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1.
Int J Mol Sci ; 20(18)2019 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-31500108

RESUMO

The chloroplast RNA splicing and ribosome maturation (CRM) domain proteins are involved in the splicing of chloroplast gene introns. Numerous CRM domain proteins have been reported to play key roles in chloroplast development in several plant species. However, the functions of CRM domain proteins in chloroplast development in rice remain poorly understood. In the study, we generated oscaf1 albino mutants, which eventually died at the seedling stage, through the editing of OsCAF1 with two CRM domains using CRISPR/Cas9 technology. The mesophyll cells in oscaf1 mutant had decreased chloroplast numbers and damaged chloroplast structures. OsCAF1 was located in the chloroplast, and transcripts revealed high levels in green tissues. In addition, the OsCAF1 promoted the splicing of group IIA and group IIB introns, unlike orthologous proteins of AtCAF1 and ZmCAF1, which only affected the splicing of subgroup IIB introns. We also observed that the C-terminal of OsCAF1 interacts with OsCRS2, and OsCAF1-OsCRS2 complex may participate in the splicing of group IIA and group IIB introns in rice chloroplasts. OsCAF1 regulates chloroplast development by influencing the splicing of group II introns.


Assuntos
Cloroplastos/fisiologia , Proteínas de Plantas/metabolismo , Domínios e Motivos de Interação entre Proteínas , Fatores de Processamento de RNA/metabolismo , Cloroplastos/ultraestrutura , Regulação da Expressão Gênica de Plantas , Mutação , Oryza/genética , Oryza/metabolismo , Fenótipo , Proteínas de Plantas/química , Proteínas de Plantas/genética , Ligação Proteica , Processamento de RNA , Fatores de Processamento de RNA/química , Fatores de Processamento de RNA/genética , Espécies Reativas de Oxigênio , Ribossomos/metabolismo , Plântula/genética , Plântula/metabolismo
2.
J Clin Pathol ; 72(11): 778-782, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31473630

RESUMO

SF3B1 is the largest subunit of the Spliceosome Factor 3b (SF3B) complex and part of the U2 small nuclear ribosomal protein. It functions as an important part of spliceosomal assembly, converting precursor messenger RNA (mRNA) to mRNA ready for ribosomal translation. Mutations of SF3B1 are commonly seen in myelodysplastic syndromes with ring sideroblasts (MDS-RS)and MDS/myeloproliferative neoplasm (MPN-RS-T). These mutations are typically heterozygous missense substitutions, of which, 55% involve K700E. MDS-RS and MDS/MPN-RS-T usually carry a more favourable prognosis than other subtypes of MDS. SF3B1 itself does not influence survival in these conditions, but does correlate with increased thrombotic risk. Mutated SF3B1 is present in 9%-15% of chronic lymphocytic leukaemia cases and on its own correlates with improved responsiveness to ibrutinib, but is associated with additional adverse genetic abnormalities including TP53 and ATM mutations, which traditionally confer adverse outcomes.


Assuntos
Biomarcadores Tumorais/genética , Eritroblastos/patologia , Leucemia Linfocítica Crônica de Células B/genética , Mutação , Síndromes Mielodisplásicas/genética , Fosfoproteínas/genética , Fatores de Processamento de RNA/genética , Predisposição Genética para Doença , Humanos , Leucemia Linfocítica Crônica de Células B/metabolismo , Leucemia Linfocítica Crônica de Células B/patologia , Leucemia Linfocítica Crônica de Células B/terapia , Síndromes Mielodisplásicas/metabolismo , Síndromes Mielodisplásicas/patologia , Síndromes Mielodisplásicas/terapia , Fenótipo , Fosfoproteínas/química , Fosfoproteínas/metabolismo , Prognóstico , Conformação Proteica , Fatores de Processamento de RNA/química , Fatores de Processamento de RNA/metabolismo , Spliceossomos/genética , Spliceossomos/metabolismo , Relação Estrutura-Atividade
3.
Mol Cell ; 76(1): 82-95.e7, 2019 10 03.
Artigo em Inglês | MEDLINE | ID: mdl-31474574

