Neurospora crassa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA283990 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2026380.fastq.gz | Fastqsanger.gz | |||
| SRR2026390.fastq.gz | Fastqsanger.gz | |||
| SRR2026371.fastq.gz | Fastqsanger.gz | |||
| SRR2026381.fastq.gz | Fastqsanger.gz | |||
| SRR2026391.fastq.gz | Fastqsanger.gz |
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Project description:Methylated lysine 27 on histone H3 (H3K27me) marks repressed "facultative heterochromatin", including developmentally regulated genes in plants and animals. The mechanisms responsible for localization of H3K27me are largely unknown, perhaps in part because of the complexity of epigenetic regulatory networks. We used a relatively simple model organism bearing both facultative and constitutive heterochromatin, Neurospora crassa, to explore possible interactions between elements of heterochromatin. In higher eukaryotes, reductions of H3K9me3 and DNA methylation in constitutive heterochromatin have been variously reported to cause redistribution of H3K27me3. In Neurospora, we found that elimination of any member of the DCDC H3K9 methylation complex (DIM-5, DIM-7, CUL4, DDB1/DIM-8 or DIM-9) caused massive changes in the distribution of H3K27me; regions of facultative heterochromatin lost H3K27me3 while regions that are normally marked by H3K9me3 became methylated at H3K27. Elimination of DNA methylation by deletion of the DNA methyltransferase gene, dim-2, had no obvious effect on the distribution of H3K27me. Elimination of HP1, which "reads" H3K9me3, also caused major changes in the distribution of H3K27me, indicating that HP1 is important for normal localization of facultative heterochromatin. Because loss of HP1 caused redistribution of H3K27me2/3 but not H3K9me3, these normally non-overlapping marks became superimposed. Indeed, mass spectrometry revealed substantial cohabitation of H3K9me3 and H3K27me2 on H3 molecules from an hpo strain. Loss of H3K27me machinery (e.g. the methyltransferase SET-7) did not impact constitutive heterochromatin, but partially rescued the slow growth of the DCDC mutants, suggesting that the poor growth of these mutants is partly attributable to ectopic H3K27me. Altogether, our findings with Neurospora clarify interactions of facultative and constitutive heterochromatin in eukaryotes.
2015-11-03 | GSE68897 | GEO
Project description:Facultative heterochromatin in the filamentous fungus Neurospora crassa is identified by the repressive histone mark H3K27me3 and is primarily subtelomeric, while constitutive heterochromatin, marked by the DIM-5-catalzyed H3K9me3, is found at centromeres, telomeres, and smaller dispersed regions. In strains lacking constitutive heterochromatin (e.g., Δdim-5), H3K27me2/3 relocalizes to the regions formerly marked by H3K9me3. H3K27me3 is catalyzed by the SET-7 histone methyltransferase subunit of the Polycomb Repressive Complex 2 (PRC2); another PRC2 member, Neurospora p55 (NPF) regulates subtelomeric H3K27me2/3. Despite the de-repression of >70 genes, a Δset-7 strain has no distinguishable phenotype. To investigate the facultative heterochromatin contribution to genome organization, we performed high-throughput “chromosome conformation capture” (Hi-C) on mutants with impacted H3K27me2/3 deposition. A Δset-7 strain has decreased inter-/intra-subtelomeric contacts among others; this pattern is mirrored in a Δnpf strain, which lacks subtelomeric H3K27me3. In a Δset-7 strain, telomere bundles were often uncoupled from the nuclear membrane and de-repressed genes were subtelomeric. The chromosome conformation of a Δset-7;Δdim-5 double mutant was similar to Δset-7, suggesting that facultative heterochromatin relocalization does not compensate for H3K9me3 loss and rescue the Neurospora genome organization in strains with defective constitutive heterochromatin.
