Comparison of nucleosome positioning among two yeast species and their hybrid for wild-type and deletion mutant strains
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces paradoxus
SUBMITTER: Itay Tirosh
PROVIDER: E-GEOD-18939 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences.
Tirosh Itay I Sigal Nadejda N Barkai Naama N
Molecular systems biology 20100501
Gene regulation differs greatly between related species, constituting a major source of phenotypic diversity. Recent studies characterized extensive differences in the gene expression programs of closely related species. In contrast, virtually nothing is known about the evolution of chromatin structure and how it influences the divergence of gene expression. Here, we compare the genome-wide nucleosome positioning of two closely related yeast species and, by profiling their inter-specific hybrid, ...[more]
Similar Datasets
Project description:Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified. We profiled a compendium of 50 yeast strains carrying conditional alleles or complete deletions of genes involved in transcriptional regulation, histone biology and chromatin remodeling, as well as compounds that target transcription and histone deacetylases, to assess their respective roles in nucleosome positioning and transcription. We find that nucleosome patterning in genes is affected by many factors including the CAF-1 complex, Spt10 and Spt21, in addition to previously reported remodeler ATPases and histone chaperones. Disruption of these factors or reductions in histone levels led genic nucleosomes to assume positions more consistent with their intrinsic sequence preferences, with pronounced and specific shifts of the +1 nucleosome relative to the transcription start site. These shifts of +1 nucleosomes appear to have functional consequences, as several affected genes in Ino80 mutants exhibited altered expression responses. Our parallel expression profiling compendium revealed extensive transcription changes in intergenic and antisense regions, most of which occur in regions with altered nucleosome occupancy and positioning. We show that the nucleosome-excluding transcription factors Reb1, Abf1, Tbf1, and Rsc3 suppress cryptic transcripts at their target promoters, while a combined analysis of nucleosome and expression profiles identified 36 novel transcripts that are normally repressed by Tup1/Cyc8. Our data confirm and extend the roles of chromatin remodelers and chaperones as major determinants of genic nucleosome positioning and these data provide a valuable resource for future studies. We examined 50 single-gene loss-of-function strains, comprised of gene deletions (del) and temperature-sensitive (ts) or tetracycline promoter-shutoff (tet) alleles. These genes were selected based on their known or potential role in nucleosome biology and include remodeler ATPases and chaperones, histones and histone modifiers, transcription and elongation factors, and components of RNA polymerase I and II. The compendium also includes 4 compounds targeting transcription and histone deacetylases, as well as a histone depletion time course performed with a strain in which H4 gene expression is exclusively under the control of a GAL1 promoter. Genome-wide nucleosome occupancy profiles were generated using Affymetrix Tiling arrays with probes spaced every 4 bp [PMID:16569694], or next-generation sequencing. Identically prepared samples for each strain and treatment were analyzed on the same tiling arrays for strand-specific expression differences. Each compendium condition was compared to a matched wild-type (WT) reference grown in parallel.
2013-05-22 | E-GEOD-44878 | biostudies-arrayexpress
Project description:The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA. Here we show that the combined action of Isw1 and Chd1 nucleosome spacing enzymes is required to maintain this organization. In the absence of these enzymes regular positioning of the majority of nucleosomes is lost. Exceptions include the region upstream of the promoter, the +1 nucleosome and a subset of locations distributed throughout coding regions where other factors are likely to be involved. These observations indicated that ATP-dependent remodeling enzymes are responsible for directing the positioning of the majority of nucleosomes within the Saccharomyces cerevisiae genome. Examination of nucleosome positioning in mutants of snf2-related enzymes Other data used in this study are provided in GEO Series GSE31301 and GSE31833.
2011-09-16 | E-GEOD-31015 | biostudies-arrayexpress
Project description:The budding yeast genome is marked by 250-350 origins of DNA replication. These origins are bound by the origin recognition complex (ORC) throughout the cell cycle. ORC has known DNA binding sequence preferences which, though necessary for binding, are not sufficient to fully specify a genomic locus as being bound by ORC, indicating that the cell must use additional chromosomal cues to specify ORC binding sites and origins of replication. Using high-throughput sequencing to precisely locate both ORC binding sites and nucleosome locations genome-wide, we find that a nucleosome depleted region (NDR) and precisely positioned nucleosomes are a ubiquitous feature of yeast replication origins. The ARS consensus sequence (ACS) and adjacent sequences are sufficient to maintain the nucleosome-free properties of the NDR. We use a temperature sensitive ORC1 mutant to demonstrate that ORC is required to maintain precisely positioned nucleosomes at origins of replication. These findings demonstrate the importance of local nucleosome positioning at replication origins, and that chromatin organization is an important determinant of origin selection. Examination of nucleosome positioning in wild-type and orc1-161ts mutant S. cerevisiae at room temperature and heatshock temperatures. Examination of ORC binding locations by ChIP-seq. All reported coordinates are based on the SGD genome build released 12/16/2005.