RESUMO

SF3B1, which encodes an essential spliceosomal protein, is frequently mutated in myelodysplastic syndromes (MDS) and many cancers. However, the defect of mutant SF3B1 is unknown. Here, we analyzed RNA sequencing data from MDS patients and confirmed that SF3B1 mutants use aberrant 3' splice sites. To elucidate the underlying mechanism, we purified complexes containing either wild-type or the hotspot K700E mutant SF3B1 and found that levels of a poorly studied spliceosomal protein, SUGP1, were reduced in mutant spliceosomes. Strikingly, SUGP1 knockdown completely recapitulated the splicing errors, whereas SUGP1 overexpression drove the protein, which our data suggest plays an important role in branchsite recognition, into the mutant spliceosome and partially rescued splicing. Other hotspot SF3B1 mutants showed similar altered splicing and diminished interaction with SUGP1. Our study demonstrates that SUGP1 loss is a common defect of spliceosomes with disease-causing SF3B1 mutations and, because this defect can be rescued, suggests possibilities for therapeutic intervention.


Assuntos
Leucemia Eritroblástica Aguda/metabolismo , Mutação , Síndromes Mielodisplásicas/metabolismo , Fosfoproteínas/metabolismo , Fatores de Processamento de RNA/metabolismo , Processamento de RNA , Spliceossomos/metabolismo , Regulação Neoplásica da Expressão Gênica , Predisposição Genética para Doença , Células HEK293 , Humanos , Células K562 , Leucemia Eritroblástica Aguda/genética , Leucemia Eritroblástica Aguda/patologia , Síndromes Mielodisplásicas/genética , Síndromes Mielodisplásicas/patologia , Fenótipo , Fosfoproteínas/genética , Ligação Proteica , Fatores de Processamento de RNA/genética , Spliceossomos/genética , Spliceossomos/patologia
4.
Nature ; 572(7770): 543-548, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31391587

RESUMO

The synthesis of pre-mRNA by RNA polymerase II (Pol II) involves the formation of a transcription initiation complex, and a transition to an elongation complex1-4. The large subunit of Pol II contains an intrinsically disordered C-terminal domain that is phosphorylated by cyclin-dependent kinases during the transition from initiation to elongation, thus influencing the interaction of the C-terminal domain with different components of the initiation or the RNA-splicing apparatus5,6. Recent observations suggest that this model provides only a partial picture of the effects of phosphorylation of the C-terminal domain7-12. Both the transcription-initiation machinery and the splicing machinery can form phase-separated condensates that contain large numbers of component molecules: hundreds of molecules of Pol II and mediator are concentrated in condensates at super-enhancers7,8, and large numbers of splicing factors are concentrated in nuclear speckles, some of which occur at highly active transcription sites9-12. Here we investigate whether the phosphorylation of the Pol II C-terminal domain regulates the incorporation of Pol II into phase-separated condensates that are associated with transcription initiation and splicing. We find that the hypophosphorylated C-terminal domain of Pol II is incorporated into mediator condensates and that phosphorylation by regulatory cyclin-dependent kinases reduces this incorporation. We also find that the hyperphosphorylated C-terminal domain is preferentially incorporated into condensates that are formed by splicing factors. These results suggest that phosphorylation of the Pol II C-terminal domain drives an exchange from condensates that are involved in transcription initiation to those that are involved in RNA processing, and implicates phosphorylation as a mechanism that regulates condensate preference.


