Genome-wide maps of heterochromatin state (H3K9me2) in kinetochore and other centromere related mutants.
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PROVIDER: PRJNA483785 | ENA |
REPOSITORIES: ENA
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Project description:We report the high-throughput profiling of histone modification (H3K9me2) in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide H3K9me2 maps of fission yeast mutants with either deletions of non-essential kinetochore genes or conditional inactivation (temperature sensitive, ts) mutations in essential ones. We find that the impairment of the kinetochore componnets cause various levels (from no to prominent) of heterochroamatin spreading into centromeric core regions. Hence, we conclude that the integrity of the inner kinetochore is required to maintain normal centromeric chromatin organization as well as distinct centromere identity.
2019-09-28 | GSE117948 | GEO
Project description:We report the high-throughput profiling of histone modification (H3K9me2) or histone variant CNEP-A/Cnp1 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide H3K9me2 or CENP-A/Cnp1 maps of both mhf2∆ and mhf2+ carrying the inactivated Centromere 1 or Centromere 2 in fission yeast. We find that neocemtromeres are formed preferably at pericentromeric regions in single depletion of CENP-T-W-X-S.
2019-09-28 | GSE117955 | GEO
Project description:Chromosome segregation depends on proper attachment of sister kinetochores to microtubules. Merotelic kinetochore orientation is an error which occurs when a single kinetochore is attached to microtubules emanating form opposite poles. Mechanisms preventing or correcting the merotelic attachment must operate to avoid chromosome missegregation. Pcs1 has been implicated in preventing merotelic attachment in mitosis and meiosis II. We describe here the identification of Mde4 protein which forms a complex with the Pcs1. Both Mde4 and Pcs1 localize to the central core of the centromere. Similarly to the pcs1 mutant, in the absence of mde4 lagging chromosomes are frequently observed during mitosis and meiosis II . We provide the first evidence that the lagging chromosomes in pcs1 and mde4 mutants are due to merotelic kinetochore orientation. Keywords: ChIP-chip analysis ChIP-chip analysis: In all cases, hybridization data for ChIP fraction was compared with that of SUP (supernatant) fraction. Pombe whole chromosome array was used.
2010-06-10 | E-GEOD-5257 | biostudies-arrayexpress
Project description:Chromosome segregation depends on proper attachment of sister kinetochores to microtubules. Merotelic kinetochore orientation is an error which occurs when a single kinetochore is attached to microtubules emanating form opposite poles. Mechanisms preventing or correcting the merotelic attachment must operate to avoid chromosome missegregation. Pcs1 has been implicated in preventing merotelic attachment in mitosis and meiosis II. We describe here the identification of Mde4 protein which forms a complex with the Pcs1. Both Mde4 and Pcs1 localize to the central core of the centromere. Similarly to the pcs1 mutant, in the absence of mde4 lagging chromosomes are frequently observed during mitosis and meiosis II . We provide the first evidence that the lagging chromosomes in pcs1 and mde4 mutants are due to merotelic kinetochore orientation. Keywords: ChIP-chip analysis
2007-06-18 | GSE5257 | GEO
Project description:Heterochromatin is a tightly packed form of DNA, which is associated with histone 3 lysine 9 methylation (H3K9me). Here, we identify an H3K9me2 binding protein, Agenet domain (AGD)-containing protein 1 (AGDP1), in Arabidopsis thaliana. Our biochemical studies revealed that the AGDP1 can specifically recognize the H3K9me2 marks by the three pairs of tandem-AGDs. We determined the crystal structure of the AGD12 of Raphanus sativus AGDP1 in complex with an H3K9me2 peptide. In the complex, the histone peptide adopts a unique helical conformation. AGD12 employs a newly defined interacting interface to specifically recognize the H3K4me0 and H3K9me2 marks. In addition, we found that AGDP1 is required for transcriptional gene silencing, non-CG DNA methylation, and H3K9 dimethylation. Our ChIP-seq data showed that AGDP1 is enriched in TE regions and associated with the heterochromatin marks. Our findings suggest that, as a heterochromatin binding protein, AGDP1 links H3K9me2 to DNA methylation in heterochromatin regions.
