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1.
Genes Cells ; 29(5): 361-379, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38403935

RESUMO

Constitutive heterochromatin is transcriptionally repressed and densely packed chromatin, typically harboring histone H3 Lys9 trimethylation (H3K9me3) and heterochromatin protein 1 (HP1). SUV420H2, a histone H4 Lys20 methyltransferase, is recruited to heterochromatin by binding to HP1 through its Heterochromatic Targeting Module (HTM). Here, we have identified three HP1 binding motifs within the HTM. Both the full-length HTM and its N-terminal region (HTM-N), which contains the first and second motifs, stabilized HP1 on heterochromatin. The intervening region between the first and second HP1 binding motifs in HTM-N was also crucial for HP1 binding. In contrast, the C-terminal region of HTM (HTM-C), containing the third motif, destabilized HP1 on chromatin. An HTM V374D mutant, featuring a Val374 to Asp substitution in the second HP1 binding motif, localizes to heterochromatin without affecting HP1 stability. These data suggest that the second HP1 binding motif in the SUV420H2 HTM is critical for locking HP1 on H3K9me3-enriched heterochromatin. HTM V374D, tagged with a fluorescent protein, can serve as a live-cell probe to visualize HP1-bound heterochromatin.


Assuntos
Homólogo 5 da Proteína Cromobox , Proteínas Cromossômicas não Histona , Heterocromatina , Histona-Lisina N-Metiltransferase , Ligação Proteica , Heterocromatina/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , Homólogo 5 da Proteína Cromobox/metabolismo , Humanos , Histona-Lisina N-Metiltransferase/metabolismo , Histona-Lisina N-Metiltransferase/genética , Histonas/metabolismo , Motivos de Aminoácidos , Células HeLa , Sítios de Ligação
2.
Nucleic Acids Res ; 50(22): 12702-12722, 2022 12 09.
Artigo em Inglês | MEDLINE | ID: mdl-36537242

RESUMO

Heterochromatin protein 1α (HP1α) is a crucial element of chromatin organization. It has been proposed that HP1α functions through liquid-liquid phase separation (LLPS), which allows it to compact chromatin into transcriptionally repressed heterochromatin regions. In vitro, HP1α can undergo phase separation upon phosphorylation of its N-terminus extension (NTE) and/or through interactions with DNA and chromatin. Here, we combine computational and experimental approaches to elucidate the molecular interactions that drive these processes. In phosphorylation-driven LLPS, HP1α can exchange intradimer hinge-NTE interactions with interdimer contacts, which also leads to a structural change from a compacted to an extended HP1α dimer conformation. This process can be enhanced by the presence of positively charged HP1α peptide ligands and disrupted by the addition of negatively charged or neutral peptides. In DNA-driven LLPS, both positively and negatively charged peptide ligands can perturb phase separation. Our findings demonstrate the importance of electrostatic interactions in HP1α LLPS where binding partners can modulate the overall charge of the droplets and screen or enhance hinge region interactions through specific and non-specific effects. Our study illuminates the complex molecular framework that can fine-tune the properties of HP1α and that can contribute to heterochromatin regulation and function.


Assuntos
Homólogo 5 da Proteína Cromobox , Proteínas Cromossômicas não Histona , Heterocromatina , Cromatina , Homólogo 5 da Proteína Cromobox/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , DNA/metabolismo , Ligantes , Fosforilação , Fatores de Transcrição/metabolismo , Humanos
3.
Proc Natl Acad Sci U S A ; 119(25): e2118796119, 2022 06 21.
Artigo em Inglês | MEDLINE | ID: mdl-35704756

RESUMO

Position-effect variegation (PEV) results from the juxtaposition of euchromatic and heterochromatic components of eukaryotic genomes, silencing genes near the new euchromatin/heterochromatin junctions. Silencing is itself heritable through S phase, giving rise to distinctive random patterns of cell clones expressing the genes intermixed with clones in which the genes are silenced. Much of what we know about epigenetic inheritance in the soma stems from work on PEV aimed at identifying the components of the silencing machinery and its mechanism of inheritance. The roles of two central gene activities-the Su(var)3-9-encoded histone H3-lysine-9 methyltransferase and the Su(var)205-encoded methyl-H3-lysine-9 binding protein heterochromatin protein 1 (HP1a)-have been inferred from terminal phenotypes, leaving considerable gaps in understanding of how PEV behaves through development. Here, we investigate the PEV phenotypes of Su(var)3-9 and Su(var)205 mutations in live developing tissues. We discovered that mutation in Su(var)205 compromises the initial establishment of PEV in early embryogenesis. Later gains of heterochromatin-induced gene silencing are possible but are unstable and lost rapidly. In contrast, a strain with mutation in Su(var)3-9 exhibits robust silencing early in development but fails to maintain it through subsequent cell divisions. Our analyses show that, while the terminal phenotypes of these mutations may appear identical, they have arrived at them through different developmental trajectories. We discuss how our findings expand and clarify existing models for epigenetic inheritance of heterochromatin-induced gene silencing.


