Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA132441 | ENA |
REPOSITORIES: ENA
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Project description:Histone variant H2A.Z-containing nucleosomes are incorporated at most eukaryotic promoters. This incorporation is mediated by the conserved SWR1 complex, which replaces histone H2A in canonical nucleosomes with H2A.Z in an ATP-dependent manner. Here, we show that promoter-proximal nucleosomes are highly heterogeneous for H2A.Z in Saccharomyces cerevisiae, with substantial representation of nucleosomes containing one, two, or no H2A.Z molecules. SWR1-catalyzed H2A.Z replacement in vitro occurs in a stepwise and unidirectional fashion, one H2A.Z-H2B dimer at a time, producing heterotypic nucleosomes as intermediates and homotypic H2A.Z nucleosomes as end products. The ATPase activity of SWR1 is specifically stimulated by H2A-containing nucleosomes without ensuing histone H2A eviction. Remarkably, further addition of free H2A.Z-H2B dimer leads to hyperstimulation of ATPase activity, eviction of nucleosomal H2A-H2B and deposition of H2A.Z-H2B. These results suggest that the combination of H2A-containing nucleosome and free H2A.Z-H2B dimer acting as both effector and substrate for SWR1 governs the specificity and outcome of the replacement reaction. Total nucleosomes from MNase-treated nuclear extracts were fractionated by sequential immunoprecipitation into homotypic H2A/H2A (AA), heterotypic H2A/H2A.Z (AZ), and homotypic H2A.Z/H2A.Z (ZZ) nucleosomes.
2010-10-12 | E-GEOD-24618 | biostudies-arrayexpress
Project description:Histone variant H2A.Z-containing nucleosomes are incorporated at most eukaryotic promoters. This incorporation is mediated by the conserved SWR1 complex, which replaces histone H2A in canonical nucleosomes with H2A.Z in an ATP-dependent manner. Here, we show that promoter-proximal nucleosomes are highly heterogeneous for H2A.Z in Saccharomyces cerevisiae, with substantial representation of nucleosomes containing one, two, or no H2A.Z molecules. SWR1-catalyzed H2A.Z replacement in vitro occurs in a stepwise and unidirectional fashion, one H2A.Z-H2B dimer at a time, producing heterotypic nucleosomes as intermediates and homotypic H2A.Z nucleosomes as end products. The ATPase activity of SWR1 is specifically stimulated by H2A-containing nucleosomes without ensuing histone H2A eviction. Remarkably, further addition of free H2A.Z-H2B dimer leads to hyperstimulation of ATPase activity, eviction of nucleosomal H2A-H2B and deposition of H2A.Z-H2B. These results suggest that the combination of H2A-containing nucleosome and free H2A.Z-H2B dimer acting as both effector and substrate for SWR1 governs the specificity and outcome of the replacement reaction.
2010-10-12 | GSE24618 | GEO
Project description:The site-specific chromatin incorporation of eukaryotic histone variant H2A.Z is driven by the multi-component chromatin remodeling complex SWR1/SRCAP/ p400. The budding yeast SWR1 complex replaces the H2A-H2B dimer in the canonical nucleosome with the H2A.Z-H2B dimer, but the mechanism governing the directionality of H2A-to-H2A.Z exchange remains elusive. Here, we use single-molecule force spectroscopy to dissect the disassembly/ reassembly of H2A-nucleosome and H2A.Z-nucleosome. We find that the N-terminal 1-135 residues of yeast SWR1-complex-protein-2 (previously termed Swc2-Z) facilitate the disassembly of nucleosomes containing H2A but not H2A.Z. The Swc2-mediated nucleosome disassembly/reassembly requires the inherently unstable H2A-nucleosome, whose instability is conferred by three H2A α2-helix residues Gly47, Pro49 and Ile63 as they selectively weaken the structural rigidity of H2A-H2B dimer. It also requires Swc2-ZN (residues 1-37) that directly anchors to H2A-nucleosome and functions in the SWR1-catalyzed H2A.Z replacement in vitro and yeast H2A.Z deposition in vivo. Our findings providecrucial insights into how SWR1 complex discriminates between the H2A-nucleosome and H2A.Z-nucleosome, establishing a simple paradigm for the governace of unidirectional H2A.Z exchange.
2021-04-12 | GSE171844 | GEO
Project description:The SWR1 complex replaces the canonical histone H2A with the variant H2A.Z (Htz1 in yeast) at specific chromatin regions. This dynamic alteration in nucleosome structure provides a molecular mechanism to regulate transcription. Here we analysed the transcription profiles of single and double mutants and wild-type cells by whole-genome microarray analysis. Our results indicate that genome-wide transcriptional misregulation in htz1∆ can be partially or totally suppressed if SWR1 is not formed (swr1∆), if it forms but cannot bind to chromatin (swc2∆), or if it binds to chromatin but has no histone replacement activity (swc5∆). These results suggest that in htz1∆ the nucleosome remodelling activity of SWR1 affects chromatin integrity because of an attempt to replace H2A with Htz1 in the absence of the latter. Three biological independent replicates were use for each strain
2011-05-18 | E-GEOD-21571 | biostudies-arrayexpress
Project description:The SWR1 complex replaces the canonical histone H2A with the variant H2A.Z (Htz1 in yeast) at specific chromatin regions. This dynamic alteration in nucleosome structure provides a molecular mechanism to regulate transcription. Here we analysed the transcription profiles of single and double mutants and wild-type cells by whole-genome microarray analysis. Our results indicate that genome-wide transcriptional misregulation in htz1∆ can be partially or totally suppressed if SWR1 is not formed (swr1∆), if it forms but cannot bind to chromatin (swc2∆), or if it binds to chromatin but has no histone replacement activity (swc5∆). These results suggest that in htz1∆ the nucleosome remodelling activity of SWR1 affects chromatin integrity because of an attempt to replace H2A with Htz1 in the absence of the latter.