Assuntos
Complexo Mediador/química , Complexo Mediador/metabolismo , RNA Polimerase II/química , RNA Polimerase II/metabolismo , Processamento de RNA , Transcrição Genética , Animais , Linhagem Celular , Elementos Facilitadores Genéticos/genética , Regulação da Expressão Gênica/genética , Humanos , Complexo Mediador/genética , Camundongos , Fosforilação , Domínios Proteicos , RNA Polimerase II/genética , Fatores de Processamento de RNA/química , Fatores de Processamento de RNA/genética , Fatores de Processamento de RNA/metabolismo
5.
RNA ; 25(11): 1509-1521, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31383795

RESUMO

During splicing of pre-mRNA, 5' and 3' splice sites are brought within proximity by interactions between the pre-mRNA bound U1 and U2 snRNPs, followed by recruitment of the tri-snRNP for assembly of the mature spliceosome. Previously, we identified an interaction between the U2 snRNP-specific protein SF3A1 and the stem-loop 4 (SL4) of the U1 snRNA that occurs during the early steps of spliceosome assembly. Although harboring many annotated domains, SF3A1 lacks a canonical RNA binding domain. To identify the U1-SL4 binding region in SF3A1, we expressed amino- and carboxy-terminal deletion constructs using a HeLa cell-based cell free expression system. UV-crosslinking of the truncated proteins with 32P-U1-SL4 RNA identified the carboxy-terminal ubiquitin-like (UBL) domain of SF3A1 as the RNA binding region. Characterization of the interaction between SF3A1-UBL and U1-SL4 by electrophoretic mobility shift assay and surface plasmon resonance determined high binding affinity (K D = ∼97 nM), and revealed the double-stranded G-C rich stem of U1-SL4 as an important feature for binding to the UBL domain. Further, mutations of two conserved tyrosine residues, Y772 and Y773, were found to cause a two- and fivefold decrease in the binding affinity for U1-SL4, respectively. Finally, we found that SF3A1-UBL can specifically pull down the U1 snRNP from HeLa nuclear extract, demonstrating its capacity to bind U1-SL4 in the context of the intact snRNP. Thus, the data show that the UBL domain of SF3A1 can function as an RNA binding domain and that mutations in this region may interfere with U1-SL4 binding.


Assuntos
Fatores de Processamento de RNA/metabolismo , RNA/metabolismo , Sítios de Ligação , Ensaio de Desvio de Mobilidade Eletroforética , Células HeLa , Humanos , Ligação Proteica , RNA Nuclear Pequeno/metabolismo , Ubiquitina/metabolismo
6.
Int J Mol Sci ; 20(14)2019 Jul 19.
Artigo em Inglês | MEDLINE | ID: mdl-31331069

RESUMO

Mutant mice with respect to the splicing factor Zrsr1 present altered spermatogenesis and infertility. To investigate whether Zrsr1 is involved in the homeostatic control that the hypothalamus exerts over reproductive functions, we first analyzed both differential gene and isoform expression and alternative splicing alterations in Zrsr1 mutant (Zrsr1mu) hypothalamus; second, we analyzed the spontaneous and social behavior of Zrsr1mu mice; and third, we analyzed adult cell proliferation and survival in the Zrsr1mu hypothalamus. The Zrsr1mu hypothalamus showed altered expression of genes and isoforms related to the glutathione metabolic process, synaptonemal complex assembly, mRNA transport, and altered splicing events involving the enrichment of U12-type intron retention (IR). Furthermore, increased IR in U12-containing genes related with the prolactin, progesterone, and gonadotropin-releasing hormone (GnRH) reproductive signaling pathway was observed. This was associated with a hyperactive phenotype in both males and females, with an anxious phenotype in females, and with increased social interaction in males, instead of the classical aggressive behavior. In addition, Zrsr1mu females but not males exhibited reduced cell proliferation in both the hypothalamus and the subventricular zone. Overall, these results suggest that Zrsr1 expression and function are relevant to organization of the hypothalamic cell network controlling behavior.


