Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Antisense Transcripts in Mutant Strains

ABSTRACT: The positioning of the nucleosome by ATP-dependent nucleosome remodelers provides the fundamental chromatin environment for the regulation of diverse cellular processes acting on the underlying DNA. Here, we report that the fission yeast CHD remodeler, Hrp3, is a global regulator that drives higher-order chromatin structure and genomic stability. The loss of Hrp3 resulted in the production of antisense transcripts and perturbation of the nucleosome in an ATPase mutant of Hrp3 was also associated with destabilization of the DNA-histone interaction. Furthermore, the effect of Hrp3 in the pericentric region was found to be accomplished via a physical interaction with Swi6, and appeared to cooperate with other heterochromatin factors for gene silencing. Taken together, our data indicate that a well-positioned nucleosome is important for the spatial-temporal control of transcription-associated processes, and show that this is accomplished by the chromatin remodeler, Hrp3, in fission yeast.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE37697 | GEO | 2012/05/08

SECONDARY ACCESSION(S): PRJNA163863

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Antisense Transcripts in Mutant Strains

Project description:The positioning of the nucleosome by ATP-dependent nucleosome remodelers provides the fundamental chromatin environment for the regulation of diverse cellular processes acting on the underlying DNA. Here, we report that the fission yeast CHD remodeler, Hrp3, is a global regulator that drives higher-order chromatin structure and genomic stability. The loss of Hrp3 resulted in the production of antisense transcripts and perturbation of the nucleosome in an ATPase mutant of Hrp3 was also associated with destabilization of the DNA-histone interaction. Furthermore, the effect of Hrp3 in the pericentric region was found to be accomplished via a physical interaction with Swi6, and appeared to cooperate with other heterochromatin factors for gene silencing. Taken together, our data indicate that a well-positioned nucleosome is important for the spatial-temporal control of transcription-associated processes, and show that this is accomplished by the chromatin remodeler, Hrp3, in fission yeast. Two-condition experiment, Mutant vs Wild-type (control)

2012-05-07 | E-GEOD-37697 | biostudies-arrayexpress

Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin [MNase-Seq]

Project description:We report that the Schizosaccharomyces pombe CHD remodeler, Hrp3, is a global regulator that drives higher-order chromatin structure and genomic stability. The loss of Hrp3 resulted in nucleosome perturbation across the chromosome, and the production of antisense transcripts in the hrp3∆ cells emphasized the importance of nucleosome architecture for proper transcription

2012-10-02 | GSE40451 | GEO

Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin [MNase-Seq]

Project description:We report that the Schizosaccharomyces pombe CHD remodeler, Hrp3, is a global regulator that drives higher-order chromatin structure and genomic stability. The loss of Hrp3 resulted in nucleosome perturbation across the chromosome, and the production of antisense transcripts in the hrp3M-bM-^HM-^F cells emphasized the importance of nucleosome architecture for proper transcription Examination of nucleosome positions in wild-type and mutants using the MNase-seq method

2012-10-02 | E-GEOD-40451 | biostudies-arrayexpress

Hrp3-TAP_Purification from Schizosaccharomyces pombe

Project description:Hrp3_Purification from Schizosaccharomyces pombe 972h- Eukaryotic genome is composed of repeating units of nucleosomes to form chromatin arrays. A canonical gene is marked by nucleosome free region (NFR) at its 5’ end followed by uniformly spaced arrays of nucleosomes. In fission yeast we show both biochemically and in vivo that both Hrp1 and Hrp3 are key determinants of uniform spacing of genic arrays.

2014-05-16 | PXD000041 | Pride

Molecular mechanism of repression of meiotic recombination around centromeres

Project description:In most eukaryotes, meiotic crossovers are essential for error-free chromosome segregation but are specifically repressed near centromeres to prevent missegregation. Recognized for >85 years, the molecular mechanism of this repression has remained unknown. Meiotic chromosomes contain two distinct cohesin complexes: pericentric complex (for segregation) and chromosomal arm complex (for crossing-over). We show that the pericentric-specific complex also actively represses pericentric meiotic double-strand break (DSB) formation and, consequently, crossovers. The fission yeast pericentric regions contain heterochromatin, removal of which can result in derepression in double-strand break formation and recombination during meiosis. We uncover the mechanism by which fission yeast heterochromatin protein Swi6 (mammalian HP1-homolog) prevents recruitment of activators of meiotic DSB formation such as Rec10. Localizing these missing activators to wild-type pericentromeres bypasses repression and generates abundant crossovers but reduces gamete viability.The molecular mechanism elucidated here likely extends to other species including humans, where pericentric crossovers can result in disorders such as Down syndrome. These mechanistic insights provide new clues to understand the roles played by multiple cohesin complexes, especially in human infertility and birth defects.