2011-05-18 | GSE21571 | GEO
Project description:The histone variant H2A.Z is a genome-wide signature of nucleosomes proximal to eukaryotic regulatory DNA. While the multi-subunit SWR1 chromatin remodeling complex is known to catalyze ATP-dependent deposition of H2A.Z, the mechanism of recruitment to S. cerevisiae promoters has been unclear. A sensitive assay for competitive binding of di-nucleosome substrates revealed that SWR1 preferentially binds long nucleosome-free DNA adjoining core particles, allowing discrimination of gene promoters over gene bodies. We traced the critical DNA binding component of SWR1 to the conserved Swc2/YL1 subunit, whose activity is required for both SWR1 binding and H2A.Z incorporation in vivo. Histone acetylation by NuA4 enhances SWR1 binding, but the interaction with nucleosome-free DNA is the major determinant. ‘Hierarchical cooperation’ between high affinity DNA- and low affinity histone modification-binding factors may reconcile the large disparity in affinities for chromatin substrates, and unify classical control by DNA-binding factors with post-translational histone modifications and ATP-dependent nucleosome mobility. Swr1 TAP IF of various mutants
2013-09-16 | E-GEOD-49183 | biostudies-arrayexpress
Project description:In eukaryotes, DNA wraps around histones to form nucleosomes, which are compacted into chromatin. DNA-templated processes, including transcription, require chromatin disassembly and reassembly mediated by histone chaperones. Additionally, distinct histone variants can replace core histones to regulate chromatin structure and function. Although replacement of H2A with the evolutionarily conserved H2A.Z via the SWR1 histone chaperone complex has been extensively studied, in plants little is known about how a reduction of H2A.Z levels can be achieved. Here, we show that NRP proteins cause a decrease of H2A.Z-containing nucleosomes in Arabidopsis under standard growing conditions. nrp1-1 nrp2-2 double mutants show an over-accumulation of H2A.Z genome-wide, especially at heterochromatic regions normally H2A.Z-depleted in wild-type plants. Our work suggests that NRP proteins regulate gene expression by counteracting SWR1, thereby preventing excessive accumulation of H2A.Z.
2020-05-18 | PXD019248 | Pride
Project description:The histone variant H2A.Z is a genome-wide signature of nucleosomes proximal to eukaryotic regulatory DNA. While the multi-subunit SWR1 chromatin remodeling complex is known to catalyze ATP-dependent deposition of H2A.Z, the mechanism of recruitment to S. cerevisiae promoters has been unclear. A sensitive assay for competitive binding of di-nucleosome substrates revealed that SWR1 preferentially binds long nucleosome-free DNA adjoining core particles, allowing discrimination of gene promoters over gene bodies. We traced the critical DNA binding component of SWR1 to the conserved Swc2/YL1 subunit, whose activity is required for both SWR1 binding and H2A.Z incorporation in vivo. Histone acetylation by NuA4 enhances SWR1 binding, but the interaction with nucleosome-free DNA is the major determinant. ‘Hierarchical cooperation’ between high affinity DNA- and low affinity histone modification-binding factors may reconcile the large disparity in affinities for chromatin substrates, and unify classical control by DNA-binding factors with post-translational histone modifications and ATP-dependent nucleosome mobility.
2013-09-16 | GSE49183 | GEO
Project description:To investigate the incorporation dynamics of histone variant H2A.Z, we determined its genomic localization at single nucleosome resolution, as well as the localization of its chromatin remodelers Swr1 and Ino80. We find that Swr1 binding alone is a poor predictor of H2A.Z occupancy levels, and that normal Swr1 and Ino80 localization are actually dependent on H2A.Z. Additionally, we find that H2A.Z’s bimodal incorporation on either side of the NDR is not a general feature of TSS, but is specifically a marker for bidirectional transcription, such that the upstream flanking -1 H2A.Z-containing nucleosome is more appropriately considered as a +1 H2A.Z nucleosome for antisense transcription.
2019-10-29 | GSE104147 | GEO
Project description:A cascade of histone acetylation events with subsequent incorporation of a histone H2A variant plays an essential part in transcription regulation in various model organisms. A key player in this cascade is the chromatin remodellling complex SWR1, which replaces the canonical histone H2A with its variant H2A.Z. Transcriptional regulation of polycistronic transcription units in the unicellular parasite Trypanosoma brucei has been shown to be highly dependent on acetylation of H2A.Z, which is mediated by the histone-acetyltransferase HAT2. The chromatin remodellling complex, which mediates H2A.Z incorporation is not known and an SWR1 orthologue in trypanosomes has not yet been reported. In this study, we identified and characterised an SWR1-like remodelller complex in T. brucei that is responsible for Pol II-dependent transcriptional regulation. Bioinformatic analysis of potential SNF2 DEAD/Box helicases, the key component of SWR1 complexes, identified a 1211 amino acids-long protein that exhibits key structural characteristics of the SWR1 subfamily. Systematic protein-protein interaction analysis revealed the existence of a novel complex exhibiting key features of an SWR1-like chromatin remodelller. RNAi-mediated depletion of the ATPase subunit of this complex resulted in a significant reduction of H2A.Z incorporation at transcription start sites and a subsequent decrease of steady-state mRNA levels. Furthermore, depletion of SWR1 and RNA-polymerase II (Pol II) caused massive chromatin condensation. The potential function of several proteins associated with the SWR1-like complex and with HAT2, the key factor of H2A.Z incorporation, is discussed.
2022-08-12 | PXD026796 | Pride