Assuntos
Íntrons , Mutação , Neurogênese , Fatores de Processamento de RNA/genética , Processamento de RNA , Processamento Alternativo , Animais , Comportamento Animal , Linhagem Celular Tumoral , Proliferação de Células , Sobrevivência Celular/genética , Regulação da Expressão Gênica , Humanos , Hipotálamo/metabolismo , Camundongos , Camundongos Knockout , Fenótipo , Fatores de Processamento de RNA/metabolismo , Comportamento Social
7.
Medicine (Baltimore) ; 98(30): e16534, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31348270

RESUMO

BACKGROUND: High-grade prostate cancer (PCa) has a poor prognosis, and up to 15% of patients worldwide experience lymph node invasion (LNI). To further improve the prediction lymph node invasion in prostate cancer, we adopted risk scores of the genes expression based on the nomogram in guidelines. METHODS: We analyzed clinical data from 320 PCa patients from the Cancer Genome Atlas database. Weighted gene coexpression network analysis was used to identify the genes that were significantly associated with LNI in PCa (n = 390). Analyses using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases were performed to identify the activated signaling pathways. Univariate and multivariate logistic regression analyses were performed to identify the independent risk factors for the presence of LNI. RESULTS: We found that patients with actual LNI and predicted LNI had the worst survival outcomes. The 7 most significant genes (CTNNAL1, ENSA, MAP6D1, MBD4, PRCC, SF3B2, TREML1) were selected for further analysis. Pathways in the cell cycle, DNA replication, oocyte meiosis, and 9 other pathways were dramatically activated during LNI in PCa. Multivariate analyses identified that the risk score (odds ratio [OR] = 1.05 for 1% increase, 95% confidence interval [CI]: 1.04-1.07, P < .001), serum PSA level, clinical stage, primary biopsy Gleason grade (OR = 2.52 for a grade increase, 95% CI: 1.27-5.22, P = .096), and secondary biopsy Gleason grade were independent predictors of LNI. A nomogram built using these predictive variables showed good calibration and a net clinical benefit, with an area under the curve (AUC) value of 90.2%. CONCLUSIONS: In clinical practice, the application of our nomogram might contribute significantly to the selection of patients who are good candidates for surgery with extended pelvic lymph node dissection.


Assuntos
Biomarcadores Tumorais/genética , Metástase Linfática/genética , Nomogramas , Neoplasias da Próstata/genética , Idoso , Área Sob a Curva , Proteínas de Ciclo Celular/metabolismo , Bases de Dados Genéticas , Endodesoxirribonucleases/metabolismo , Humanos , Peptídeos e Proteínas de Sinalização Intercelular , Modelos Logísticos , Linfonodos/patologia , Masculino , Proteínas Associadas aos Microtúbulos/metabolismo , Pessoa de Meia-Idade , Análise Multivariada , Gradação de Tumores , Proteínas de Neoplasias/metabolismo , Razão de Chances , Peptídeos/metabolismo , Valor Preditivo dos Testes , Neoplasias da Próstata/patologia , Fatores de Processamento de RNA/metabolismo , Receptores Imunológicos/metabolismo , Reprodutibilidade dos Testes , Fatores de Risco , alfa Catenina/metabolismo
8.
BMC Biol ; 17(1): 56, 2019 07 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311534

RESUMO

BACKGROUND: Adaptive responses to stress are essential for cell and organismal survival. In metazoans, little is known about the impact of environmental stress on RNA homeostasis. RESULTS: By studying the regulation of a cadmium-induced gene named numr-1 in Caenorhabditis elegans, we discovered that disruption of RNA processing acts as a signal for environmental stress. We find that NUMR-1 contains motifs common to RNA splicing factors and influences RNA splicing in vivo. A genome-wide screen reveals that numr-1 is strongly and specifically induced by silencing of genes that function in basal RNA metabolism including subunits of the metazoan integrator complex. Human integrator processes snRNAs for functioning with splicing factors, and we find that silencing of C. elegans integrator subunits disrupts snRNA processing, causes aberrant pre-mRNA splicing, and induces the heat shock response. Cadmium, which also strongly induces numr-1, has similar effects on RNA and the heat shock response. Lastly, we find that heat shock factor-1 is required for full numr-1 induction by cadmium. CONCLUSION: Our results are consistent with a model in which disruption of integrator processing of RNA acts as a molecular damage signal initiating an adaptive stress response mediated by heat shock factor-1. When numr-1 is induced via this pathway in C. elegans, its function in RNA metabolism may allow it to mitigate further damage and thereby promote tolerance to cadmium.