Assuntos
Homólogo 5 da Proteína Cromobox , Proteínas de Drosophila , Drosophila , Metiltransferases , Animais , Homólogo 5 da Proteína Cromobox/genética , Homólogo 5 da Proteína Cromobox/metabolismo , Drosophila/genética , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Heterocromatina/genética , Lisina/genética , Metiltransferases/genética , Metiltransferases/metabolismo
4.
J Biol Chem ; 298(6): 102053, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35605661

RESUMO

miRNA-based cellular fate reprogramming offers an opportunity to investigate the mechanisms of long-term gene silencing. To further understand how genes are silenced in a tissue-specific manner, we leveraged our miRNA-based method of reprogramming fibroblasts into cardiomyocytes. Through screening approaches, we identified three proteins that were downregulated during reprogramming of fibroblasts into cardiomyocytes: heterochromatin protein Cbx1, transcriptional activator protein PurB, and transcription factor Sp3. We show that knockdown of Cbx1, PurB, and Sp3 was sufficient to induce cardiomyocyte gene expression in fibroblasts. Similarly, gene editing to ablate Cbx1, PurB, and Sp3 expression induced fibroblasts to convert into cardiomyocytes in vivo. Furthermore, high-throughput DNA sequencing and coimmunoprecipitation experiments indicated that Cbx1, PurB, and Sp3 also bound together as a complex and were necessary to localize nucleosomes to cardiomyocyte genes on the chromosome. Finally, we found that the expression of these genes led to nucleosome modification via H3K27me3 (trimethylated histone-H3 lysine-27) deposition through an interaction with the polycomb repressive PRC2 complex. In summary, we conclude that Cbx1, PurB, and Sp3 control cell fate by actively repressing lineage-specific genes.


Assuntos
Reprogramação Celular , Homólogo 5 da Proteína Cromobox , Proteínas de Ligação a DNA , Inativação Gênica , Fator de Transcrição Sp3 , Animais , Homólogo 5 da Proteína Cromobox/genética , Homólogo 5 da Proteína Cromobox/metabolismo , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Heterocromatina/metabolismo , Humanos , Camundongos , MicroRNAs/genética , Miócitos Cardíacos/metabolismo , Proteínas do Grupo Polycomb/genética , Proteínas do Grupo Polycomb/metabolismo , Fator de Transcrição Sp3/genética , Fator de Transcrição Sp3/metabolismo
5.
Kidney Blood Press Res ; 47(5): 329-340, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35249038

RESUMO

BACKGROUND: Circular RNAs (circRNAs) were demonstrated to have roles in the carcinogenesis of renal cell carcinoma (RCC). Hence, this work aimed to determine the functions and molecular mechanism of circ_0037866 in regulating the progression of RCC. METHODS: Quantitative real-time polymerase chain reaction and Western blotting were used to detect the levels of genes and proteins. In vitro assays, including colony formation, 5-ethynyl-2'-deoxyuridine, flow cytometry, transwell assays, and in vivo tumor formation, were conducted to investigate the effects of circ_0037866 on RCC tumorigenesis. Dual-luciferase reporter assay, RNA pull-down, and RNA immunoprecipitation assay were used to confirm the interaction between miR-384 and circ_0037866 or Chromobox 5 (CBX5). RESULTS: Circ_0037866 is a stable circRNA and was found to be increased in RCC tissues and cells. Functionally, circ_0037866 silencing suppressed RCC cell survival, invasion, and migration in vitro, and impeded RCC cell tumorigenesis in the subcutaneous xenograft model. Mechanistically, circ_0037866 could function as a sponge for miR-384 to elevate the expression of its target CBX5. Furthermore, a series of rescue experiments showed that miR-384 inhibition reversed the anticancer effects of circ_0037866 knockdown on RCC cells; besides that, miR-384 restoration suppressed RCC cell growth and mobility, which were attenuated by CBX5 overexpression. CONCLUSION: Circ_0037866 knockdown restrains the tumorigenesis of RCC by miR-384/CBX5, revealing a promising molecular target for RCC therapy.


Assuntos
Carcinoma de Células Renais , Homólogo 5 da Proteína Cromobox , Neoplasias Renais , MicroRNAs , RNA Circular , Carcinogênese/genética , Carcinoma de Células Renais/genética , Carcinoma de Células Renais/metabolismo , Carcinoma de Células Renais/patologia , Proliferação de Células , Homólogo 5 da Proteína Cromobox/genética , Homólogo 5 da Proteína Cromobox/metabolismo , Feminino , Humanos , Neoplasias Renais/genética , Neoplasias Renais/metabolismo , Neoplasias Renais/patologia , Masculino , MicroRNAs/genética , MicroRNAs/metabolismo , RNA Circular/genética , RNA Circular/metabolismo
6.
EMBO Rep ; 23(4): e53581, 2022 04 05.
Artigo em Inglês | MEDLINE | ID: mdl-35166421

