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1.
Genes Cells ; 2024 Apr 17.
Article in English | MEDLINE | ID: mdl-38629626

ABSTRACT

In fission yeast, Schizosaccharomyces pombe, constitutive heterochromatin defined by methylation of histone H3 lysine 9 (H3K9me) and its binding protein Swi6/HP1 localizes at the telomere, centromere, and mating-type loci. These loci contain DNA sequences called dg and dh, and the RNA interference (RNAi)-dependent system establishes and maintains heterochromatin at dg/dh. Bi-directional transcription at dg/dh induced by RNA polymerase II is critical in RNAi-dependent heterochromatin formation because the transcribed RNAs provide substrates for siRNA synthesis and a platform for assembling RNAi factors. However, a regulator of dg/dh transcription during the establishment of heterochromatin is not known. Here, we found that a zinc-finger protein Moc3 localizes dh and activates dh-forward transcription in its zinc-finger-dependent manner when heterochromatin structure or heterochromatin-dependent silencing is compromised. However, Moc3 does not localize at normal heterochromatin and does not activate the dh-forward transcription. Notably, the loss of Moc3 caused a retarded heterochromatin establishment, showing that Moc3-dependent dh-forward transcription is critical for RNAi-dependent heterochromatin establishment. Therefore, Moc3 is a transcriptional activator that induces RNAi to establish heterochromatin.

2.
Commun Biol ; 6(1): 796, 2023 08 04.
Article in English | MEDLINE | ID: mdl-37542144

ABSTRACT

Motivated by our recent experiments that demonstrate that the tandemly repeated genes become heterochromatin, here we show a theory of heterochromatin assembly by taking into account the connectivity of these genes along the chromatin in the kinetic equations of small RNA production and histone methylation, which are the key biochemical reactions involved in the heterochromatin assembly. Our theory predicts that the polymeric nature of the tandemly repeated genes ensures the steady production of small RNAs because of the stable binding of nascent RNAs produced from the genes to RDRC/Dicers at the surface of nuclear membrane. This theory also predicts that the compaction of the tandemly repeated genes suppresses the production of small RNAs, consistent with our recent experiments. This theory can be extended to the small RNA-dependent gene silencing in higher organisms.


Subject(s)
Schizosaccharomyces pombe Proteins , Schizosaccharomyces , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , Heterochromatin/genetics , Heterochromatin/metabolism , RNA, Small Interfering/genetics , Schizosaccharomyces pombe Proteins/genetics , RNA Interference
3.
Biomolecules ; 13(2)2023 02 16.
Article in English | MEDLINE | ID: mdl-36830746

ABSTRACT

DNA is stored in the nucleus of a cell in a folded state; however, only the necessary genetic information is extracted from the required group of genes. The key to extracting genetic information is chromatin ambivalence. Depending on the chromosomal region, chromatin is characterized into low-density "euchromatin" and high-density "heterochromatin", with various factors being involved in its regulation. Here, we focus on chromatin regulation and gene expression by the yeast FACT complex, which functions in both euchromatin and heterochromatin. FACT is known as a histone H2A/H2B chaperone and was initially reported as an elongation factor associated with RNA polymerase II. In budding yeast, FACT activates promoter chromatin by interacting with the transcriptional activators SBF/MBF via the regulation of G1/S cell cycle genes. In fission yeast, FACT plays an important role in the formation of higher-order chromatin structures and transcriptional repression by binding to Swi6, an HP1 family protein, at heterochromatin. This FACT property, which refers to the alternate chromatin-regulation depending on the binding partner, is an interesting phenomenon. Further analysis of nucleosome regulation within heterochromatin is expected in future studies.


