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Small RNA profiles in wt and swi6 deletion strains

ABSTRACT: 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.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE70945 | GEO | 2015/10/07

SECONDARY ACCESSION(S): PRJNA290002

REPOSITORIES: GEO

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Genome wide map of heterochromatin state in fission yeast Schizosaccharomcyces pombe (S. pombe)

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

Identification of a novel, tunable interface in the S.pombe HP1 protein, Swi6, that underpins epigenetic inheritance.

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.

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DamID for Cid14 in wild-type and swi6∆

Project description:HP1 proteins are major components of heterochromatin, which is generally perceived to be an inert and transcriptionally inactive chromatin structure. Yet, HP1 binding to chromatin is highly dynamic and robust silencing of heterochromatic genes can involve RNA processing. Here we demonstrate by a combination of in vivo and in vitro experiments that the fission yeast HP1Swi6 protein guarantees tight repression of heterochromatic genes through RNA sequestration and degradation. Stimulated by positively charged residues in the hinge region, RNA competes with methylated histone H3K9 for binding to the chromodomain of HP1Swi6. Hence, HP1Swi6 binding to RNA is incompatible with stable heterochromatin association. We propose a model in which an ensemble of HP1Swi6 proteins functions as a heterochromatin-specific checkpoint capturing and priming heterochromatic RNAs for the RNA degradation machinery. Sustaining a functional checkpoint requires continuous exchange of HP1Swi6 within heterochromatin, which explains the dynamic localization of HP1 proteins on heterochromatin.

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The establishment of HP1-independent heterochromatin reveals an essential role for HP1 proteins in maintaining epigenetic memory

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

The establishment of HP1-independent heterochromatin reveals an essential role for HP1 proteins in maintaining epigenetic memory.

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Uncoupling the distinct functions of HP1 proteins during heterochromatin establishment and maintenance

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An RNA Endonuclease-Kinase Complex Required for Spreading and Epigenetic Inheritance of Heterochromatin

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

Genome-wide localization of Swi6 and H3-Lys9-me2 in wt and mutant starins of S. pombe

Project description:ChIP-on-ChIP experiments were performed to quantitate the genome-wide localization of heterochromatin proteins Swi6 and H3-Lys9-me2 in wild type versus polalpha mutant swi7H4, Pol delta mutant, dts2 and cut4 mutant cut4-993. Our results indicate that the localization of Swi6 and H3-Lys7-me2 at heterochromaitn regions, like centromere, telomere and mating-type is abrogated in the swi7H4, dts2 and cut4 mutants.

2023-03-05 | GSE198590 | GEO

HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila

Project description:Heterochromatin is important for the maintenance of genome stability and regulation of gene expression, yet our knowledge of heterochromatin structure and function is incomplete. We identified four novel Drosophila heterochromatin proteins. Three of these proteins (HP3, HP4, and HP5) interact directly with HP1, while HP6 in turn binds to each of these three proteins. Immunofluorescence microscopy and genome-wide mapping of in vivo binding sites shows that all four proteins are components of heterochromatin. Depletion of HP1 causes redistribution of all four proteins, indicating that HP1 is essential for their heterochromatic targeting. Finally, mutants of HP4 and HP5 are dominant suppressors of position effect variegation, demonstrating their importance in heterochromatic gene silencing. These results indicate that HP1 acts as a docking platform for several mediator proteins that contribute to heterochromatin function. Keywords: DamID knock-down

2007-02-02 | GSE6411 | GEO

Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa

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

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