Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide maps of heterochromatin state (H3K9me2) in kinetochore and other centromere related mutants.

ABSTRACT: 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.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE117948 | GEO | 2019/09/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

CENP-A chaperone Scm3HJURP contains a cysteine-rich domain required for centromere targeting and kinetochore integrity

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

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.

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

Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs

Project description:Retrotransposons have invaded eukaryotic centromeres in cycles of repeat expansion and purging, but the function of centromeric retrotransposons, if any, has remained unclear. In Arabidopsis, centromeric ATHILA retrotransposons give rise to epigenetically activated short interfering RNAs (easiRNAs) in mutants in DECREASE IN DNA METHYLATION1 (DDM1), which promote histone H3 lysine-9 di-methylation (H3K9me2). Here, we show that mutants which lose both DDM1 and RNA dependent RNA polymerase (RdRP) have pleiotropic developmental defects and mis-segregation of chromosome 5 during mitosis. Fertility defects are epigenetically inherited with the centromeric region of chromosome 5, and can be rescued by directing artificial small RNAs to a single family of ATHILA5 retrotransposons specifically embedded within this centromeric region. easiRNAs and H3K9me2 promote pericentromeric condensation, chromosome cohesion and proper chromosome segregation in mitosis. Insertion of ATHILA silences transcription, while simultaneously making centromere function dependent on retrotransposon small RNAs, promoting the selfish survival and spread of centromeric retrotransposons. Parallels are made with the fission yeast S. pombe, where chromosome segregation depends on RNAi, and with humans, where chromosome segregation depends on both RNAi and HELLSDDM1.

2022-10-24 | GSE132005 | GEO

Heat-shock molecular chaperone Hsp90 is involved in heterochromatin assembly in Schizosaccharomyces pombe.

Project description:Here, we report the high-throughput profiling of histone modification (H3K9me2) in fission yeast Schizosaccharomyces pombe. We generated genome-wide H3K9me2 maps of fission yeast mutants in swo1-26 (temperature sensitive, ts) cells at 25℃ and 37℃. We find that H3K9me2 enrichment at heterochromatin regions, especially at the mating-type locus and subtelomeres, is compromised, suggesting heterochromatin assembly defects.

2020-06-18 | GSE140617 | GEO

Centromere-Like Regions in Budding Yeast

Project description:Accurate chromosome segregation requires centromeres (CENs), the chromosomal sites where kinetochores form, to bridge DNA and attach to microtubules. In contrast to most eukaryotes, Saccharomyces cerevisiae possesses sequence-defined point centromeres. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) of four kinetochore components reveals regions of overlapping, extra-centromeric protein localization upon overproduction of the centromeric histone, Cse4 (CENP-A or CenH3). These identified sequences enhance proper plasmid and chromosome segregation, and are termed Centromere-like Regions (CLRs). CLRs form in close proximity to S. cerevisiae CENs and share characteristics typical of point and regional centromeres. CLR sequences are conserved among related budding yeasts, suggesting a role in vivo. These studies provide new insights into the origin and evolution of centromeres. ChIP-Seq analysis of the kinetochore components Cse4, Mif2, Ndc10 and Ndc80 in budding yeast strains (Saccharomyces cerevisiae) with normal and elevated levels of Cse4

2013-01-18 | E-GEOD-31466 | biostudies-arrayexpress

Genome wide map of H3K9me2 in fission yeast Schizosaccharomyces pombe.

Project description:Genome wide map of H3K9me2 in 4 different strains of fission yeast Schizosaccharomyces pombe.

2019-01-03 | GSE119604 | GEO

Abo1 is required for H3K9me2 to H3K9me3 transition in telomeric and centromeric heterochromatin [ChIP-seq]

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

Genome-wide maps of heterochromatin state (H3K9me2) in kinetochore and other centromere related mutants.

Project description:Genome-wide maps of heterochromatin state (H3K9me2) in kinetochore and other centromere related mutants.

| PRJNA483785 | ENA

The Ino80 complex mediates epigenetic centromere propagation via active removal of histone H3

Project description:Centromere is the chromosomal locus at which kinetochore is assembled to direct chromosome segregation. Histone H3 variant CENP-A epigenetically marks active centromeres; however, the mechanism by which CENP-A propagates at the centromere, replacing histone H3, remains poorly understood. Using fission yeast, we find that CENP-ACnp1 chromatin assembly at the centromere requires the Ino80 ATP-dependent chromatin remodeling complex which removes histone H3-containing nucleosomes from associated chromatin. CENP-ACnp1 chromatin actively recruits the Ino80 complex to centromeres to elicit eviction of histone H3-containing nucleosomes. Artificial targeting of Ino80 subunits to a non-centromeric DNA placed in a native centromere enhances the spreading of CENP-ACnp1 chromatin into the non-centromeric DNA. Based on these results, we propose that CENP-ACnp1 chromatin employs the Ino80 complex to mediate replacement of histone H3 with CENP-ACnp1, and thereby reinforces itself.

2017-07-14 | GSE99589 | GEO

Bub1 and CENP-U redundantly recruit Plk1 to stabilize kinetochore-microtubule attachments and ensure accurate chromosome segregation

Project description:Bub1 is required for the kinetochore/centromere localization of two essential mitotic kinases Plk1 and Aurora B. Surprisingly, stable depletion of Bub1 by ~95% in human cells marginally affects whole chromosome segregation fidelity. We show that CENP-U, which is recruited to kinetochores by the CENP-P and CENP-Q subunits of the CENP-O complex, is required to prevent chromosome mis-segregation in Bub1-depleted cells. Mechanistically, Bub1 and CENP-U redundantly recruit Plk1 to kinetochores to stabilize kinetochore-microtubule attachments, thereby ensuring accurate chromosome segregation. Furthermore, unlike its budding yeast homolog, the CENP-O complex does not regulate centromeric localization of Aurora B. Consistently, depletion of Bub1 or CENP-U sensitizes cells to the inhibition of Plk1 but not Aurora B kinase activity. Taken together, our findings provide mechanistic insight into the regulation of kinetochore function, which may have implications for targeted treatment of cancer cells with mutations perturbing kinetochore recruitment of Plk1 by Bub1 or the CENP-O complex.

2021-08-29 | GSE182827 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data