Assuntos
Cádmio/toxicidade , Caenorhabditis elegans/fisiologia , Regulação da Expressão Gênica , Resposta ao Choque Térmico/fisiologia , Processamento Pós-Transcricional do RNA/fisiologia , Processamento de RNA , Animais , Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Resposta ao Choque Térmico/genética , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Fatores de Processamento de RNA/genética , Fatores de Processamento de RNA/metabolismo , RNA Nuclear Pequeno/genética , RNA Nuclear Pequeno/metabolismo , Estresse Fisiológico
9.
Genes Cells ; 24(8): 585-590, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31166646

RESUMO

Noncoding (nc) RNA called satellite I is transcribed from the human centromere region. Depletion of this ncRNA results in abnormal nuclear morphology because of defects in chromosome segregation. Some protein factors interact with this ncRNA and function as a component of a nc ribonucleoprotein (RNP) complex in mitotic regulation. Here, we found that DHX38, a pre-mRNA splicing-related DEAH box RNA helicase, interacts with satellite I ncRNA. Depletion of DHX38 resulted in defective chromosome segregation similar to knockdown of satellite I ncRNA. Interaction between DHX38 and ncRNA was interphase-specific, but DHX38 depletion affected the function of Aurora B, which associated with satellite I ncRNA at mitotic phase. Based on these findings, we suggest that DHX38 has a role in mitotic regulation as a component of the satellite I ncRNP complex at interphase.


Assuntos
Centrômero/genética , Segregação de Cromossomos , RNA Helicases DEAD-box/metabolismo , DNA Satélite , Fatores de Processamento de RNA/metabolismo , RNA não Traduzido/genética , Linhagem Celular , Técnicas de Silenciamento de Genes , Humanos
10.
Retrovirology ; 16(1): 12, 2019 04 29.
Artigo em Inglês | MEDLINE | ID: mdl-31036027

RESUMO

BACKGROUND: The different interactions between viral proteins and cellular host proteins are required for efficient replication of HIV-1. Various reports implicated host cellular proteins as a key factor that either interact directly with HIV-1 integrase (IN) or get involved in the integration process of virus resulting in the modulation of integration step. Polypyrimidine tract binding protein and associated splicing factor (PSF) has diverse functions inside the cell such as transcriptional regulation, DNA repair, acts as nucleic acids binding protein and regulate replication and infectivity of different viruses. RESULTS: The protein binding study identified the association of host protein PSF with HIV-1 integrase. The siRNA knockdown (KD) of PSF resulted in increased viral replication in TZM-bl cells, suggesting PSF has negative influence on viral replication. The quantitative PCR of virus infected PSF knockdown TZM-bl cells showed more integrated DNA and viral cDNA as compared to control cells. We did not observe any significant difference between the amount of early reverse transcription products as well as infectivity of virus in the PSF KD and control TZM-bl cells. Molecular docking study supported the argument that PSF hinders the binding of viral DNA with IN. CONCLUSION: In an attempt to study the host interacting protein of IN, we have identified a new interacting host protein PSF which is a splicing factor and elucidated its role in integration and viral replication. Experimental as well as in silico analysis inferred that the host protein causes not only change in the integration events but also targets the incoming viral DNA or the integrase-viral DNA complex. The role of PSF was also investigated at early reverse transcript production as well as late stages. The PSF is causing changes in integration events, but it does not over all make any changes in the virus infectivity. MD trajectory analyses provided a strong clue of destabilization of Integrase-viral DNA complex occurred due to PSF interaction with the conserved bases of viral DNA ends that are extremely crucial contact points with integrase and indispensable for integration. Thus our study emphasizes the negative influence of PSF on HIV-1 replication.