2010-03-19 | E-GEOD-16926 | biostudies-arrayexpress
Project description:modENCODE_submission_5173 This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include key histone modifications and histone variants. We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: fem-2(b245); Developmental Stage: Germline containing young adult; Genotype: fem-2(b245)III; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage Germline containing young adult; temp (temperature) 20 degree celsius; Strain fem-2(b245); Antibody AB2621 H3K79me3:361576 (target is H3K79me3)
2013-07-26 | E-GEOD-49208 | biostudies-arrayexpress
Project description:Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified. We profiled a compendium of 50 yeast strains carrying conditional alleles or complete deletions of genes involved in transcriptional regulation, histone biology and chromatin remodeling, as well as compounds that target transcription and histone deacetylases, to assess their respective roles in nucleosome positioning and transcription. We find that nucleosome patterning in genes is affected by many factors including the CAF-1 complex, Spt10 and Spt21, in addition to previously reported remodeler ATPases and histone chaperones. Disruption of these factors or reductions in histone levels led genic nucleosomes to assume positions more consistent with their intrinsic sequence preferences, with pronounced and specific shifts of the +1 nucleosome relative to the transcription start site. These shifts of +1 nucleosomes appear to have functional consequences, as several affected genes in Ino80 mutants exhibited altered expression responses. Our parallel expression profiling compendium revealed extensive transcription changes in intergenic and antisense regions, most of which occur in regions with altered nucleosome occupancy and positioning. We show that the nucleosome-excluding transcription factors Reb1, Abf1, Tbf1, and Rsc3 suppress cryptic transcripts at their target promoters, while a combined analysis of nucleosome and expression profiles identified 36 novel transcripts that are normally repressed by Tup1/Cyc8. Our data confirm and extend the roles of chromatin remodelers and chaperones as major determinants of genic nucleosome positioning and these data provide a valuable resource for future studies. We examined 50 single-gene loss-of-function strains, comprised of gene deletions (del) and temperature-sensitive (ts) or tetracycline promoter-shutoff (tet) alleles. These genes were selected based on their known or potential role in nucleosome biology and include remodeler ATPases and chaperones, histones and histone modifiers, transcription and elongation factors, and components of RNA polymerase I and II. The compendium also includes 4 compounds targeting transcription and histone deacetylases, as well as a histone depletion time course performed with a strain in which H4 gene expression is exclusively under the control of a GAL1 promoter. Genome-wide nucleosome occupancy profiles were generated using Affymetrix Tiling arrays with probes spaced every 4 bp [PMID:16569694], or next-generation sequencing. Identically prepared samples for each strain and treatment were analyzed on the same tiling arrays for strand-specific expression differences. Each compendium condition was compared to a matched wild-type (WT) reference grown in parallel.
2013-05-22 | E-GEOD-44877 | biostudies-arrayexpress
Project description:Meiotic recombination is initiated by developmentally programmed DNA double-strand breaks (DSBs). In S. cerevisiae, the vast majority of DSBs occur in the nucleosome-depleted regions at gene promoters, where transcription factors (TFs) bind. It has been proposed that TF binding can stimulate DSB formation nearby by modulating local chromatin structure. However, a prior study in TF bas1 mutant suggested that the role of TF binding in determining break formation is complex. Here, we examined fine-scale DSB distributions in TF mutant (bas1Δ and ino4Δ) strains. In bas1Δ mutants, 239 out of the 2468 hotspots showed reduced DSB activity, whereas 87 hotspots showed increased DSB activity. Similarly, in ino4Δ mutant, 415 out of the 2468 hotspots showed reduced DSB activity, whereas 322 hotspots showed increased DSB activity. We also mapped Bas1 and Ino4 binding sites in meiosis and found that only a small portion of the affected hotspots contained TF binding sites. This indicates that TF can influence DSB distribution both directly and indirectly. Surprisingly, these DSB changes in TF mutants did not correlate with change in chromatin structure and histone H3K4me3 modification, suggesting that the role of TF on DSB distribution cannot be simply explained by affecting local chromatin status. Four samples total: Bas1-Myc (ChIP and input samples), Ino4-Myc (ChIP and input samples)
2015-08-21 | E-GEOD-67912 | biostudies-arrayexpress
Project description:To study the evolution of nucleosome positioning we mapped nucleosome positioning in two species of yeasts. Identified differences in nucleosome positioning were classified into cis-based changes or trans-bseed changes based on the pattern of nucleosomes in the hybrid. This analysis was performed for wild-type strains as well as for strains deleted of 5 chromatin regulatoirs allolwing us to examine their roles in determining nucleosome positioning.