RESUMO

Di- or tri-methylated H3K9 (H3K9me2/3) is an epigenetic mark of heterochromatin. Heterochromatin protein 1 (HP1) specifically recognizes H3K9me2/3, contributing to transcriptional suppression and spread of H3K9me2/3. Here, we demonstrate another role of HP1 in heterochromatin organization: regulation of protein stability of H3K9 methyltransferases (H3K9 MTs) and demethylases (H3K9 DMs). We show that HP1 interaction-defective mutants of H3K9 MTs, Suv39h1 and Setdb1, undergo protein degradation. We further establish mouse embryonic stem cell lines lacking all three HP1 paralogs. In the HP1-deficient cells, Suv39h1, Suv39h2, Setdb1, and G9a/GLP complex decrease at the protein level, and the enzymes are released from chromatin. HP1 mutants that cannot recognize H3K9me2/3 or form dimers cannot stabilize these enzymes, indicating that the tethering of H3K9 MTs to chromatin is critical for their protein stability. We show that HP1 also stabilizes H3K9 DMs, Jmjd1a and Jmjd1b. Our study indicates that mammalian HP1 forms a heterochromatin hub that governs protein stability of H3K9 MTs and H3K9 DMs.


Assuntos
Homólogo 5 da Proteína Cromobox , Histonas , Metiltransferases , Animais , Cromatina/genética , Homólogo 5 da Proteína Cromobox/genética , Homólogo 5 da Proteína Cromobox/metabolismo , Estabilidade Enzimática , Heterocromatina , Histonas/metabolismo , Metiltransferases/metabolismo , Camundongos
7.
Nat Commun ; 13(1): 360, 2022 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-35042897

RESUMO

Human 53BP1 is primarily known as a key player in regulating DNA double strand break (DSB) repair choice; however, its involvement in other biological process is less well understood. Here, we report a previously uncharacterized function of 53BP1 at heterochromatin, where it undergoes liquid-liquid phase separation (LLPS) with the heterochromatin protein HP1α in a mutually dependent manner. Deletion of 53BP1 results in a reduction in heterochromatin centers and the de-repression of heterochromatic tandem repetitive DNA. We identify domains and residues of 53BP1 required for its LLPS, which overlap with, but are distinct from, those involved in DSB repair. Further, 53BP1 mutants deficient in DSB repair, but proficient in LLPS, rescue heterochromatin de-repression and protect cells from stress-induced DNA damage and senescence. Our study suggests that in addition to DSB repair modulation, 53BP1 contributes to the maintenance of heterochromatin integrity and genome stability through LLPS.


Assuntos
Heterocromatina/metabolismo , Proteína 1 de Ligação à Proteína Supressora de Tumor p53/metabolismo , Animais , Linhagem Celular , Núcleo Celular/metabolismo , Homólogo 5 da Proteína Cromobox/metabolismo , Quebras de DNA de Cadeia Dupla , Reparo do DNA , Proteínas de Fluorescência Verde/metabolismo , Camundongos , Camundongos Knockout , Mutação/genética , Domínios Proteicos , Estresse Fisiológico , Proteína 1 de Ligação à Proteína Supressora de Tumor p53/química
8.
J Med Chem ; 65(3): 2646-2655, 2022 02 10.
Artigo em Inglês | MEDLINE | ID: mdl-35014255

RESUMO

Development of inhibitors for histone methyllysine reader proteins is an active area of research due to the importance of reader protein-methyllysine interactions in transcriptional regulation and disease. Optimized peptide-based chemical probes targeting methyllysine readers favor larger alkyllysine residues in place of methyllysine. However, the mechanism by which these larger substituents drive tighter binding is not well understood. This study describes the development of a two-pronged approach combining genetic code expansion (GCE) and structure-activity relationships (SAR) through systematic variation of both the aromatic binding pocket in the protein and the alkyllysine residues in the peptide to probe inhibitor recognition in the CBX5 chromodomain. We demonstrate a novel change in driving force for larger alkyllysines, which weaken cation-π interactions but increases dispersion forces, resulting in tighter binding. This GCE-SAR approach establishes discrete energetic contributions to binding from both ligand and protein, providing a powerful tool to gain mechanistic understanding of SAR trends.


Assuntos
Homólogo 5 da Proteína Cromobox/metabolismo , Lisina/análogos & derivados , Peptidomiméticos/metabolismo , Homólogo 5 da Proteína Cromobox/química , Homólogo 5 da Proteína Cromobox/genética , Código Genético , Humanos , Ligantes , Estrutura Molecular , Mutagênese Sítio-Dirigida , Peptidomiméticos/química , Ligação Proteica/efeitos dos fármacos , Ligação Proteica/genética , Eletricidade Estática , Relação Estrutura-Atividade
9.
EMBO Rep ; 23(1): e51041, 2022 01 05.
Artigo em Inglês | MEDLINE | ID: mdl-34758190