Subject(s)
Saccharomyces cerevisiae Proteins , Schizosaccharomyces pombe Proteins , Schizosaccharomyces , Heterochromatin/metabolism , Saccharomyces cerevisiae/metabolism , Euchromatin/metabolism , Chromosomal Proteins, Non-Histone/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Chromatin/metabolism , Schizosaccharomyces/metabolism , DNA-Binding Proteins/metabolism , High Mobility Group Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Transcriptional Elongation Factors/genetics , Transcriptional Elongation Factors/metabolism
4.
Biochem Biophys Res Commun ; 638: 58-65, 2023 01 01.
Article in English | MEDLINE | ID: mdl-36442233

ABSTRACT

Cell migration is a cytoskeleton-driven cellular process involved in physiological and pathological events such as embryonic development and cancer metastasis. Fibroblasts have often been used to elucidate the mechanism of cell migration due to their high morphological polarity and migratory activity. We recently reported that human lung fibroblasts migrate straight for a long duration without external stimuli, which phenomenon we named intrinsic and directed migration (IDM) of fibroblasts. In this study, we explored proteins involved in IDM in order to elucidate the molecular mechanism. First, we focused on the differences in morphology and migratory behaviors between normal and immortalized fibroblasts-the former exhibit obvious polarity and IDM; the latter exhibit poorly polarized morphology and random migration. We compared the abundance of proteins functioning as the cytoskeletal components between them through proteomic analysis and found that LIM domain only protein 7 (LMO7) is overwhelmingly incorporated into the cytoskeletons of normal fibroblasts. Depletion of LMO7 inhibited the directed migration of normal fibroblast on the fibronectin (FN)-rich surface, suggesting that LMO7 is important for IDM. Moreover, on the FN-free surface, LMO7-depleted fibroblasts often failed to establish morphological polarity and hardly migrated. Thus, the present study identified LMO7 as a positive regulator of fibroblast polarization and IDM, especially in an environment where integrin-mediated substrate attachment is insufficient.


Subject(s)
Fibronectins , Proteomics , Humans , Cytoskeleton/metabolism , Fibroblasts/metabolism , Cell Movement , Integrins , Transcription Factors/metabolism , LIM Domain Proteins/metabolism
5.
Nucleic Acids Res ; 50(19): 10914-10928, 2022 10 28.
Article in English | MEDLINE | ID: mdl-36200823

ABSTRACT

Centromeres of most eukaryotes consist of two distinct chromatin domains: a kinetochore domain, identified by the histone H3 variant, CENP-A, and a heterochromatic domain. How these two domains are separated is unclear. Here, we show that, in Schizosaccharomyces pombe, mutation of the chromatin remodeler RSC induced CENP-ACnp1 misloading at pericentromeric heterochromatin, resulting in the mis-assembly of kinetochore proteins and a defect in chromosome segregation. We find that RSC functions at the kinetochore boundary to prevent CENP-ACnp1 from spreading into neighbouring heterochromatin, where deacetylated histones provide an ideal environment for the spread of CENP-ACnp1. In addition, we show that RSC decompacts the chromatin structure at this boundary, and propose that this RSC-directed chromatin decompaction prevents mis-propagation of CENP-ACnp1 into pericentromeric heterochromatin. Our study provides an insight into how the distribution of distinct chromatin domains is established and maintained.


Subject(s)
Schizosaccharomyces pombe Proteins , Schizosaccharomyces , Heterochromatin/metabolism , Chromatin/metabolism , Centromere Protein A/metabolism , Chromosomal Proteins, Non-Histone/genetics , Chromosomal Proteins, Non-Histone/metabolism , Centromere/metabolism , Kinetochores/metabolism , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces pombe Proteins/metabolism , Histones/metabolism
6.
Genes Cells ; 27(2): 93-112, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34910346

