Uncoupling the distinct functions of HP1 proteins during heterochromatin establishment and maintenance
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ABSTRACT:
ORGANISM(S): Schizosaccharomyces pombe
PROVIDER: GSE244017 | GEO | 2023/09/26
REPOSITORIES: GEO
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Project description:H3K9 methylation (H3K9me) marks transcriptionally silent genomic regions called heterochromatin. A conserved class of HP1 proteins are critically required to establish and maintain heterochromatin. HP1 proteins bind to H3K9me, recruit factors that promote heterochromatin formation, and oligomerize to form phase-separated condensates. We do not understand how HP1 protein binding to heterochromatin establishes and maintains transcriptional silencing. Here, we demonstrate that the S.pombe HP1 homolog, Swi6, can be completely bypassed to establish silencing at ectopic and endogenous loci when an H3K4 methyltransferase, Set1 and an H3K14 acetyltransferase, Mst2 are deleted. Deleting Set1 and Mst2 enhances Clr4 enzymatic activity, leading to higher H3K9me levels and increased spreading. In contrast, Swi6 and its capacity to oligomerize were indispensable during epigenetic maintenance. Our results demonstrate the role of HP1 proteins in regulating histone modification crosstalk during establishment and identifies a genetically separable function in maintaining epigenetic memory.
2023-05-10 | GSE231618 | GEO
Project description:H3K9 methylation (H3K9me) marks transcriptionally silent genomic regions called heterochromatin. A conserved class of HP1 proteins are critically required to establish and maintain heterochromatin. HP1 proteins bind to H3K9me, recruit factors that promote heterochromatin formation, and oligomerize to form phase-separated condensates. We do not understand how HP1 protein binding to heterochromatin establishes and maintains transcriptional silencing. Here, we demonstrate that the S.pombe HP1 homolog, Swi6, can be completely bypassed to establish silencing at ectopic and endogenous loci when an H3K4 methyltransferase, Set1 and an H3K14 acetyltransferase, Mst2 are deleted. Deleting Set1 and Mst2 enhances Clr4 enzymatic activity, leading to higher H3K9me levels and increased spreading. In contrast, Swi6 and its capacity to oligomerize were indispensable during epigenetic maintenance. Our results demonstrate the role of HP1 proteins in regulating histone modification crosstalk during establishment and identifies a genetically separable function in maintaining epigenetic memory.
2023-05-24 | GSE233333 | GEO
Project description:HP1 proteins bind dynamically to H3K9 methylation and are essential for establishing and maintaining transcriptionally silent epigenetic states, known as heterochromatin. HP1 proteins can dimerize, forming a binding interface that interacts with and recruits diverse chromatin-associated factors. HP1 proteins rapidly evolve through sequence changes and gene duplications, but the extent of variation required to achieve functional specialization is unknown. To investigate how changes in amino acid sequence impact epigenetic inheritance, we performed a targeted mutagenesis screen of the dimerization and protein interaction domain of the S.pombe HP1 homolog Swi6. We discovered that substitutions mapping to an auxiliary motif in Swi6 outside the dimerization interface can lead to complete functional divergence. Specifically, we identified point mutations at a single amino acid residue that resulted in either persistent gain or loss of function in epigenetic inheritance without affecting heterochromatin establishment. These substitutions increase Swi6 chromatin occupancy in vivo and alter Swi6-protein interactions that selectively affect H3K9me inheritance. Based on our findings, we propose that relatively minor changes in Swi6 amino acid composition can lead to profound changes in epigenetic inheritance, underscoring the remarkable plasticity associated with HP1 proteins and their ability to evolve new functions.
2023-11-27 | GSE248428 | GEO
Project description:Heterochromatin, a highly compact chromatin state characterized by histone H3 lysine 9 methylation (H3K9me) and HP1 protein binding, epigenetically silences the underlying DNA and influences the expression of neighboring genes. Therefore the sites of heterochromatin assembly and its subsequent spreading are generally precisely determined. Here we show that in fission yeast, the combined absence of anti-silencing factors Mst2 and Epe1 results in uncontrolled heterochromatin spreading and severe growth defects. Interestingly, these cells quickly recover by accumulating H3K9me at the clr4+ locus, which encodes the H3K9 methyltransferase essential for heterochromatin assembly, thereby leading to reduced expression of Clr4 to restrain heterochromatin spreading. Preventing H3K9me at the clr4+ locus resulted in the accumulation of H3K9me at the rik1+ locus, which encodes another component of the Clr4 complex essential for H3K9me. Our results demonstrate that promiscuous heterochromatin assembly enables fast adaptation in response to changes in chromatin landscape and illustrate a negative feedback mechanism by which cells counteract toxic heterochromatin accumulation.