RESUMO

The heterochromatin protein HP1 plays a central role in the maintenance of genome stability but little is known about how HP1 is controlled. Here, we show that the zinc finger protein POGZ promotes the presence of HP1 at DNA double-strand breaks (DSBs) in human cells. POGZ depletion delays the resolution of DSBs and sensitizes cells to different DNA-damaging agents, including cisplatin and talazoparib. Mechanistically, POGZ promotes homology-directed DNA repair by retaining the BRCA1/BARD1 complex at DSBs in an HP1-dependent manner. In vivo CRISPR inactivation of Pogz is embryonically lethal. Pogz haploinsufficiency (Pogz+ /delta) results in developmental delay, impaired intellectual abilities, hyperactive behaviour and a compromised humoral immune response in mice, recapitulating the main clinical features of the White Sutton syndrome (WHSUS). Pogz+ /delta mice are further radiosensitive and accumulate DSBs in diverse tissues, including the spleen and brain. Altogether, our findings identify POGZ as an important player in homology-directed DNA repair both in vitro and in vivo.


Assuntos
Homólogo 5 da Proteína Cromobox , Reparo do DNA , Deficiência Intelectual , Reparo de DNA por Recombinação , Transposases , Animais , Homólogo 5 da Proteína Cromobox/genética , Homólogo 5 da Proteína Cromobox/metabolismo , Proteínas Cromossômicas não Histona/genética , Proteínas Cromossômicas não Histona/metabolismo , DNA , Quebras de DNA de Cadeia Dupla , Humanos , Deficiência Intelectual/genética , Camundongos , Transposases/genética , Transposases/metabolismo
10.
Gene ; 813: 146092, 2022 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-34896523

RESUMO

BACKGROUND: Diffuse large B-cell lymphoma (DLBCL) is the main pathological type of non-Hodgkin lymphoma (NHL). Chromobox (CBX) family proteins are classical components of polycomb group (PcG) complexes in many cancer types, resulting in accelerated carcinogenesis. Nevertheless, the prognostic, functional and expression significance of these CBX family members in DLBCL remain unclear and elusive. METHODS: CBX transcriptional levels were confirmed using Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA) and Cancer Cell Line Encyclopedia (CCLE) databases. The protein levels of CBX family members were analysed using The Human Protein Atlas (HPA) database. Information on the PPI network, functional enrichment, drug sensitivity, prognostic value, miRNA network, protein structure, genetic alteration and immune cell infiltration were generated using the GeneMANIA, Metascape, GSCALite, GEPIA, PDB, cBioPortal, and TIMER databases, and the correlation of these factors with CBX expression levels in DLBCL was assessed. RESULTS: CBX1/2/3/5/6/8 mRNA levels were significantly enhanced in DLBCL tissues compared to corresponding normal tissues. CBX1/3/4/5/8 protein expression levels were obviously increased, whereas CBX7 was obviously decreased. This difference might be attributed to miRNA regulation based on the miRNA network. Overall survival (OS) analysis showed that CBX levels were not correlated with prognosis in DLBCL patients, indicating that CBXs are not good biomarkers for DLBCL patients. Furthermore, functional enrichment analyses indicated that CBXs were closely related to DNA duplex unwinding, covalent chromatin modification, and histone lysine methylation. The levels of CBXs were also significantly associated with diverse immune cell infiltration in DLBCL. CONCLUSIONS: This study reveals that dysregulated CBXs are involved in DLBCL development and might represent potential therapeutic targets for DLBCL.


Assuntos
Homólogo 5 da Proteína Cromobox/genética , Linfoma Difuso de Grandes Células B/genética , Proteínas do Grupo Polycomb/genética , Biomarcadores Tumorais/biossíntese , Biomarcadores Tumorais/genética , Homólogo 5 da Proteína Cromobox/biossíntese , Homólogo 5 da Proteína Cromobox/metabolismo , Bases de Dados Genéticas , Bases de Dados de Proteínas , Expressão Gênica , Humanos , Linfoma Difuso de Grandes Células B/metabolismo , Mutação , Complexo Repressor Polycomb 1/biossíntese , Complexo Repressor Polycomb 1/genética , Proteínas do Grupo Polycomb/biossíntese , Proteínas do Grupo Polycomb/metabolismo , Prognóstico , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Análise de Sobrevida , Transcriptoma
11.
FASEB J ; 36(1): e22074, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34859928

RESUMO

Cell adhesion molecule L1 regulates multiple cell functions and L1 deficiency is linked to several neural diseases. Proteolytic processing generates functionally decisive L1 fragments, which are imported into the nucleus. By computational analysis, we found at L1's C-terminal end the chromo shadow domain-binding motif PxVxL, which directs the binding of nuclear proteins to the heterochromatin protein 1 (HP1) isoforms α, ß, and É£. By enzyme-linked immunosorbent assay, we show that the intracellular L1 domain binds to all HP1 isoforms. These interactions involve the HP1 chromo shadow domain and are mediated via the sequence 1158 KDET1161 in the intracellular domain of murine L1, but not by L1's C-terminal PxVxL motif. Immunoprecipitation using nuclear extracts from the brain and from cultured cerebellar and cortical neurons indicates that HP1 isoforms interact with a yet unknown nuclear L1 fragment of approximately 55 kDa (L1-55), which carries ubiquitin residues. Proximity ligation indicates a close association between L1-55 and the HP1 isoforms in neuronal nuclei. This association is reduced after the treatment of neurons with inhibitors of metalloproteases, ß-site of amyloid precursor protein cleaving enzyme (BACE1), or É£-secretase, suggesting that cleavage of full-length L1 by these proteases generates L1-55. Reduction of HP1α, -ß, or -É£ expression by siRNA decreases L1-dependent neurite outgrowth from cultured cortical neurons and decreases the L1-dependent migration of L1-transfected HEK293 cells in a scratch assay. These findings indicate that the interaction of the novel fragment L1-55 with HP1 isoforms in nuclei affects L1-dependent functions, such as neurite outgrowth and neuronal migration.