ABSTRACT

H2A.Z, an evolutionally well-conserved histone H2A variant, is involved in many biological processes. Although the function of H2A.Z in euchromatic gene regulation is well known, its function and deposition mechanism in heterochromatin are still unclear. Here, we report that H2A.Z plays multiple roles in fission yeast heterochromatin. While a small amount of H2A.Z localizes at pericentromeric heterochromatin, loss of methylation of histone H3 at Lys9 (H3K9me) induces the accumulation of H2A.Z, which is dependent on the H2A.Z loader, SWR complex. The accumulated H2A.Z suppresses heterochromatic non-coding RNA transcription. This transcriptional repression activity requires the N-terminal tail of H2A.Z, which is involved in the regulation of euchromatic gene transcription. RNAi-defective cells, in which a substantial amount of H3K9me is retained by RNAi-independent heterochromatin assembly, also accumulate H2A.Z at heterochromatin, and the additional loss of H2A.Z in these cells triggers a further decrease in H3K9me. Our results suggest that H2A.Z facilitates RNAi-independent heterochromatin assembly by antagonizing the demethylation activity of Epe1, an eraser of H3K9me. Furthermore, H2A.Z suppresses Epe1-mediated transcriptional activation, which is required for subtelomeric gene repression. Our results provide novel evidence that H2A.Z plays diverse roles in chromatin silencing.


Subject(s)
Schizosaccharomyces pombe Proteins , Schizosaccharomyces , Chromatin Assembly and Disassembly , Heterochromatin/genetics , Histones/metabolism , Nuclear Proteins/genetics , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces pombe Proteins/metabolism
7.
Genes Dev ; 36(21-24): 1145-1159, 2022.
Article in English | MEDLINE | ID: mdl-36617881

ABSTRACT

In most eukaryotes, constitutive heterochromatin, defined by histone H3 lysine 9 methylation (H3K9me), is enriched on repetitive DNA, such as pericentromeric repeats and transposons. Furthermore, repetitive transgenes also induce heterochromatin formation in diverse model organisms. However, the mechanisms that promote heterochromatin formation at repetitive DNA elements are still not clear. Here, using fission yeast, we show that tandemly repeated mRNA genes promote RNA interference (RNAi)-mediated heterochromatin formation in cooperation with an antisilencing factor, Epe1. Although the presence of tandemly repeated genes itself does not cause heterochromatin formation, once complementary small RNAs are artificially supplied in trans, the RNAi machinery assembled on the repeated genes starts producing cognate small RNAs in cis to autonomously maintain heterochromatin at these sites. This "repeat-induced RNAi" depends on the copy number of repeated genes and Epe1, which is known to remove H3K9me and derepress the transcription of genes underlying heterochromatin. Analogous to repeated genes, the DNA sequence underlying constitutive heterochromatin encodes widespread transcription start sites (TSSs), from which Epe1 activates ncRNA transcription to promote RNAi-mediated heterochromatin formation. Our results suggest that when repetitive transcription units underlie heterochromatin, Epe1 generates sufficient transcripts for the activation of RNAi without disruption of heterochromatin.


Subject(s)
Schizosaccharomyces pombe Proteins , Schizosaccharomyces , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , RNA Interference , Heterochromatin/genetics , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces pombe Proteins/metabolism , Histones/genetics , Histones/metabolism , Nuclear Proteins/genetics , Nuclear Proteins/metabolism
8.
Cell Rep ; 36(7): 109540, 2021 08 17.
Article in English | MEDLINE | ID: mdl-34407404

ABSTRACT

FACT (facilitate chromatin transcription) is involved in heterochromatic silencing, but its mechanisms and function remain unclear. We reveal that the Spt16 recruitment mechanism operates in two distinct ways in heterochromatin. First, Pob3 mediates Spt16 recruitment onto the heterochromatin through its Spt16 dimerization and tandem PH domains. Without Pob3, Spt16 recruitment is partially reduced, exhibiting a silencing defect and impaired H2A/H2B organization. Second, heterochromatin protein 1 (HP1)/Swi6 mediates Spt16 recruitment onto the heterochromatin by physical interaction of the Swi6 chromo-shadow domain (CSD) and Spt16 peptidase-like domains. Several CSD mutants are tested for Spt16 binding activity, and the charged loop connecting ß1 and ß2 is critical for Spt16 binding and heterochromatic silencing. Loss of these pathways causes a severe defect in H3K9 methylation and HP1/Swi6 localization in the pericentromeric region, exhibiting transcriptional silencing defects and disordered heterochromatin. Our findings suggest that FACT and HP1/Swi6 work intimately to regulate heterochromatin organization.


