Transcriptional impact of removing H2A.Z
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE46535 | GEO | 2016/06/01
SECONDARY ACCESSION(S): PRJNA200795
REPOSITORIES: GEO
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Project description:We profiled the strand-specific transcriptome of Saccharomyces cerevisiae lacking SWR1 and HTZ1 and compared it to the wild-type transcriptome 3'-end RNA-seq was performed on RNA from Saccharomyces cerevisiae wild-type and swr1 htz1 strains (two biological replicates each)
2016-06-01 | E-GEOD-46535 | 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. 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:Among the collection of chromatin modifications that influence its function and structure, the substitution of canonical histones by the so-called histone variants is one of the most prominent actions. Since crucial meiotic transactions are modulated by chromatin, here we investigate the functional contribution of the H2A.Z histone variant during both unperturbed meiosis and upon challenging conditions where the meiotic recombination checkpoint is triggered in budding yeast by the absence of the synaptonemal complex component Zip1. We have found that H2A.Z localizes to meiotic chromosomes in an SWR1-dependent manner. Although meiotic recombination is not substantially altered, the htz1 mutant (lacking H2A.Z) shows slower meiotic progression, impaired sporulation and reduced spore viability. These phenotypes are likely accounted for by the misregulation of meiotic gene expression landscape observed in htz1. In the zip1 mutant, the absence of H2A.Z results in a tighter meiotic arrest imposed by the meiotic recombination checkpoint. We have found that Mec1-dependent Hop1-T318 phosphorylation and the ensuing Mek1 activation are not significantly altered in zip1 htz1; however, downstream checkpoint targets, such as the meiosis I-promoting factors Ndt80, Cdc5 and Clb1, are drastically down-regulated. The study of the checkpoint response in zip1 htz1 has also allowed us to reveal the existence of an additional function of the Swe1 kinase, independent of CDK inhibitory phosphorylation, which is relevant to restrain meiotic cell cycle progression. In summary, our study shows that the H2A.Z histone variant impacts various aspects of meiotic development adding further insight into the relevance of chromatin dynamics for accurate gametogenesis.
2018-02-02 | GSE110022 | GEO
Project description:The goals of this study are to compare Next-Generation-Sequecing (NGS)-derived genome-wide occupancy of TAF (Taf1) comparing with other basal initiation components (TBP and TFIIB), histones (H3, H4, Htz1 and H4 acetylation) and histone regulator complexes (Swr1, Bdf1) in S. cerevisiae.
2017-02-14 | GSE94851 | GEO
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:Actin-related proteins are ubiquitous components of chromatin remodelers, and are conserved from yeast to man. We have examined the role of the budding yeast actin-related protein Arp6 in gene expression, both as a component of the SWR1 complex (SWR-C) and in its absence. We mapped Arp6-binding sites genome-wide using chromatin immunoprecipitation in mutant and wild-type cells. We find that the majority of Arp6-binding sites in euchromatin coincide with binding sites of Swr1, the catalytic subunit of SWR-C, and with the histone H2A variant Htz1. However, the remaining Arp6 binding in telomeres, centromeres, and the promoters of ribosomal protein (RP) genes are independent of Swr1 and Htz1 deposition. We show that Arp6 can position chromatin at nuclear pores, and is required for the pore association of the RP genes to which it binds. This anchoring is also independent of Swr1. Loss of Arp6, but not Htz1, leads to an up-regulation of RP genes and loss of relocalization. This is in contrast to the Htz1-mediated pore-association of GAL1, for which loss of Arp6 impairs activation. Given that Arp6 is required for SWR-C dependent deposition of Htz1, we conclude that Arp6 contributes to both H2AZ-dependent and H2AZ-independent association with nuclear pores and subsequent effects on gene expression. These data illustrate how nuclear actin-related proteins contribute to the long-range organization of chromatin domains in the interphase nucleus. Four replicates for the arp6 deletion mutant and three replicates for the swr1 deletion mutant compared to wild-type.
2010-05-01 | E-GEOD-17780 | biostudies-arrayexpress
Project description:The H2A.Z histone variant is deposited into chromatin by the SWR1 complex affecting multiple aspects of meiosis. Here we describe a SWR1-independent localization of H2A.Z at meiotic telomeres and the centrosome. We demonstrate that H2A.Z colocalizes and interacts with Mps3, the SUN component of the LINC complex that spans the nuclear envelope and links meiotic telomeres to the cytoskeleton promoting meiotic chromosome movement. H2A.Z also interacts with the meiosis-specific Ndj1 protein that anchors telomeres to the nuclear periphery via Mps3. Telomeric localization of H2A.Z depends on Ndj1 and the N-terminal domain of Mps3. Although telomeric attachment to the nuclear envelope is maintained in the absence of H2A.Z, the distribution of Mps3 is altered. The velocity of chromosome movement during meiotic prophase I is reduced in the htz1? mutant lacking H2A.Z, but it is unaffected in swr1? cells. We reveal that H2A.Z is an additional LINC-associated factor that contributes to promote telomere-driven chromosome motion critical for error-free gametogenesis.
2020-11-16 | GSE153003 | GEO
Project description:Actin-related proteins are ubiquitous components of chromatin remodelers, and are conserved from yeast to man. We have examined the role of the budding yeast actin-related protein Arp6 in gene expression, both as a component of the SWR1 complex (SWR-C) and in its absence. We mapped Arp6-binding sites genome-wide using chromatin immunoprecipitation in mutant and wild-type cells. We find that the majority of Arp6-binding sites in euchromatin coincide with binding sites of Swr1, the catalytic subunit of SWR-C, and with the histone H2A variant Htz1. However, the remaining Arp6 binding in telomeres, centromeres, and the promoters of ribosomal protein (RP) genes are independent of Swr1 and Htz1 deposition. We show that Arp6 can position chromatin at nuclear pores, and is required for the pore association of the RP genes to which it binds. This anchoring is also independent of Swr1. Loss of Arp6, but not Htz1, leads to an up-regulation of RP genes and loss of relocalization. This is in contrast to the Htz1-mediated pore-association of GAL1, for which loss of Arp6 impairs activation. Given that Arp6 is required for SWR-C dependent deposition of Htz1, we conclude that Arp6 contributes to both H2AZ-dependent and H2AZ-independent association with nuclear pores and subsequent effects on gene expression. These data illustrate how nuclear actin-related proteins contribute to the long-range organization of chromatin domains in the interphase nucleus.
2010-05-01 | GSE17780 | GEO