2015-03-13 | GSE60521 | GEO
Project description:Proteins of the conserved HP1 family are elementary components of heterochromatin and are generally assumed to play a central role in creating a rigid heterochromatic network that is densely packed and inaccessible to the transcription machinery. In this study we demonstrate that the fission yeast HP1 protein Swi6 exists as a single highly dynamic population and rapidly exchanges in cis and in trans between different heterochromatic regions. Binding to methylated H3K9 or to heterochromatic RNA decelerates Swi6 mobility. We further show that Swi6 is largely dispensable to maintain heterochromatin domains. In contrast, our results disclose an unexpected role of Swi6 in demarcating constitutive heterochromatin from neighboring euchromatin. Our results are consistent with a stochastic model of heterochromatin and imply that heterochromatin is permissive for transcription throughout the cell cycle. Rather than promoting maintenance and spreading of heterochromatin, Swi6 appears to limit these processes to ensure that heterochromatin is appropriately confined.
2015-10-07 | GSE61136 | GEO
Project description:Proteins of the conserved HP1 family are elementary components of heterochromatin and are generally assumed to play a central role in creating a rigid heterochromatic network that is densely packed and inaccessible to the transcription machinery. In this study we demonstrate that the fission yeast HP1 protein Swi6 exists as a single highly dynamic population and rapidly exchanges in cis and in trans between different heterochromatic regions. Binding to methylated H3K9 or to heterochromatic RNA decelerates Swi6 mobility. We further show that Swi6 is largely dispensable to maintain heterochromatin domains. In contrast, our results disclose an unexpected role of Swi6 in demarcating constitutive heterochromatin from neighboring euchromatin. Our results are consistent with a stochastic model of heterochromatin and imply that heterochromatin is permissive for transcription throughout the cell cycle. Rather than promoting maintenance and spreading of heterochromatin, Swi6 appears to limit these processes to ensure that heterochromatin is appropriately confined.
2015-10-07 | GSE70945 | GEO
Project description:The highly conserved multienzyme Rix1-containing complex (hereafter referred to as the rixosome), is required for ribosomal RNA (rRNA) processing and also localizes to heterochromatin in fission yeast, but its role in heterochromatin formation is unknown. Here we report the isolation of separation of function mutations in subunits of the rixosome that abolish its physical association with Swi6/HP1 and localization to heterochromatin, but do not affect growth or rRNA processing. These mutations abolish the epigenetic inheritance of silencing and histone H3 lysine 9 methylation (H3K9me), accumulate heterochromatic RNAs, and cannot spread H3K9me and silencing away from nucleation sites into an inserted transgene. We further show that the rixosome acts upstream of the conserved 5’-3’ exoribonuclease Dhp1/XRN2 to promote heterochromatic RNA degradation. These findings reveal a new RNA degradation pathway that specifically localizes to heterochromatin to degrade nascent transcripts and enable heterochromatin spreading and inheritance.