2016-10-27 | GSE82222 | GEO
Project description:Polycomb group proteins assemble into chromatin modifying complexes that regulate stem cell identity and multicellular development. The trimethylation of lysine 27 on histone H3 (H3K27me3) is catalyzed by the conserved Polycomb Repressive Complex 2 (PRC2). In Neurospora crassa, the typically-subtelomeric pattern of H3K27me3 depends on other chromatin regulators including the H3K36 methyltransferase ASH1, the chromatin remodeling enzyme IMITATION SWITCH, and components of constitutive heterochromatin including the H3K9 methyltransferase DEFECTIVE IN METHYLATION-5 and the H3K9me3-binding protein HETEROCHROMATIN PROTEIN 1 (HP1). How constitutive heterochromatin impacts PRC2 activity is unclear. HP1 forms multiple protein complexes including the HCHC complex, which removes acetyl groups from histones in constitutive heterochromatin, and contains the proteins Histone Deacetylase 1(HDA-1) and Chromodomain Protein-2 (CDP-2). To identify genes required for Polycomb repression in N. crassa, we performed a genetic screen and identified HDA-1 as necessary for PRC2-targeted gene silencing. In the absence of HDA-1, H3K27me2/3 is lost from the subtelomeres and aberrantly accumulates at constitutive heterochromatin domains normally enriched for H3K9me3; CDP-2 is also important for wildtype H3K27me3 localization. The H3K27me2/3 redistribution in Δhda-1 or Δcdp-2 strains is variable and incomplete, and mutant progeny obtained following a sexual cross displayed wild-type H3K27me3 patterns, consistent with HCHC loss leading to progressive changes in H3K27me3 enrichment. Indeed, a newly constructed ∆hda-1 deletion strain displays a wild-type H3K27me3 pattern that relocalizes to constitutive heterochromatic regions after sequential passages. Thus, HCHC-specific deacetylation prevents aberrant recruitment of PRC2 to constitutive heterochromatin.
2025-01-21 | GSE286535 | GEO
Project description:Polycomb group proteins assemble into chromatin modifying complexes that regulate stem cell identity and multicellular development. The trimethylation of lysine 27 on histone H3 (H3K27me3) is catalyzed by the conserved Polycomb Repressive Complex 2 (PRC2). In Neurospora crassa, the typically-subtelomeric pattern of H3K27me3 depends on other chromatin regulators including the H3K36 methyltransferase ASH1, the chromatin remodeling enzyme IMITATION SWITCH, and components of constitutive heterochromatin including the H3K9 methyltransferase DEFECTIVE IN METHYLATION-5 and the H3K9me3-binding protein HETEROCHROMATIN PROTEIN 1 (HP1). How constitutive heterochromatin impacts PRC2 activity is unclear. HP1 forms multiple protein complexes including the HCHC complex, which removes acetyl groups from histones in constitutive heterochromatin, and contains the proteins Histone Deacetylase 1(HDA-1) and Chromodomain Protein-2 (CDP-2). To identify genes required for Polycomb repression in N. crassa, we performed a genetic screen and identified HDA-1 as necessary for PRC2-targeted gene silencing. In the absence of HDA-1, H3K27me2/3 is lost from the subtelomeres and aberrantly accumulates at constitutive heterochromatin domains normally enriched for H3K9me3; CDP-2 is also important for wildtype H3K27me3 localization. The H3K27me2/3 redistribution in Δhda-1 or Δcdp-2 strains is variable and incomplete, and mutant progeny obtained following a sexual cross displayed wild-type H3K27me3 patterns, consistent with HCHC loss leading to progressive changes in H3K27me3 enrichment. Indeed, a newly constructed ∆hda-1 deletion strain displays a wild-type H3K27me3 pattern that relocalizes to constitutive heterochromatic regions after sequential passages. Thus, HCHC-specific deacetylation prevents aberrant recruitment of PRC2 to constitutive heterochromatin.