Assuntos
DNA Viral/metabolismo , Integrase de HIV/metabolismo , Interações entre Hospedeiro e Microrganismos , Proteína de Ligação a Regiões Ricas em Polipirimidinas/metabolismo , Fatores de Processamento de RNA/metabolismo , Replicação Viral , DNA Viral/genética , Técnicas de Silenciamento de Genes , Células HEK293 , Integrase de HIV/genética , HIV-1/fisiologia , Humanos , Simulação de Acoplamento Molecular , Proteína de Ligação a Regiões Ricas em Polipirimidinas/genética , Ligação Proteica , Processamento de RNA , Fatores de Processamento de RNA/genética , RNA Interferente Pequeno , Transcrição Reversa , Integração Viral
11.
Genetics ; 212(3): 931-951, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31073019

RESUMO

MicroRNAs (miRNAs) are known to modulate gene expression, but their activity at the tissue-specific level remains largely uncharacterized. To study their contribution to tissue-specific gene expression, we developed novel tools to profile putative miRNA targets in the Caenorhabditis elegans intestine and body muscle. We validated many previously described interactions and identified ∼3500 novel targets. Many of the candidate miRNA targets curated are known to modulate the functions of their respective tissues. Within our data sets we observed a disparity in the use of miRNA-based gene regulation between the intestine and body muscle. The intestine contained significantly more putative miRNA targets than the body muscle highlighting its transcriptional complexity. We detected an unexpected enrichment of RNA-binding proteins targeted by miRNA in both tissues, with a notable abundance of RNA splicing factors. We developed in vivo genetic tools to validate and further study three RNA splicing factors identified as putative miRNA targets in our study (asd-2, hrp-2, and smu-2), and show that these factors indeed contain functional miRNA regulatory elements in their 3'UTRs that are able to repress their expression in the intestine. In addition, the alternative splicing pattern of their respective downstream targets (unc-60, unc-52, lin-10, and ret-1) is dysregulated when the miRNA pathway is disrupted. A reannotation of the transcriptome data in C. elegans strains that are deficient in the miRNA pathway from past studies supports and expands on our results. This study highlights an unexpected role for miRNAs in modulating tissue-specific gene isoforms, where post-transcriptional regulation of RNA splicing factors associates with tissue-specific alternative splicing.


Assuntos
Processamento Alternativo , Proteínas de Caenorhabditis elegans/metabolismo , Mucosa Intestinal/metabolismo , Músculo Esquelético/metabolismo , Fatores de Processamento de RNA/metabolismo , Proteínas de Ligação a RNA/metabolismo , Animais , Caenorhabditis elegans , Proteínas de Caenorhabditis elegans/genética , Ribonucleoproteínas Nucleares Heterogêneas Grupo A-B/genética , Ribonucleoproteínas Nucleares Heterogêneas Grupo A-B/metabolismo , Peptídeos e Proteínas de Sinalização Intracelular/genética , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , MicroRNAs/genética , MicroRNAs/metabolismo , Especificidade de Órgãos , Fatores de Processamento de RNA/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Proteínas de Ligação a RNA/genética
12.
Hepatol Int ; 13(4): 454-467, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31140152

RESUMO

PURPOSE: Trans-acting splicing factors (SF) shape the eukaryotic transcriptome by regulating alternative splicing (AS). This process is recurrently modulated in liver cancer suggesting its direct contribution to the course of liver disease. The aim of our study was to investigate the relationship between the regulation of SFs expression and liver damage. METHODS: The expression profile of 10 liver-specific SF and the AS events of 7 genes associated with liver disorders was assessed by western-blotting in 6 murine models representing different stages of liver damage, from inflammation to hepatocellular carcinoma (HCC). Relevant SFs (PSF, SRSF3, and SRSF6) and target genes (INSR, SRSF3, and SLK) modulated in mice were investigated in a cohort of 179 HCC patients. RESULTS: Each murine model of liver disease was characterized by a unique SF expression profile. Changes in the SF profile did not affect AS events of the selected genes despite the presence of corresponding splicing sites. In human HCC expression of SFs, including the tumor-suppressor SRSF3, and AS regulation of genes studied were frequently upregulated in tumor versus non-tumor tissues. Risk of tumor recurrence positively correlated with AS isoform of the INSR gene. In contrast, increased levels of SFs expression correlated with an extended overall survival of patients. CONCLUSIONS: Dysregulation of SF expression is an early event occurring during liver injury and not just at the stage of HCC. Besides impacting on AS regulation, overexpression of SF may contribute to preserving hepatocyte homeostasis during liver pathogenesis.