2020-06-08 | GSE140920 | GEO
Project description:Heterochromatin protein 1 (HP1) proteins are important regulators of heterochromatin mediated gene silencing and chromosome structure and it is well known as the reader of the heterochromatin mark methylation of histone H3 lysine 9 (H3K9me). In Drosophila three different histone lysine methyl transferases (HKMTs) are associated with the methylation of H3K9; Su(var)3-9, Setdb1 and G9a. To gain insights on the dependence of HP1a on the three different HKMTs, the division of labor between these methyl transferases and the dependence of HP1a on H3K9me we have studied HP1a binding in relation to H3K9me in mutants of these HKMTs. We show that Su(var)3-9 is responsible for the HP1a H3K9me-dependent binding in pericentromeric regions while Setdb1 controls the HP1a H3K9me-dependent binding to cytological region 2L:31 and together with POF chromosome 4. HP1a binds to the promoters and within gene bodies of active genes in these three regions. More importantly, HP1a bound at promoters of active genes are independent of H3K9me and POF and is associated to heterochromatin protein 2 (HP2) and open chromatin. Our results supports a model where HP1a nucleates with high affinity independent of H3K9me in promoters of active genes and then spreads via H3K9 methylation and transient looping contacts with those H3K9me target sites. In total 44 samples; 2 replicates for each genotype and for each ChIP (HP1a, H3K9me2 and H3K9me3)
2012-12-21 | E-GEOD-38366 | biostudies-arrayexpress
Project description:H3K9 methylation (H3K9me) is a conserved marker of heterochromatin, a transcriptionally silent chromatin structure. Knowledge of the mechanisms for regulating heterochromatin distribution is limited. The fission yeast JmjC domain-containing protein Epe1 localizes to heterochromatin mainly through its interaction with Swi6, a homologue of heterochromatin protein 1 (HP1), and directs JmjC-mediated H3K9me demethylation in vivo. Here, we found that loss of epe1 (epe1∆) induced a red-white variegated phenotype in a red-pigment accumulation background that generated uniform red colonies. Analysis of isolated red and white colonies revealed that silencing of genes involved in pigment accumulation by stochastic ectopic heterochromatin formation led to white colony formation. In addition, genome-wide analysis of red- and white-isolated clones revealed that epe1∆ resulted in a heterogeneous heterochromatin distribution among clones. We found that Epe1 had an N-terminal domain distinct from its JmjC domain, which activated transcription in both fission and budding yeasts. The N-terminal transcriptional activation (NTA) domain was involved in suppression of ectopic heterochromatin-mediated red-white variegation. We introduced a single copy of Epe1 into epe1∆ clones harboring ectopic heterochromatin, and found that Epe1 could reduce H3K9me from ectopic heterochromatin but some of the heterochromatin persisted. This persistence was due to a latent H3K9me source embedded in ectopic heterochromatin. Epe1H297A, a canonical JmjC mutant, suppressed red-white variegation, but entirely failed to remove already-established ectopic heterochromatin, suggesting that Epe1 prevented stochastic de novo deposition of ectopic H3K9me in an NTA-dependent but JmjC-independent manner, while its JmjC domain mediated removal of H3K9me from established ectopic heterochromatin. Our results suggest that Epe1 not only limits the distribution of heterochromatin but also controls the balance between suppression and retention of heterochromatin-mediated epigenetic diversification.
2019-04-24 | GSE108448 | GEO
Project description:Both RNAi-dependent and -independent mechanisms have been implicated in the establishment of heterochromatin domains, which may be stabilized by feedback loops involving chromatin proteins and modifications of histones and DNA. Neurospora crassa sports features of heterochromatin found in higher eukaryotes, namely cytosine methylation (5mC), methylation of histone H3 lysine9 (H3K9me) and HETEROCHROMATIN PROTEIN-1 (HP1), and provides a model to investigate heterochromatin establishment and maintenance. We mapped the distribution of HP1, 5mC, H3K9me3 and H3K4me2 at 100bp-resolution and explored their interplay. HP1, H3K9me3 and DNA methylation were extensively colocalized and defined 44 heterochromatic domains on linkage group VII, all relics of repeat-induced point mutation (RIP). Interestingly, the centromere was found in a striking ~350kb heterochromatic domain with no detectable H3K4me2. 5mC was not found in genes, in contrast to the situation in plants and animals. H3K9me3 is required for HP1 localization and DNA methylation. Here, we show that localization of H3K9me3 is independent of 5mC or HP1 at virtually all heterochromatin regions. In addition, we observed complete restoration of DNA methylation patterns after depletion and reintroduction of the H3K9 methylation machinery, indicating that the signals for de novo heterochromatin formation lie upstream of H3K9 methylation. These data show that A:T rich RIPâd DNA efficently directs methylation of H3K9, which in turn, directs methylation of associated cytosines. Immunoprecipitation experiments using antibodies to 5mC, H3K9me3, epitope-tagged HP1, and H3K4me2 were performed. The immunoprecipitate fraction was labeled with Cy5 and the total input was labeled with Cy3. Samples were hybridized to a N. crassa LGVII tiling path microarray.
2010-05-15 | E-GEOD-12690 | biostudies-arrayexpress