Assuntos
Movimento Celular , Homólogo 5 da Proteína Cromobox/metabolismo , Molécula L1 de Adesão de Célula Nervosa/metabolismo , Neuritos/metabolismo , Motivos de Aminoácidos , Animais , Homólogo 5 da Proteína Cromobox/genética , Feminino , Masculino , Camundongos , Camundongos Mutantes , Molécula L1 de Adesão de Célula Nervosa/genética , Domínios Proteicos , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo
12.
Bioengineered ; 12(2): 10596-10607, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34895048

RESUMO

To probe into the potential mechanism of microRNA (miR)-98-5p inhibiting the biological progress of cervical cancer (CC) cells via regulating PI3K/Akt pathway. Reverse transcription quantitative polymerase chain reaction was applied to detect miR-98-5p expression in CC tissues and cell lines; Cell counting kit-8 and Edu analysis were performed for checking cell proliferation, flow cytometry for cell apoptosis, transwell for cell invasion and migration, Western blot for proliferation-related proteins Ki67 and Proliferating cell nuclear antigen expression, apoptosis-related proteins Bcl-2 and Bax expression, epithelial-mesenchymal transition (EMT)-related proteins Snail, matrix metalloproteinase-3, E-cadherin and N-cadherin expression, as well as PI3K/Akt pathway-related proteins PTEN, PI3K as well as Akt expression levels, and the nude mouse tumor xenograft experiment was applied to verify in vivo. The result clarified, miR-98-5p was reduced in CC. Overexpression miR-98-5p could inhibit CC cell proliferation, invasion, migration and EMT, whereas promoted its apoptosis, but silencing miR-98-5p was opposite. Overexpression miR-98-5p could depress the activation of PI3K/Akt pathway in CC in vivo and in vitro. MiR-98-5p targeted CBX5. In short, miR-98-5p is able to be used as a potential target for treating CC in future research.


Assuntos
Progressão da Doença , MicroRNAs/metabolismo , Fosfatidilinositol 3-Quinases/metabolismo , Proteínas Proto-Oncogênicas c-akt/metabolismo , Neoplasias do Colo do Útero/genética , Neoplasias do Colo do Útero/patologia , Animais , Apoptose/genética , Linhagem Celular Tumoral , Movimento Celular/genética , Proliferação de Células/genética , Homólogo 5 da Proteína Cromobox/metabolismo , Transição Epitelial-Mesenquimal/genética , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Camundongos Endogâmicos BALB C , Camundongos Nus , MicroRNAs/genética , Pessoa de Meia-Idade , Invasividade Neoplásica , Transdução de Sinais
13.
Int J Mol Sci ; 22(24)2021 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-34948223

RESUMO

Insertions of transposable elements (TEs) in eukaryotic genomes are usually associated with repressive chromatin, which spreads to neighbouring genomic sequences. In ovaries of Drosophila melanogaster, the Piwi-piRNA pathway plays a key role in the transcriptional silencing of TEs considered to be exerted mostly through the establishment of H3K9me3 histone marks recruiting Heterochromatin Protein 1a (HP1a). Here, using RNA-seq, we investigated the expression of TEs and the adjacent genomic regions upon Piwi and HP1a germline knockdowns sharing a similar genetic background. We found that the depletion of Piwi and HP1a led to the derepression of only partially overlapping TE sets. Several TEs were silenced predominantly by HP1a, whereas the upregulation of some other TEs was more pronounced upon Piwi knockdown and, surprisingly, was diminished upon a Piwi/HP1a double-knockdown. We revealed that HP1a loss influenced the expression of thousands of protein-coding genes mostly not adjacent to TE insertions and, in particular, downregulated a putative transcriptional factor required for TE activation. Nevertheless, our results indicate that Piwi and HP1a cooperatively exert repressive effects on the transcription of euchromatic loci flanking the insertions of some Piwi-regulated TEs. We suggest that this mechanism controls the silencing of a small set of TE-adjacent tissue-specific genes, preventing their inappropriate expression in ovaries.