Subject(s)
Heterochromatin/metabolism , Multiprotein Complexes/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/metabolism , Amino Acid Sequence , Euchromatin/metabolism , Gene Silencing , Histones/metabolism , Multiprotein Complexes/chemistry , Mutation/genetics , Nucleosomes/metabolism , Protein Binding , Protein Domains , Protein Multimerization , Protein Structure, Secondary , Schizosaccharomyces pombe Proteins/chemistry , Transcription, Genetic
9.
Genes Cells ; 26(4): 203-218, 2021 Apr.
Article in English | MEDLINE | ID: mdl-33527595

ABSTRACT

In fission yeast, siRNA generated by RNA interference (RNAi) factors plays critical roles in establishment and maintenance of heterochromatin. To achieve efficient siRNA synthesis, RNAi factors assemble on heterochromatin via association with Swi6, a homologue of heterochromatin protein 1 (HP1), and heterochromatic noncoding RNA (hncRNA) retained on chromatin. In addition, spliceosomes formed on hncRNA introns recruit RNAi factors to hncRNA and heterochromatin. Small nuclear RNAs, components of the spliceosome, have a trimethylguanosine (TMG) cap that is generated by Tgs1-dependent hypermethylation of the normal m7G cap; this cap is required for efficient splicing of some mRNAs in budding yeast and Drosophila. In this study, we found that loss of Tgs1 in fission yeast destabilizes centromeric heterochromatin. Tgs1 was required for Swi6-independent siRNA synthesis, as well as for the establishment of centromeric heterochromatin. Loss of Tgs1 affected the splicing efficiency of hncRNA introns in the absence of Swi6. Furthermore, some hncRNAs have a TMG cap, and we found that loss of Tgs1 diminished the chromatin binding of these hncRNAs. Together, these results suggest that the Tgs1-dependent TMG cap plays critical roles in establishment of heterochromatin by ensuring spliceosome-dependent recruitment of RNAi factors and regulating the binding between chromatin and hncRNA.


Subject(s)
Chromosomal Proteins, Non-Histone/metabolism , Heterochromatin/metabolism , RNA, Small Interfering/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/metabolism , tRNA Methyltransferases/metabolism , Centromere/metabolism , Gene Silencing , Introns/genetics , Models, Biological , Protein Domains , RNA Splicing/genetics , RNA, Antisense/metabolism , RNA, Fungal/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , Schizosaccharomyces pombe Proteins/chemistry , tRNA Methyltransferases/chemistry
10.
Yeast ; 38(4): 251-261, 2021 04.
Article in English | MEDLINE | ID: mdl-33245560

ABSTRACT

Gene expression vectors are useful and important tools that are commonly used in a variety of experiments, including expression of foreign genes, functional analysis of genes of interest and complementation experiments. In this study, a hybrid promoter, combining the adh1+ upstream activating sequence (UAS) of fission yeast and the GAL10 core promoter of budding yeast, was constructed to enable high level expression depending on the presence of zinc in culture medium for fission yeast. When the hybrid promoter was cloned on the multicopy plasmid, it was fully induced and repressed within 10 h in the presence and absence of zinc, respectively. The kinetics of induction and reduction were similar to those of the endogenous adh1+ mRNA. In contrast, native adh1+ promoter lost its tight repression in zinc-depleted condition when it was cloned on the plasmid. Because adh1+ UAS-specific transcription factors have not yet been identified, we identified UAS elements involved in zinc sensing by characterizing this hybrid promoter. We also found that the expression level increased by the TATA box mutation, GATAA, in the presence of zinc.