2025-01-21 | GSE286537 | GEO
Project description:Eukaryotic chromatin is organized into compartments for gene expression regulation, but the underlying mechanisms remain unclear. Here, we demonstrate that multivalent H3K27me3 and its reader, CBX7-PRC1, regulate facultative heterochromatin via a phase separation mechanism, similar to constitutive heterochromatin. Facultative and constitutive heterochromatin represent distinct, coexisting repressive condensates in nuclei. H3K27me3- and H3K9me3-marked nucleosomal arrays and their reader complexes phase separate into immiscible condensates, analogous to the relationship between facultative and constitutive heterochromatin in vivo. Overexpression of CBX7-PRC1 causes aberrant chromatin compartmentalization in vivo and up-regulation of cancer-related genes. CBX7 inhibitor effectively inhibits cancer cell proliferation possibly through phase separation-mediated compartment reorganization. Our data suggest that histone marks mediate chromatin compartmentalization via phase separation, and offer potential epigenetic mechanistic insights into tumor development and cancer therapy.
2025-04-07 | GSE241262 | GEO
Project description:Facultative heterochromatin is formed by Polycomb repressive complex 2 (PRC2)-deposited H3K27 tri-methylation (H3K27me3) and PRC1-deposited H2AK119 mono-ubiquitylation (H2AK119ub1). How it is newly established after fertilization remains unclear. To delineate the establishment kinetics, here we profiled the temporal dynamics of H3K27 di-methylation (H3K27me2), which represents the de novo PRC2 catalysis, in mouse preimplantation embryos. H3K27me2 is newly deposited at CpG islands (CGIs), the paternal X-chromosome (Xp), and putative enhancers during the 8-cell-to-morula transition, all of which follow H2AK119ub1 deposition. We found that JARID2, a PRC2.2-specific accessory protein possessing an H2AK119ub1-binding ability, colocalizes with SUZ12 at CGIs and Xp in morula embryos. Upon JARID2 depletion, SUZ12 chromatin binding and H3K27me2 deposition were attenuated and H3K27 acetylation was increased at putative enhancers in morulae, and subsequently H3K27me3 failed to be deposited in blastocysts. These data reveal that facultative heterochromatin is established by PRC2.2-driven stepwise H3K27 methylation along pre-deposited H2AK119ub1 during early embryogenesis.
2024-09-05 | GSE263441 | GEO
Project description:Facultative heterochromatin is formed by Polycomb repressive complex 2 (PRC2)-deposited H3K27 tri-methylation (H3K27me3) and PRC1-deposited H2AK119 mono-ubiquitylation (H2AK119ub1). How it is newly established after fertilization remains unclear. To delineate the establishment kinetics, here we profiled the temporal dynamics of H3K27 di-methylation (H3K27me2), which represents the de novo PRC2 catalysis, in mouse preimplantation embryos. H3K27me2 is newly deposited at CpG islands (CGIs), the paternal X-chromosome (Xp), and putative enhancers during the 8-cell-to-morula transition, all of which follow H2AK119ub1 deposition. We found that JARID2, a PRC2.2-specific accessory protein possessing an H2AK119ub1-binding ability, colocalizes with SUZ12 at CGIs and Xp in morula embryos. Upon JARID2 depletion, SUZ12 chromatin binding and H3K27me2 deposition were attenuated and H3K27 acetylation was increased at putative enhancers in morulae, and subsequently H3K27me3 failed to be deposited in blastocysts. These data reveal that facultative heterochromatin is established by PRC2.2-driven stepwise H3K27 methylation along pre-deposited H2AK119ub1 during early embryogenesis.