Assuntos
Proteínas Argonautas/metabolismo , Homólogo 5 da Proteína Cromobox/metabolismo , Elementos de DNA Transponíveis , Proteínas de Drosophila/metabolismo , Células Germinativas/metabolismo , Ovário/metabolismo , RNA-Seq , Animais , Proteínas Argonautas/genética , Homólogo 5 da Proteína Cromobox/genética , Proteínas de Drosophila/genética , Drosophila melanogaster , Feminino
14.
Front Immunol ; 12: 738958, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34721405

RESUMO

Immune checkpoint blockade (ICB) relieves CD8+ T-cell exhaustion in most mutated tumors, and TCF-1 is implicated in converting progenitor exhausted cells to functional effector cells. However, identifying mechanisms that can prevent functional senescence and potentiate CD8+ T-cell persistence for ICB non-responsive and resistant tumors remains elusive. We demonstrate that targeting Cbx3/HP1γ in CD8+ T cells augments transcription initiation and chromatin remodeling leading to increased transcriptional activity at Lef1 and Il21r. LEF-1 and IL-21R are necessary for Cbx3/HP1γ-deficient CD8+ effector T cells to persist and control ovarian cancer, melanoma, and neuroblastoma in preclinical models. The enhanced persistence of Cbx3/HP1γ-deficient CD8+ T cells facilitates remodeling of the tumor chemokine/receptor landscape ensuring their optimal invasion at the expense of CD4+ Tregs. Thus, CD8+ T cells heightened effector function consequent to Cbx3/HP1γ deficiency may be distinct from functional reactivation by ICB, implicating Cbx3/HP1γ as a viable cancer T-cell-based therapy target for ICB resistant, non-responsive solid tumors.


Assuntos
Linfócitos T CD8-Positivos/metabolismo , Homólogo 5 da Proteína Cromobox/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , Linfócitos do Interstício Tumoral/metabolismo , Fator 1 de Ligação ao Facilitador Linfoide/metabolismo , Melanoma Experimental/metabolismo , Neuroblastoma/metabolismo , Neoplasias Ovarianas/metabolismo , Animais , Linfócitos T CD8-Positivos/imunologia , Linfócitos T CD8-Positivos/transplante , Diferenciação Celular , Linhagem Celular Tumoral , Homólogo 5 da Proteína Cromobox/genética , Proteínas Cromossômicas não Histona/genética , Técnicas de Cocultura , Feminino , Regulação Neoplásica da Expressão Gênica , Imunoterapia Adotiva , Subunidade alfa de Receptor de Interleucina-21/genética , Subunidade alfa de Receptor de Interleucina-21/metabolismo , Ativação Linfocitária , Linfócitos do Interstício Tumoral/imunologia , Fator 1 de Ligação ao Facilitador Linfoide/genética , Melanoma Experimental/genética , Melanoma Experimental/imunologia , Melanoma Experimental/terapia , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Camundongos Transgênicos , Neuroblastoma/genética , Neuroblastoma/imunologia , Neuroblastoma/terapia , Neoplasias Ovarianas/genética , Neoplasias Ovarianas/imunologia , Neoplasias Ovarianas/terapia , Transdução de Sinais , Linfócitos T Reguladores/imunologia , Linfócitos T Reguladores/metabolismo , Carga Tumoral , Microambiente Tumoral
15.
Cell ; 184(23): 5775-5790.e30, 2021 11 11.
Artigo em Inglês | MEDLINE | ID: mdl-34739832

RESUMO

RNA, DNA, and protein molecules are highly organized within three-dimensional (3D) structures in the nucleus. Although RNA has been proposed to play a role in nuclear organization, exploring this has been challenging because existing methods cannot measure higher-order RNA and DNA contacts within 3D structures. To address this, we developed RNA & DNA SPRITE (RD-SPRITE) to comprehensively map the spatial organization of RNA and DNA. These maps reveal higher-order RNA-chromatin structures associated with three major classes of nuclear function: RNA processing, heterochromatin assembly, and gene regulation. These data demonstrate that hundreds of ncRNAs form high-concentration territories throughout the nucleus, that specific RNAs are required to recruit various regulators into these territories, and that these RNAs can shape long-range DNA contacts, heterochromatin assembly, and gene expression. These results demonstrate a mechanism where RNAs form high-concentration territories, bind to diffusible regulators, and guide them into compartments to regulate essential nuclear functions.


Assuntos
Núcleo Celular/metabolismo , RNA/metabolismo , Animais , Núcleo Celular/efeitos dos fármacos , Homólogo 5 da Proteína Cromobox/metabolismo , Cromossomos/metabolismo , DNA/metabolismo , DNA Satélite/metabolismo , Proteínas de Ligação a DNA/metabolismo , Dactinomicina/farmacologia , Feminino , Genoma , Células HEK293 , Heterocromatina/metabolismo , Humanos , Camundongos , Modelos Biológicos , Família Multigênica , RNA Polimerase II/metabolismo , Processamento Pós-Transcricional do RNA/efeitos dos fármacos , Processamento Pós-Transcricional do RNA/genética , Splicing de RNA/genética , RNA Longo não Codificante/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Ribossômico/genética , Proteínas de Ligação a RNA/metabolismo , Transcrição Gênica/efeitos dos fármacos
16.
EMBO J ; 40(21): e104543, 2021 11 02.
Artigo em Inglês | MEDLINE | ID: mdl-34533226