2018-06-14 | GSE115726 | GEO

Small RNA expression in swi6 mutants or dcr1 delta fission yeast Schizosaccharomyces pombe

Project description:Small RNA expression in swi6 mutants, dcr1 delta, and wild type fission yeast Schizosaccharomcyces pombe wild type, swi6 mutant, and dcr1 delta mutant

2013-07-20 | E-GEOD-42849 | biostudies-arrayexpress

Small RNA expression in swi6 mutants or dcr1 delta fission yeast Schizosaccharomyces pombe

Project description:Small RNA expression in swi6 mutants, dcr1 delta, and wild type fission yeast Schizosaccharomcyces pombe

2013-07-20 | GSE42849 | GEO

Nucleosome recognition and DNA distortion by the Chd1 remodeler revealed at 2.6 Å resolution

Project description:Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. The Chd1 remodeler specializes in shifting nucleosomes into evenly spaced arrays, a defining characteristic of chromatin in gene bodies that blocks spurious transcription initiation. Linked to some forms of autism and commonly mutated in prostate cancer, Chd1 is essential for maintaining pluripotency in stem cells. Here we report a complex of yeast Chd1 bound to a nucleosome in a nucleotide-free state, determined by cryo-electron microscopy (cryo-EM) to 2.6 Å resolution. The structure shows a bulge of the DNA tracking strand where the ATPase motor engages the nucleosome, consistent with an initial stage in DNA translocation. Unlike other remodeler-nucleosome complexes, nucleosomal DNA compensates for the remodeler-induced bulge with a bulge of the complementary DNA strand one helical turn downstream from the ATPase motor. Unexpectedly, the structure also reveals an N-terminal binding motif, called ChEx, which binds on the exit-side acidic patch of the nucleosome. The ChEx motif can displace a LANA-based peptide from the acidic patch, which suggests a means by which Chd1 remodelers may block competing chromatin remodelers from acting on the opposite side of the nucleosome.

2022-02-23 | PXD025287 | Pride

Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription

Project description:Proper chromatin organization is essential for defining transcription units and maintaining genomic integrity in eukaryotes. Mutations affecting the chromatin structure can lead to increased cryptic transcription and genomic instability. In this study we found that deletion of the Schizosaccharomyces pombe Chd1-type chromatin remodelers, hrp1 and hrp3, causes strong, genome-wide accumulation of antisense transcripts, while the amount of coding mRNA transcripts is mostly unaffected. Nucleosome mapping revealed a specific role for Chd1-remodelers in the positioning of nucleosomes in gene coding regions. While the arrangement of nucleosomes in promoter regions was similar to WT, nucleosome organization within coding regions was remarkably irregular in hrp1∆hrp3∆ strain. We extended our analysis to other mutations associated with enhanced cryptic transcription activity, such as set2∆, alp13∆, and FACT complex subunit pob3∆. While nucleosomes were severely depleted in the pob3∆ strain, nucleosome positioning was less affected. In sharp contrast, nucleosome organization in the alp13∆ and set2∆ strains was indistinguishable from WT. These data indicate multiple mechanisms in the repression of cryptic promoter activity in eukaryotic cells. Genome-wide profiling of H3K9/K14 acetylation Genome-wide expression analysis of either Alp13-, Set2-, Hrp3 or Hrp1 and Hrp3-deficient cells Genome-wide expression analysis of either Hrp1, Hrp3, or Hrp1 and Hrp3-deficient cells Nucleosome mapping experiments

2012-09-15 | GSE40872 | GEO

The INO80 complex regulates epigenetic inheritance of heterochromatin (ChIP-seq, Mnase-seq)

Project description:One key aspect of epigenetic inheritance is that chromatin structure can be stably inherited through generations even after removal of the signal that establishes such structure. In fission yeast, the RNA interference (RNAi) machinery is critical for initial targeting of histone methyltransferase Clr4 to pericentric repeats to establish heterochromatin. However, pericentric heterochromatin cannot be properly inherited in the absence of RNAi, suggesting the existence of mechanisms that counteract chromatin structure inheritance. Here we show that in the absence of certain components of the INO80 chromatin-remodeling complex, pericentric heterochromatin can be properly inherited in RNAi mutants. The ability of INO80 to counter heterochromatin inheritance is attributed to one accessory subunit Iec5, which promotes histone turnover at heterochromatin regions, but has little effects on nucleosome positioning at heterochromatin, gene expression, or the DNA damage response. Slow histone turnover preserves parental histones at repeat regions to enhance epigenetic inheritance of heterochromatin not only in RNAi mutants but also in wild type cells. Our analyses demonstrate the importance of INO80 in controlling heterochromatin inheritance and maintaining the proper heterochromatin landscape of the genome.

2020-11-18 | GSE150542 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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