2024-09-05 | GSE264193 | GEO
Project description:Heterochromatin remodeling is critical for various cell processes. In particular, the “loss of heterochromatin” phenotype in cellular senescence engages with the progress of aging and age-related disorders. Although biological processes of senescent cells including senescence-associated heterochromatin foci (SAHF) formation, chromosome compaction and entry into senescence have been closely associated with high-order chromatin structure. the relationship between the high-order chromatin organization and the loss of heterochromatin phenotype during senescence has not been fully understood. By using senescent and late senescent fibroblasts induced by DNA damage harboring the “loss of heterochromatin” phenotype, we observed progressive 3D reorganization of heterochromatin during senescence. Facultative and constitutive heterochromatin marked by H3K27me3 and H3K9me3, respectively, showed different alterations. Facultative heterochromatin tends to switch from the repressive B-compartment to the active A-compartment, whereas constitutive heterochromatin shows no significant changes at the compartment level but enhanced interactions between themselves. Interestingly, both types show increased chromatin accessibility and gene expression leakage during senescence. Furthermore, increased chromatin accessibility in potential CTCF binding sites accompanies by the establishment of novel loops in constitutive heterochromatin. Finally, we also observed aberrant expression of repetitive elements, including LTR (long terminal repeat) and satellite classes. Overall, facultative and constitutive heterochromatin show multiscale but distinct alterations in the 3D map, meanwhile they also share the same features of increased chromatin accessibility and gene expression leakage. This study provides an epigenomic map of heterochromatin reorganization during senescence.
2019-12-31 | GSE133292 | GEO
Project description:Development in higher organisms requires selective gene silencing, directed in part by di-/tri-methylation of lysine 27 on histone H3 (H3K27me2/3). Knowledge of the cues that control formation of such repressive Polycomb domains is extremely limited. We exploited natural and engineered chromosomal rearrangements in the fungus Neurospora crassa to elucidate the control of H3K27me2/3. Analyses of H3K27me2/3 in strains bearing chromosomal rearrangements revealed both position-dependent and position-independent facultative heterochromatin. We found that proximity to chromosome ends is necessary to maintain, and sufficient to induce, transcriptionally repressive, subtelomeric H3K27me2/3. We ascertained that such telomere-proximal facultative heterochromatin requires native telomere repeats and found that a short array of ectopic telomere repeats, (TTAGGG)17, can induce a large domain (~225 kb) of H3K27me2/3. This provides an example of a cis-acting sequence that directs H3K27 methylation. Our findings provide new insight into the relationship between genome organization and control of heterochromatin formation.
2017-12-29 | GSE104019 | GEO
Project description:Polycomb group (PcG) proteins assemble into chromatin modifying complexes that regulate stem cell identity and multicellular development. The trimethylation of lysine 27 on histone H3 (H3K27me3) is catalyzed by the conserved Polycomb Repressive Complex 2 (PRC2). In Neurospora crassa, the typically-subtelomeric pattern of H3K27me3 depends on other chromatin regulators including the H3K36 methyltransferase ASH1, the chromatin remodeling enzyme IMITATION SWITCH, and components of constitutive heterochromatin including the H3K9 methyltransferase DEFECTIVE IN METHYLATION-5 (DIM-5) and the H3K9me3-binding protein HETEROCHROMATIN PROTEIN 1 (HP1). How constitutive heterochromatin impacts PRC2 activity is unclear. We performed a genetic screen to identify histone deacetylase genes required to repress PRC2-methylated genes in N. crassa. We found that HISTONE DEACETYLASE-1 (HDA-1) is required for transcriptional repression in PcG-repressed domains and for normal patterns of H3K27me3. In the absence of HDA-1, H3K27me3 is lost from typical PRC2-methylated domains and instead is enriched at a subset of constitutive heterochromatin domains normally marked for H3K9me3. In addition to altered H3K27me3 patterns, HDA-1-deficient mutants displayed aberrant patterns of H3K9me3, H3K36me3, and lysine acetylation (Kac). Mutants lacking the HP1/HDA-1-interacting protein CHROMO DOMAIN PROTEIN-2 (CDP-2) displayed a similar but non-identical phenotype, and we observed variable patterns of aberrant H3K7me3 enrichment in genetically identical ∆hda-1 strains, raising the possibility that loss of HDA-1 activity leads to progressive changes in H3K27me3 enrichment. Indeed, a newly constructed ∆hda-1 deletion strain displayed a near-wild type H3K27me3 chromatin modification profile that decayed over multiple strain passages corresponding to hundreds of nuclear divisions. Together, our data indicate that HDA-1 is a critical regulator of epigenome stability in N. crassa.
2025-01-16 | GSE286914 | GEO