RESUMO

The DNA polymerase zeta (Polζ) plays a critical role in bypassing DNA damage. REV3L, the catalytic subunit of Polζ, is also essential in mouse embryonic development and cell proliferation for reasons that remain incompletely understood. In this study, we reveal that REV3L protein interacts with heterochromatin components including repressive histone marks and localizes in pericentromeric regions through direct interaction with HP1 dimer. We demonstrate that Polζ/REV3L ensures progression of replication forks through difficult-to-replicate pericentromeric heterochromatin, thereby preventing spontaneous chromosome break formation. We also find that Rev3l-deficient cells are compromised in the repair of heterochromatin-associated double-stranded breaks, eliciting deletions in late-replicating regions. Lack of REV3L leads to further consequences that may be ascribed to heterochromatin replication and repair-associated functions of Polζ, with a disruption of the temporal replication program at specific loci. This is correlated with changes in epigenetic landscape and transcriptional control of developmentally regulated genes. These results reveal a new function of Polζ in preventing chromosome instability during replication of heterochromatic regions.


Assuntos
Replicação do DNA , Proteínas de Ligação a DNA/genética , DNA Polimerase Dirigida por DNA/genética , DNA/genética , Células-Tronco Embrionárias/metabolismo , Epigênese Genética , Heterocromatina/metabolismo , Animais , Linhagem Celular , Linhagem Celular Transformada , Proliferação de Células , Homólogo 5 da Proteína Cromobox/genética , Homólogo 5 da Proteína Cromobox/metabolismo , Instabilidade Cromossômica , DNA/metabolismo , Quebras de DNA de Cadeia Dupla , Proteínas de Ligação a DNA/metabolismo , DNA Polimerase Dirigida por DNA/metabolismo , Embrião de Mamíferos , Células-Tronco Embrionárias/citologia , Fibroblastos/citologia , Fibroblastos/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Células HeLa , Heterocromatina/química , Humanos , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Células NIH 3T3 , Transdução de Sinais
17.
Cell Rep ; 36(11): 109694, 2021 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-34525372

RESUMO

Chromatin organization plays a crucial role in tissue homeostasis. Heterochromatin relaxation and consequent unscheduled mobilization of transposable elements (TEs) are emerging as key contributors of aging and aging-related pathologies, including Alzheimer's disease (AD) and cancer. However, the mechanisms governing heterochromatin maintenance or its relaxation in pathological conditions remain poorly understood. Here we show that PIN1, the only phosphorylation-specific cis/trans prolyl isomerase, whose loss is associated with premature aging and AD, is essential to preserve heterochromatin. We demonstrate that this PIN1 function is conserved from Drosophila to humans and prevents TE mobilization-dependent neurodegeneration and cognitive defects. Mechanistically, PIN1 maintains nuclear type-B Lamin structure and anchoring function for heterochromatin protein 1α (HP1α). This mechanism prevents nuclear envelope alterations and heterochromatin relaxation under mechanical stress, which is a key contributor to aging-related pathologies.


Assuntos
Proteínas de Drosophila/metabolismo , Heterocromatina/metabolismo , Lamina Tipo B/metabolismo , Peptidilprolil Isomerase de Interação com NIMA/metabolismo , Peptidilprolil Isomerase/metabolismo , Estresse Mecânico , Doença de Alzheimer/metabolismo , Doença de Alzheimer/patologia , Animais , Células Cultivadas , Homólogo 5 da Proteína Cromobox/genética , Homólogo 5 da Proteína Cromobox/metabolismo , Elementos de DNA Transponíveis/genética , Drosophila/metabolismo , Proteínas de Drosophila/antagonistas & inibidores , Proteínas de Drosophila/genética , Humanos , Lamina Tipo B/química , Camundongos , Camundongos Endogâmicos C57BL , Peptidilprolil Isomerase de Interação com NIMA/antagonistas & inibidores , Peptidilprolil Isomerase de Interação com NIMA/genética , Neocórtex/citologia , Neocórtex/metabolismo , Neurônios/citologia , Neurônios/metabolismo , Membrana Nuclear/química , Peptidilprolil Isomerase/antagonistas & inibidores , Peptidilprolil Isomerase/genética , Fosforilação , Interferência de RNA , RNA Interferente Pequeno/metabolismo
18.
Mol Cell ; 81(20): 4287-4299.e5, 2021 10 21.
Artigo em Inglês | MEDLINE | ID: mdl-34428454

RESUMO

Eukaryotic chromosomes feature large regions of compact, repressed heterochromatin hallmarked by Heterochromatin Protein 1 (HP1). HP1 proteins play multi-faceted roles in shaping heterochromatin, and in cells, HP1 tethering to individual gene promoters leads to epigenetic modifications and silencing. However, emergent properties of HP1 at supranucleosomal scales remain difficult to study in cells because of a lack of appropriate tools. Here, we develop CRISPR-engineered chromatin organization (EChO), combining live-cell CRISPR imaging with inducible large-scale recruitment of chromatin proteins to native genomic targets. We demonstrate that human HP1α tiled across kilobase-scale genomic DNA form novel contacts with natural heterochromatin, integrates two distantly targeted regions, and reversibly changes chromatin from a diffuse to compact state. The compact state exhibits delayed disassembly kinetics and represses transcription across over 600 kb. These findings support a polymer model of HP1α-mediated chromatin regulation and highlight the utility of CRISPR-EChO in studying supranucleosomal chromatin organization in living cells.