Subject(s)
Gene Expression Regulation, Fungal , Genetic Vectors , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , Zinc/metabolism , Genes, Fungal , Genetic Engineering/methods , Plasmids/genetics , Schizosaccharomyces/drug effects , Zinc/pharmacology
11.
Curr Genet ; 66(2): 319-325, 2020 Apr.
Article in English | MEDLINE | ID: mdl-31598751

ABSTRACT

Changes in gene expression via chromatin-mediated mechanisms are important for reprogramming and differentiation, but uncontrolled changes can potentially lead to harmful or adaptive phenotypic alteration. Thus, diversification of the genome-wide chromatin state must be strictly limited, but the underlying mechanism of this regulation is largely unknown. In this review, we focused on distribution of heterochromatin, a tight chromatin structure that negatively regulates gene expression. Heterochromatin is characterized by methylation of histone H3 at lysine 9, and its formation and spreading are controlled by H3K9-specific methyltransferases and reversal factors such as histone demethylases. We summarize recent findings and discuss how variability in the heterochromatin distribution is controlled in the unicellular eukaryote fission yeast. In this context, we recently found that the anti-silencing factor Epe1 plays a key role in the formation of the individual-specific heterochromatin distribution. In conclusion, recent studies revealed that there are many potential heterochromatin formation sites in the fission yeast genome, and several proteins contribute to suppression of spreading and genome-wide dispersal of heterochromatin; knowledge from fission yeast studies may provide insights into the mechanisms regulating epigenetic diversification in multicellular eukaryotes.


Subject(s)
Epigenesis, Genetic , Heterochromatin/metabolism , Histones/metabolism , Jumonji Domain-Containing Histone Demethylases/metabolism , Chromatin Assembly and Disassembly , Methylation , Methyltransferases/metabolism , Protein Processing, Post-Translational , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism
12.
J Biochem ; 167(1): 25-39, 2020 Jan 01.
Article in English | MEDLINE | ID: mdl-31599953

ABSTRACT

Precise regulation of cytoskeletal dynamics is important in many fundamental cellular processes such as cell shape determination. Actin and microtubule (MT) cytoskeletons mutually regulate their stability and dynamics. Nonmuscle myosin II (NMII) is a candidate protein that mediates the actin-MT crosstalk. NMII regulates the stability and dynamics of actin filaments to control cell morphology. Additionally, previous reports suggest that NMII-dependent cellular contractility regulates MT dynamics, and MTs also control cell morphology; however, the detailed mechanism whereby NMII regulates MT dynamics and the relationship among actin dynamics, MT dynamics and cell morphology remain unclear. The present study explores the roles of two well-characterized NMII isoforms, NMIIA and NMIIB, on the regulation of MT growth dynamics and cell morphology. We performed RNAi and drug experiments and demonstrated the NMII isoform-specific mechanisms-NMIIA-dependent cellular contractility upregulates the expression of some mammalian diaphanous-related formin (mDia) proteins that suppress MT dynamics; NMIIB-dependent inhibition of actin depolymerization suppresses MT growth independently of cellular contractility. The depletion of either NMIIA or NMIIB resulted in the increase in cellular morphological dynamicity, which was alleviated by the perturbation of MT dynamics. Thus, the NMII-dependent control of cell morphology significantly relies on MT dynamics.


Subject(s)
Cell Shape , Microtubules/metabolism , Nonmuscle Myosin Type IIA/metabolism , Nonmuscle Myosin Type IIB/metabolism , Cytoskeleton/metabolism , Humans , Tumor Cells, Cultured
13.
Front Biosci (Landmark Ed) ; 25(4): 632-645, 2020 01 01.
Article in English | MEDLINE | ID: mdl-31585908

ABSTRACT

In Drosophila melanogaster, in response to developmental transcription factors, and by repeated initiation of DNA replication of four chorion genes, ovarian follicle cells, form an onion skin-type structure at the replication origins. The DNA replication machinery is conserved from yeast to humans. Subunits of the origin recognition complex (ORC) is comprised of Orc1, Orc2, and Cdc6 genes. While mutations of Orc1 and Orc2 and not Cdc6can be lethal, overexpression of these genes lead to female sterility. Ecdysone, is a steroidal prohormone of the major insect molting hormone 20-hydroxyecdysone that in Drosophila, triggers molting, metamorphosis, and oogenesis. To this end, we identified several ecdysone receptor (EcR) binding sites around gene amplification loci. We also found that H3K4 was trimethylated at chorion gene amplification origins, but not at the act1 locus. Female mutants overexpressing Lsd1 (a dimethyl histone H3K4 demethylase) or Lid (a trimethyl histone H3K4 demethylase), but not a Lid mutant, were sterile. The data suggest that ecdysone signaling determines which origin initiates DNA replication and contributes to the development. Screening strategies using Drosophila offer the opportunity for development of drugs that reduce gene amplification and alter histone modification associated with epigenetic effects.