2010-03-01 | GSE18939 | GEO
Project description:Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified. We profiled a compendium of 50 yeast strains carrying conditional alleles or complete deletions of genes involved in transcriptional regulation, histone biology and chromatin remodeling, as well as compounds that target transcription and histone deacetylases, to assess their respective roles in nucleosome positioning and transcription. We find that nucleosome patterning in genes is affected by many factors including the CAF-1 complex, Spt10 and Spt21, in addition to previously reported remodeler ATPases and histone chaperones. Disruption of these factors or reductions in histone levels led genic nucleosomes to assume positions more consistent with their intrinsic sequence preferences, with pronounced and specific shifts of the +1 nucleosome relative to the transcription start site. These shifts of +1 nucleosomes appear to have functional consequences, as several affected genes in Ino80 mutants exhibited altered expression responses. Our parallel expression profiling compendium revealed extensive transcription changes in intergenic and antisense regions, most of which occur in regions with altered nucleosome occupancy and positioning. We show that the nucleosome-excluding transcription factors Reb1, Abf1, Tbf1, and Rsc3 suppress cryptic transcripts at their target promoters, while a combined analysis of nucleosome and expression profiles identified 36 novel transcripts that are normally repressed by Tup1/Cyc8. Our data confirm and extend the roles of chromatin remodelers and chaperones as major determinants of genic nucleosome positioning and these data provide a valuable resource for future studies. We examined 50 single-gene loss-of-function strains, comprised of gene deletions (del) and temperature-sensitive (ts) or tetracycline promoter-shutoff (tet) alleles. These genes were selected based on their known or potential role in nucleosome biology and include remodeler ATPases and chaperones, histones and histone modifiers, transcription and elongation factors, and components of RNA polymerase I and II. The compendium also includes 4 compounds targeting transcription and histone deacetylases, as well as a histone depletion time course performed with a strain in which H4 gene expression is exclusively under the control of a GAL1 promoter. Genome-wide nucleosome occupancy profiles were generated using Affymetrix Tiling arrays with probes spaced every 4 bp [PMID:16569694], or next-generation sequencing. Identically prepared samples for each strain and treatment were analyzed on the same tiling arrays for strand-specific expression differences. Each compendium condition was compared to a matched wild-type (WT) reference grown in parallel.
2013-05-22 | E-GEOD-44876 | biostudies-arrayexpress
Project description:Abstract: In the yeast S. pombe, multiple chromatin-modifying enzymes are required for heterochromatin formation, yet how their actions alter chromatin structure to block access to DNAby the transcriptional machinery is unknown. We constructed high-resolution nucleosome occupancy maps of heterochromatic regions in wild-type strains and in mutants lacking the H3K9 methyltransferase Clr4 or one of the two activities of the silencing effector complex SHREC. Fourier analysis reveals that these enzymes do not increase the regularity of nucleosome spacing. Rather, their principal effect was to induce the elimination of nucleosome-free regions (NFRs). Both NFRs associated with transcription initiation sites as well as those not associated with promoters are affected. As in S. cerevisiae, repressed genes in euchromatin retain their NFRs. Thus, NFR elimination cannot be explained as a secondary consequence of repression. The maps also show that TFIIIC boundary elements have NFRs resistant to silencing, suggesting a potential role in preventing lateral spread of heterochromatin. NFR elimination offers a mechanism by which heterochromatin restricts access of the transcriptional machinery to DNA. Nucleosome positions in either heterochromatin or euchromatin were mapped in various mutants to determine whether chromatin structure is altered upon heterochromatic silencing. Eight strains were assayed for nucleosome positioning in heterochromatin while two strains were assayed for nucleosome positioning in euchromatin. Two biological replicates were assayed for each strain. No dye swaps were done. RNA transcripts were also mapped using the heterochromatin tiling arrays to determine where RNA transcripts accumulate in heterochromatin. Three strains were assayed for transcripts in heterochromatin by hybridizing cy5-labeled cDNA created from total RNA against cy3-labeled cDNA created from RNA synthesized from sonicated genomic DNA. Two biological replicates were assayed for each strain.
2010-11-24 | E-GEOD-19596 | biostudies-arrayexpress
Project description:We knocked down AGO2 protein by RNAi in HeLaS3 human cell line. The current experiment aims at comparing nucleosome positioning in control and AGO2 knock down cells. HeLaS3 cell were cultured in DMEM. Cells were transfected with AGO2 siRNAs (or control siRNA) at day 1. On day 4 MNAse digestion of chromatin was performed. Mnase-digested chromatin DNA fragments were sequenced by paired-end DNA-seq.
2015-05-17 | E-MTAB-1844 | biostudies-arrayexpress