Similar Datasets
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
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: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 | GSE286916 | 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:DNA methylation, heterochromatin protein 1 (HP1), histone H3 lysine 9 (H3K9) methylation, histone deacetylation, and highly repeated sequences are prototypical heterochromatic features, but their interrelationships are not fully understood. Prior work showed that H3K9 methylation directs DNA methylation and histone deacetylation via HP1 in Neurospora crassa and that the histone deacetylase complex HCHC is required for proper DNA methylation. The complex consists of the chromodomain proteins HP1 and chromodomain protein 2 (CDP-2), the histone deacetylase HDA-1, and the AT-hook motif protein CDP-2/HDA-1-associated protein (CHAP). We show that the complex is required for proper chromosome segregation, dissect its function, and characterize interactions among its components. Our analyses revealed the existence of an HP1-based DNA methylation pathway independent of its chromodomain. The pathway partially depends on CHAP but not on the CDP-2 chromodomain. CDP-2 serves as a bridge between the recognition of H3K9 trimethylation (H3K9me3) by HP1 and the histone deacetylase activity of HDA-1. CHAP is also critical for HDA-1 localization to heterochromatin. Specifically, the CHAP zinc finger interacts directly with the HDA-1 argonaute-binding protein 2 (Arb2) domain, and the CHAP AT-hook motifs recognize heterochromatic regions by binding to AT-rich DNA. Our data shed light on the interrelationships among the prototypical heterochromatic features and support a model in which dual recognition by the HP1 chromodomain and the CHAP AT-hooks are required for proper heterochromatin formation.
| S-EPMC5068333 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-05-05 | E-GEOD-59189 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-07-03 | GSE232935 | GEO
Project description:DNA methylation is deficient in a histone deacetylase 1 (HDA1) mutant (hda-1) strain of Neurospora crassa with inactivated histone deacetylase 1. Difference two-dimensional (2D) gels identified the primary histone deacetylase 1 target as histone H2B. Acetylation was identified by LC-MS/MS at five different lysines in wild-type H2B and at 11 lysines in hda-1 H2B, suggesting Neurospora H2B is a complex combination of different acetylated species. Individual 2D gel spots were shifted by single lysine acetylations. FTICR MS-observed methylation ladders identify an ensemble of 20-25 or more modified forms for each 2D gel spot. Twelve different lysines or arginines were methylated in H2B from the wild type or hda-1; only two were in the N-terminal tail. Arginines were modified by monomethylation, dimethylation, or deimination. H2B from wild-type and hda-1 ensembles may thus differ by acetylation at multiple sites, and by additional modifications. Combined with asymmetry-generated diversity in H2B structural states in nucleosome core particles, the extensive modifications identified here can create substantial histone-generated structural diversity in nucleosome core particles.
| S-EPMC4311878 | biostudies-literature
Project description:Histone deacetylase-1 is required for epigenomic stability in Neurospora crassa [CUTnRUN]
| PRJNA1210541 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-03-17 | GSE168995 | GEO