Assuntos
Hepatopatias/metabolismo , Fatores de Processamento de RNA/metabolismo , Processamento Alternativo/genética , Animais , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/metabolismo , Carcinoma Hepatocelular/mortalidade , Modelos Animais de Doenças , Progressão da Doença , Feminino , Humanos , Hepatopatias/genética , Hepatopatias/mortalidade , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/metabolismo , Neoplasias Hepáticas/mortalidade , Masculino , Camundongos Endogâmicos C57BL , Pessoa de Meia-Idade , Recidiva Local de Neoplasia
13.
Exp Mol Pathol ; 109: 36-41, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31128090

RESUMO

BACKGROUND: Calcific tendinopathy (CT) is characterized by deposits of calcium, most commonly found in the shoulder tendons. The exact cause and pathogenesis of CT are not fully understood. This study analyzed the expression pattern of RNA-binding protein fox-1 homolog 2 (RBFOX2), a crucial splicing regulator in tissue differentiation. METHODS: Normal and calcific tendons were compared for RBFOX2 mRNA level using quantitative reverse-transcription polymerase chain reaction. Intracellular localization of RBFOX2 protein was investigated using immunofluorescence microscopy. Normal and calcific tendon cDNAs were used to clone RBFOX2. Sequencing analysis identified coding sequences of the RBFOX2 isoform. RESULTS: The intracellular localization of RBFOX2 protein differed with disease status, with RBFOX2 localized in the cytoplasm in calcific tendons and the nucleus in normal tendons. Analysis of the RBFOX2 protein-coding sequence showed that exon 10, responsible for nuclear localization, was absent in calcific tendons. Splicing of RBFOX2 target genes CHD2 and MBNL1 was significantly affected by cytoplasmic localization of RBFOX2 in calcific tendons. DISCUSSION: Given the function of RBFOX2 as a splicing regulator in the nucleus, cytoplasmic localization of RBFOX2 protein in calcific tendons may have affected overall splicing events and altered gene expression. These results provide insights for comprehension of CT pathogenesis.


Assuntos
Processamento Alternativo , Citoplasma/genética , Fatores de Processamento de RNA/genética , Proteínas Repressoras/genética , Tendinopatia/genética , Idoso , Sequência de Aminoácidos , Núcleo Celular/genética , Núcleo Celular/metabolismo , Citoplasma/metabolismo , Éxons/genética , Feminino , Células HeLa , Humanos , Masculino , Pessoa de Meia-Idade , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Fatores de Processamento de RNA/metabolismo , Proteínas Repressoras/metabolismo , Homologia de Sequência de Aminoácidos , Tendinopatia/diagnóstico , Tendinopatia/metabolismo , Tendões/metabolismo , Tendões/patologia
14.
Genome Res ; 29(5): 711-722, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30962178

RESUMO

The inclusion of exons during the splicing process depends on the binding of splicing factors to short low-complexity regulatory sequences. The relationship between exonic splicing regulatory sequences and coding sequences is still poorly understood. We demonstrate that exons that are coregulated by any given splicing factor share a similar nucleotide composition bias and preferentially code for amino acids with similar physicochemical properties because of the nonrandomness of the genetic code. Indeed, amino acids sharing similar physicochemical properties correspond to codons that have the same nucleotide composition bias. In particular, we uncover that the TRA2A and TRA2B splicing factors that bind to adenine-rich motifs promote the inclusion of adenine-rich exons coding preferentially for hydrophilic amino acids that correspond to adenine-rich codons. SRSF2 that binds guanine/cytosine-rich motifs promotes the inclusion of GC-rich exons coding preferentially for small amino acids, whereas SRSF3 that binds cytosine-rich motifs promotes the inclusion of exons coding preferentially for uncharged amino acids, like serine and threonine that can be phosphorylated. Finally, coregulated exons encoding amino acids with similar physicochemical properties correspond to specific protein features. In conclusion, the regulation of an exon by a splicing factor that relies on the affinity of this factor for specific nucleotide(s) is tightly interconnected with the exon-encoded physicochemical properties. We therefore uncover an unanticipated bidirectional interplay between the splicing regulatory process and its biological functional outcome.


