found to control TBP levels at co-regulated promoters. In contrast, Spt16 did not affect TBP recruitment. Interestingly, Mot1 was required for Spt16 recruitment to co-activated promoters. In contrast, Spt16 levels in gene coding regions were unaffected by Mot1 as well as RNA polymerase II density. The co-localization of Mot1 and Spt16 at promoters and the broad overlap in the sets of genes they control is consistent with physical and genetic interactions between them. The data support a model in which these factors participate in a regulatory pathway in which Mot1 acts upstream of Spt16. Tiling arrays covering the entirety of the S.cerevisiae genome were used to identify the effects of Mot1 and Spt16 on RNA expression genome-wide. All samples were done in biological duplicates. The average signal from the spt16-197 samples was compared to the SPT16-WT to determine changes in expression. The average signal from the double mutant mot1-42 spt16-197 was compared to both SPT16-WT and MOT1-WT. The MOT1-WT data was previously published by our lab and is available at GEO accession GSM456548. Comparisons were made from our Spt16 dataset to the previously published MOT1-WT and mot1-42 data, and the entire study is available at GEO accession GSE18283. Differential RNA (spt16-197/SPT16): spt16-197_over_SPT16-WT.bar Differential RNA (mot1-42 spt16-197/SPT16): dbl_mut_over_SPT16-WT.bar Differential RNA (mot1-42 spt16-197/MOT1): dbl_mut_over_MOT1-WT.bar
2016-05-16 | E-GEOD-72117 | biostudies-arrayexpress
Project description:Mot1 is a conserved and essential Swi2/Snf2 ATPase that can remove TATA-binding protein (TBP) from DNA using ATP hydrolysis, and in so doing exerts global effects on transcription. Spt16 is also essential and functions globally in transcriptional regulation as a component of the FACT histone chaperone complex. Here we demonstrate that Mot1 and Spt16 regulate a largely overlapping set of genes in Saccharomyces cerevisiae. As expected, Mot1 was found to control TBP levels at co-regulated promoters. In contrast, Spt16 did not affect TBP recruitment. Interestingly, Mot1 was required for Spt16 recruitment to co-activated promoters. In contrast, Spt16 levels in gene coding regions were unaffected by Mot1 as well as RNA polymerase II density. The co-localization of Mot1 and Spt16 at promoters and the broad overlap in the sets of genes they control is consistent with physical and genetic interactions between them. The data support a model in which these factors participate in a regulatory pathway in which Mot1 acts upstream of Spt16.
2016-05-16 | GSE72117 | GEO
Project description:For a typical RNA polymerase (pol) II transcribed budding yeast gene, the 5' -end is characterized by a nucleosome-free region (NFR) immediate upstream of the transcription start site (TSS), flanked by two well-positioned nucleosomes (-1 and +1) containing H2A.Z. A similar arrangement of nucleosomes containing H2A.Z is found on the genes transcribed by pol III, which reside in the NFR actively maintained by the chromatin remodeling complexes. We did genome-wide MNase-seq and ChIP-seq experiments to study the nucleosome arrangement near pol III transcribed genes. We also measured the levels of different tRNAs in the tRNA pool of the wild type and Spt16 mutant (*spt16-197*) cells using tRNA-HySeq method. Although, it is difficult to measure the primary transcripts of tRNA due to their quick processing and the sequence degeneracy of the tRNA isogenes; a comparison of the wild type and Spt16 mutant showed both increase or decrease of tRNA transcripts. The result suggest that Spt16 may not be necessary for the transcription per se of tRNA genes.
2023-12-31 | GSE109527 | GEO
Project description:Spt16-TAP ChIP-seq
2020-12-26 | GSE83086 | GEO
Project description:The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator – histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis, that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization.
2011-11-22 | GSE28613 | GEO
Project description:The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity – nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed fragile nucleosomes throughout the yeast genome, nearly one thousand of which are at previously determined “nucleosome free” loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization.
2011-01-24 | GSE26412 | GEO
Project description:The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator – histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis, that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization. Med8-TAP strain ChIPed with IgG beads vs. Input in Saccharomyces cerevisiae
2011-11-22 | E-GEOD-28613 | biostudies-arrayexpress
Project description:The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity – nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed fragile nucleosomes throughout the yeast genome, nearly one thousand of which are at previously determined “nucleosome free” loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization. Comparing nucleosome occupancy under different MNase digestion levels and growth conditions.
2011-01-24 | E-GEOD-26412 | biostudies-arrayexpress