Subject(s)
Drosophila melanogaster/genetics , Epigenesis, Genetic , Gene Amplification , Gene Expression Regulation, Developmental , Animals , Animals, Genetically Modified , Chorion/growth & development , Chorion/metabolism , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Drosophila melanogaster/growth & development , Drosophila melanogaster/metabolism , Female , Histones/metabolism , Humans , Methylation , Oogenesis/genetics , Origin Recognition Complex/genetics , Origin Recognition Complex/metabolism , Ovarian Follicle/cytology , Ovarian Follicle/growth & development , Ovarian Follicle/metabolism , Receptors, Steroid/genetics , Receptors, Steroid/metabolism
14.
Microbiol Resour Announc ; 8(45)2019 Nov 07.
Article in English | MEDLINE | ID: mdl-31699754

ABSTRACT

Staphylococcus arlettae is one coagulase-negative species in the bacterial genus Staphylococcus Here, we describe the closed complete genome sequence of S. arlettae strain P2, which was obtained using a hybrid approach combining Oxford Nanopore long-read and Illumina MiSeq short-read sequencing data.

15.
PLoS Genet ; 15(6): e1008129, 2019 06.
Article in English | MEDLINE | ID: mdl-31206516

ABSTRACT

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 (epe1Δ) 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 epe1Δ 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 epe1Δ 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.


Subject(s)
Epigenomics , Heterochromatin/genetics , Nuclear Proteins/genetics , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces/genetics , Chromatin Assembly and Disassembly/genetics , Chromosomal Proteins, Non-Histone/genetics , Gene Silencing , Histones/genetics , Jumonji Domain-Containing Histone Demethylases/genetics , Methylation , Mutation
16.
J Biochem ; 166(1): 3-6, 2019 Jul 01.
Article in English | MEDLINE | ID: mdl-31198932

ABSTRACT

Heterochromatin is a condensed and transcriptionally silent chromatin structure and that plays important roles in epigenetic regulation of the genome. Two types of heterochromatin exist: constitutive heterochromatin is primarily associated with trimethylation of histone H3 at lysine 9 (H3K9me3), and facultative heterochromatin with trimethylation of H3 at lysine 27 (H3K27me3). The methylated histones are bound by the chromodomain of histone code 'reader' proteins: HP1 family proteins for H3K9me3 and Polycomb family proteins for H3K27me3. Each repressive reader associates with various 'effector' proteins that provide the functional basis of heterochromatin. Heterochromatin regulation is primarily achieved by controlling histone modifications. However, recent studies have revealed that the repressive readers are phosphorylated, like other regulatory proteins, suggesting that phosphorylation also participates in heterochromatin regulation. Detailed studies have shown that phosphorylation of readers affects the binding specificities of chromodomains for methylated histone H3, as well as the binding of effector proteins. Thus, phosphorylation adds another layer to heterochromatin regulation. Interestingly, casein kinase 2, a strong and predominant kinase within the cell, is responsible for phosphorylation of repressive readers. In this commentary, I summarize the regulation of repressive readers by casein kinase 2-dependent phosphorylation and discuss the functional meaning of this modification.