Assuntos
Proteína 9 Associada à CRISPR/genética , Sistemas CRISPR-Cas , Montagem e Desmontagem da Cromatina , Homólogo 5 da Proteína Cromobox/metabolismo , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Heterocromatina/metabolismo , Proteína 9 Associada à CRISPR/metabolismo , Linhagem Celular Tumoral , Homólogo 5 da Proteína Cromobox/genética , Células HEK293 , Heterocromatina/genética , Humanos , Conformação de Ácido Nucleico , Conformação Proteica , RNA Guia de Cinetoplastídeos/genética , RNA Guia de Cinetoplastídeos/metabolismo , Relação Estrutura-Atividade , Fatores de Tempo
19.
Nature ; 595(7867): 444-449, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34194047

RESUMO

The size of the transcriptional program of long non-coding RNAs in the mammalian genome has engendered discussions about their biological roles1, particularly the promoter antisense (PAS) transcripts2,3. Here we report the development of an assay-referred to as chromatin isolation by RNA-Cas13a complex-to quantitatively detect the distribution of RNA in the genome. The assay revealed that PAS RNAs serve as a key gatekeeper of a broad transcriptional pause release program, based on decommissioning the 7SK small nuclear RNA-dependent inhibitory P-TEFb complex. Induction of PAS RNAs by liganded ERα led to a significant loss of H3K9me3 and the release of basally recruited HP1α and KAP1 on activated target gene promoters. This release was due to PAS RNA-dependent recruitment of H3K9me3 demethylases, which required interactions with a compact stem-loop structure in the PAS RNAs, an apparent feature of similarly regulated PAS RNAs. Activation of the ERα-bound MegaTrans enhancer, which is essential for robust pause release, required the recruitment of phosphorylated KAP1, with its transfer to the cognate promoters permitting 17ß-oestradiol-induced pause release and activation of the target gene. This study reveals a mechanism, based on RNA structure, that mediates the function of PAS RNAs in gene regulation.


Assuntos
Conformação de Ácido Nucleico , Regiões Promotoras Genéticas/genética , RNA Antissenso/química , RNA Antissenso/genética , Ativação Transcricional/genética , Linhagem Celular , Homólogo 5 da Proteína Cromobox/metabolismo , Proteína Substrato Associada a Crk , Receptor alfa de Estrogênio/metabolismo , Histonas/química , Histonas/metabolismo , Humanos , Histona Desmetilases com o Domínio Jumonji/metabolismo , Ligantes , Fator B de Elongação Transcricional Positiva/metabolismo , RNA Polimerase II/metabolismo , Estabilidade de RNA , Proteína 28 com Motivo Tripartido/metabolismo
20.
Brain Res Bull ; 176: 121-129, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34274429

RESUMO

Glioma, featured with high incidence and low survival rate, is the most common type of primary brain tumor, severely affecting human life worldwide. LINC02381 is an interesting lncRNA functioning as oncogenic lncRNA in some cancers but as tumor-suppressor in others, but no report demonstrates its association with and function in glioma. Intriguingly, we found in a bioinformatics website LncRNADisease that LINC02381 was closely related to malignant glioma, so this study aimed to figure out the expression and function of LINC02381 in glioma. By RT-qPCR, we confirmed LINC02381 upregulation in glioma cells. Functional experiments demonstrated that LINC02381 knockdown repressed glioma cell proliferation and induced apoptosis. Boinformatics tools and RT-qPCR revealed the positive correlation between LINC02381 and CBX5 in glioma cells. More importantly, we confirmed that LINC02381 could interact and work synergistically with CEBPß to bind to CBX5 promoter and activate CBX5 transcriptionally. Additionally, rescue experiments indicated that CBX5 up-regulation reversed the decline in cell proliferation and the augment in cell apoptosis caused by LINC02381 knockdown. To conclude, LINC02381 could facilitate CBX5 transcription via interaction with CEBPß, thus exerting its oncogenic role in glioma cells, which could contribute to better understanding of glioma.


Assuntos
Apoptose/genética , Neoplasias Encefálicas/genética , Proliferação de Células/genética , Homólogo 5 da Proteína Cromobox/genética , Glioma/genética , RNA Longo não Codificante/genética , Astrócitos/metabolismo , Neoplasias Encefálicas/metabolismo , Neoplasias Encefálicas/patologia , Homólogo 5 da Proteína Cromobox/metabolismo , Regulação Neoplásica da Expressão Gênica , Glioma/metabolismo , Glioma/patologia , Humanos , RNA Longo não Codificante/metabolismo , Transcrição Gênica
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