2018-10-23 | GSE111609 | GEO
Project description:Centromeric chromatin is crucial for supporting kinetochore assembly and chromosome segregation. To specify centromeres, the histone H3 variant CENP-A is loaded by the conserved chaperone Scm3/HJURP. The amino-terminus of Scm3/HJURP interacts with CENP-A, while the carboxyl-terminus contains a small domain that interacts with the Mis18 holocomplex, which facilitates centromere localization. Fungal Scm3 proteins contain an additional conserved cysteine-rich domain (CYS) with unknown function. In this study, we found that CYS is essential for the localization and function of fission yeast Scm3. Disrupting CYS prevents Scm3 from localizing to the centromere and results in cell lethality. Moreover, introducing point mutations in a predicted zinc-binding motif within CYS hinders Scm3 centromere targeting and kinetochore integrity, consistent with structural evidence that CYS binds zinc. We find that expressing only the Scm3 carboxyl-terminus is harmful as it localizes to centromeres and causes defective kinetochores. Remarkably, mutating the CYS zinc-binding motif in this construct eliminates the observed centromere localization and toxicity. Together, our findings establish this cysteine-rich domain with predicted zinc-binding capability as an essential feature of fungal Scm3 proteins and shed new light on the molecular mechanism for targeting Scm3 to centromeres.
2024-03-06 | GSE231729 | GEO
Project description:The centromere is essential for the inheritance of genetic information on eukaryotic chromosomes. Epigenetic regulation of centromere identity has been implicated in genome stability, karyotype evolution and speciation. However, little is known regarding the manner in which centromere dysfunction affects the chromosomal architectures. Here we show that in the fission yeast Schizosaccharomyces pombe, the conditional deletion of the centromere produces survivors that carry either neocentromere-acquired chromosome at the sub-telomeric region or acentric chromosome rescued by inter-telomere fusion with other chromosome. The ratio of neocentromere formation to telomere fusion is considerably decreased by inactivation of genes involved in RNA interference (RNAi)-dependent heterochromatin formation. By affecting the modes of chromosomal reorganization, the genomic distribution of heterochromatin may influence the fate of karyotype evolution. Keywords: ChIP-chip
2008-08-22 | GSE10287 | GEO
Project description:Regulation of heterochromatin is critical for genome stability. Different states of methylated H3K9 have been discovered with distinct roles in heterochromatin formation and silencing. However, the control of the transition from H3K9me2 to H3K9me3 is still unclear. Here we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining the global nucleosome organization in fission yeast. We identified several key factors involved in heterochromatin silencing to interact genetically with Abo1: the histone deacetylase Clr3, the H3K9 methyltransferase Clr4, and the HP1 homologue Swi6. Cells lacking Abo1 display an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin had increased H3K9me2 but decreased H3K9me3 levels compared to wild type. In contrast, facultative heterochromatin regions, show both reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both centromeres and subtelomeres, but not in a subset of heterochromatin islands. Our work uncovers a new role for Abo1 in supporting Clr4 activity and allowing for the transition of H3K9me2 to H3K9me3 in telomeric and centromeric heterochromatin.
2020-04-13 | GSE125911 | GEO
Project description:Regulation of heterochromatin is critical for genome stability. Different states of methylated H3K9 have been discovered with distinct roles in heterochromatin formation and silencing. However, the control of the transition from H3K9me2 to H3K9me3 is still unclear. Here we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining the global nucleosome organization in fission yeast. We identified several key factors involved in heterochromatin silencing to interact genetically with Abo1: the histone deacetylase Clr3, the H3K9 methyltransferase Clr4, and the HP1 homologue Swi6. Cells lacking Abo1 display an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin had increased H3K9me2 but decreased H3K9me3 levels compared to wild type. In contrast, facultative heterochromatin regions, show both reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both centromeres and subtelomeres, but not in a subset of heterochromatin islands. Our work uncovers a new role for Abo1 in supporting Clr4 activity and allowing for the transition of H3K9me2 to H3K9me3 in telomeric and centromeric heterochromatin. We used microarrays to detail the global gene expression in wilde typ (Hu2185) and abo1∆ (Hu2318) strain with three temperature induction: 25°C (cold stress), 30°C(standard cultivation) and 37°C heat stress. We found silencing defect under in heterochromatin in abo1∆ deletion in all three conditions.
2020-04-13 | GSE125910 | GEO
Project description:Genome-wide maps of chromatin state (heterochromatin H3K9me2 or centromeric histone H3 variant CENP-A/Cnp1) in both mhf2∆ and mhf2+ carrying the inactivated Centromere 1 or Centromere 2.
| PRJNA483790 | ENA