Subject(s)
Casein Kinase II/metabolism , Heterochromatin/metabolism , Histone Code/physiology , Histones/chemistry , Histones/metabolism , Animals , Heterochromatin/chemistry , Heterochromatin/genetics , Histones/genetics , Humans , Phosphorylation
17.
Exp Cell Res ; 376(1): 67-76, 2019 03 01.
Article in English | MEDLINE | ID: mdl-30711568

ABSTRACT

Nonmuscle myosin II (NMII) plays an important role in cytokinesis by constricting a contractile ring. However, it is poorly understood how NMII isoforms contribute to cytokinesis in mammalian cells. Here, we investigated the roles of the two major NMII isoforms, NMIIA and NMIIB, in cytokinesis using a WI-38 VA13 cell line (human immortalized fibroblast). In this cell line, NMIIB tended to localize to the contractile ring more than NMIIA. The expression level of NMIIA affected the localization of NMIIB. Most NMIIB accumulated at the cleavage furrow in NMIIA-knockout (KO) cells, and most NMIIA was displaced from this location in exogenous NMIIB-expressing cells, indicating that NMIIB preferentially localizes to the contractile ring. Specific KO of each isoform elicited opposite effects. The rate of furrow ingression was decreased and increased in NMIIA-KO and NMIIB-KO cells, respectively. Meanwhile, the length of NMII-filament stacks in the contractile ring was increased and decreased in NMIIA-KO and NMIIB-KO cells, respectively. Moreover, NMIIA helped to maintain cortical stiffness during cytokinesis. These findings suggest that appropriate ratio of NMIIA and NMIIB in the contractile ring is important for proper cytokinesis in specific cell types. In addition, two-photon excitation spinning-disk confocal microscopy enabled us to image constriction of the contractile ring in live cells in a three-dimensional manner.


Subject(s)
Cytokinesis/genetics , Muscle Contraction/genetics , Nonmuscle Myosin Type IIA/genetics , Nonmuscle Myosin Type IIB/genetics , Actin Cytoskeleton/genetics , Cell Line , Cell Lineage/genetics , Fibroblasts/metabolism , Gene Expression Regulation/genetics , Gene Knockout Techniques , Humans , Protein Isoforms/genetics
18.
Commun Biol ; 2: 17, 2019.
Article in English | MEDLINE | ID: mdl-30652128

ABSTRACT

Heterochromatin, characterized by histone H3 lysine 9 (H3K9) methylation, assembles on repetitive regions including centromeres. Although centromeric heterochromatin is important for correct segregation of chromosomes, its exact role in maintaining centromere integrity remains elusive. Here, we found in fission yeast that heterochromatin suppresses gross chromosomal rearrangements (GCRs) at centromeres. Mutations in Clr4/Suv39 methyltransferase increased the formation of isochromosomes, whose breakpoints were located in centromere repeats. H3K9A and H3K9R mutations also increased GCRs, suggesting that Clr4 suppresses centromeric GCRs via H3K9 methylation. HP1 homologs Swi6 and Chp2 and the RNAi component Chp1 were the chromodomain proteins essential for full suppression of GCRs. Remarkably, mutations in RNA polymerase II (RNAPII) or Tfs1/TFIIS, the transcription factor that facilitates restart of RNAPII after backtracking, specifically bypassed the requirement of Clr4 for suppressing GCRs. These results demonstrate that heterochromatin suppresses GCRs by repressing Tfs1-dependent transcription of centromere repeats.


Subject(s)
Centromere/metabolism , Heterochromatin/metabolism , Isochromosomes/genetics , Schizosaccharomyces/genetics , Transcription, Genetic/genetics , Transcriptional Elongation Factors/metabolism , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Chromosomal Proteins, Non-Histone/metabolism , Histone-Lysine N-Methyltransferase/genetics , Histones/genetics , Methylation , Plasmids/genetics , RNA Interference , RNA Polymerase II/genetics , Repressor Proteins/metabolism , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces pombe Proteins/metabolism
19.
Genes Cells ; 23(9): 738-752, 2018 Sep.
Article in English | MEDLINE | ID: mdl-30155942

ABSTRACT

Abp1 is a fission yeast CENP-B homologue that contributes to centromere function, silencing at pericentromeric heterochromatin and silencing of retrotransposons. We identified the sfh1 gene, encoding a core subunit of the fission yeast chromatin remodeling complex RSC as an Abp1-interacting protein. Because sfh1 is essential for growth, we isolated temperature-sensitive sfh1 mutants. These mutants showed defects in centromere functions, reflected by sensitivity to an inhibitor of spindle formation and minichromosome instability. Sfh1 localized at both kinetochore and pericentromeric heterochromatin regions. Although sfh1 mutations had minor effect on silencing at these regions, they decreased the levels of cohesin on centromeric heterochromatin. Sfh1 also localized at a retrotransposon, Tf2, in a partly Abp1-dependent manner, and assisted in silencing of Tf2 by Abp1 probably in the same pathway as a histone chaperon, HIRA, which is also known to involve in Tf2 repression. Furthermore, sfh1 mutants were sensitive to several DNA-damaging treatments (HU, MMS, UV and X-ray). Increase in spontaneous foci of Rad22, a recombination Mediator protein Rad52 homologue, in sfh1 mutant suggests that RSC functions in homologous recombination repair of double-stranded break downstream of the Rad22 recruitment. These results indicate that RSC plays multiple roles in the maintenance of genome integrity.


Subject(s)
Chromatin Assembly and Disassembly , Gene Expression Regulation, Fungal , Genomic Instability , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/genetics , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Centromere , Chromosomal Proteins, Non-Histone/genetics , Chromosomal Proteins, Non-Histone/metabolism , Chromosome Segregation , Heterochromatin , Mutation , Retroelements , Schizosaccharomyces pombe Proteins/genetics , Cohesins
20.
Epigenetics Chromatin ; 11(1): 26, 2018 06 04.
Article in English | MEDLINE | ID: mdl-29866182

ABSTRACT

BACKGROUND: Heat-shock molecular chaperone proteins (Hsps) promote the loading of small interfering RNA (siRNA) onto RNA interference (RNAi) effector complexes. While the RNAi process is coupled with heterochromatin assembly in several model organisms, it remains unclear whether the Hsps contribute to epigenetic gene regulation. In this study, we used the fission yeast Schizosaccharomyces pombe as a model organism and investigated the roles of Hsp90 and Mas5 (a nucleocytoplasmic type-I Hsp40 protein) in RNAi-dependent heterochromatin assembly. RESULTS: Using a genetic screen and biochemical analyses, we identified Hsp90 and Mas5 as novel silencing factors. Mutations in the genes encoding these factors caused derepression of silencing at the pericentromere, where heterochromatin is assembled in an RNAi-dependent manner, but not at the subtelomere, where RNAi is dispensable. The mutations also caused a substantial reduction in the level of dimethylation of histone H3 at Lys9 at the pericentromere, where association of the Argonaute protein Ago1 was also abrogated. Consistently, siRNA corresponding to the pericentromeric repeats was undetectable in these mutant cells. In addition, levels of Tas3, which is a protein in the RNA-induced transcriptional silencing complex along with Ago1, were reduced in the absence of Mas5. CONCLUSIONS: Our results suggest that the Hsps Hsp90 and Mas5 contribute to RNAi-dependent heterochromatin assembly. In particular, Mas5 appears to be required to stabilize Tas3 in vivo. We infer that impairment of Hsp90 and Hsp40 also may affect the integrity of the epigenome in other organisms.


Subject(s)
HSP40 Heat-Shock Proteins/genetics , HSP90 Heat-Shock Proteins/genetics , Heterochromatin/genetics , RNA, Small Interfering/genetics , Schizosaccharomyces/genetics , Argonaute Proteins/metabolism , Carrier Proteins/metabolism , Centromere/genetics , Chromatin Assembly and Disassembly , Epigenesis, Genetic , Gene Expression Regulation, Fungal , HSP40 Heat-Shock Proteins/metabolism , HSP90 Heat-Shock Proteins/metabolism , Methylation , Mutation , Schizosaccharomyces/metabolism , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces pombe Proteins/metabolism
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