Assuntos
Processamento Alternativo , Éxons/genética , Sítios de Splice de RNA/genética , Fatores de Processamento de RNA/metabolismo , Aminoácidos/química , Composição de Bases/genética , Linhagem Celular , Código Genético , Ribonucleoproteínas Nucleares Heterogêneas/metabolismo , Humanos , Íntrons/genética , Motivos de Nucleotídeos/genética , Análise de Sequência de Proteína , Análise de Sequência de RNA , Fatores de Processamento de Serina-Arginina/metabolismo
15.
Nat Commun ; 10(1): 1590, 2019 04 08.
Artigo em Inglês | MEDLINE | ID: mdl-30962446

RESUMO

Alternative splicing, a fundamental step in gene expression, is deregulated in many diseases. Splicing factors (SFs), which regulate this process, are up- or down regulated or mutated in several diseases including cancer. To date, there are no inhibitors that directly inhibit the activity of SFs. We designed decoy oligonucleotides, composed of several repeats of a RNA motif, which is recognized by a single SF. Here we show that decoy oligonucleotides targeting splicing factors RBFOX1/2, SRSF1 and PTBP1, can specifically bind to their respective SFs and inhibit their splicing and biological activities both in vitro and in vivo. These decoy oligonucleotides present an approach to specifically downregulate SF activity in conditions where SFs are either up-regulated or hyperactive.


Assuntos
Ribonucleoproteínas Nucleares Heterogêneas/genética , Oligonucleotídeos/farmacologia , Proteína de Ligação a Regiões Ricas em Polipirimidinas/genética , Fatores de Processamento de RNA/genética , Fatores de Processamento de Serina-Arginina/genética , Processamento Alternativo , Animais , Animais Geneticamente Modificados , Sítios de Ligação , Glioblastoma/genética , Glioblastoma/patologia , Células HEK293 , Ribonucleoproteínas Nucleares Heterogêneas/antagonistas & inibidores , Ribonucleoproteínas Nucleares Heterogêneas/metabolismo , Humanos , Sistema de Sinalização das MAP Quinases/genética , Músculo Esquelético/crescimento & desenvolvimento , Degradação do RNAm Mediada por Códon sem Sentido , Oligonucleotídeos/química , Oligonucleotídeos/metabolismo , Proteína de Ligação a Regiões Ricas em Polipirimidinas/antagonistas & inibidores , Proteína de Ligação a Regiões Ricas em Polipirimidinas/metabolismo , Fatores de Processamento de RNA/antagonistas & inibidores , Fatores de Processamento de RNA/metabolismo , Fatores de Processamento de Serina-Arginina/antagonistas & inibidores , Fatores de Processamento de Serina-Arginina/metabolismo , Sequências de Repetição em Tandem , Ensaios Antitumorais Modelo de Xenoenxerto , Peixe-Zebra/embriologia , Peixe-Zebra/genética
16.
J Biol Chem ; 294(22): 8760-8772, 2019 05 31.
Artigo em Inglês | MEDLINE | ID: mdl-31010829

RESUMO

The cohesin complex regulates sister chromatid cohesion, chromosome organization, gene expression, and DNA repair. Cohesin is a ring complex composed of four core subunits and seven regulatory subunits. In an effort to comprehensively identify additional cohesin-interacting proteins, we used gene editing to introduce a dual epitope tag into the endogenous allele of each of 11 known components of cohesin in cultured human cells, and we performed MS analyses on dual-affinity purifications. In addition to reciprocally identifying all known components of cohesin, we found that cohesin interacts with a panoply of splicing factors and RNA-binding proteins (RBPs). These included diverse components of the U4/U6.U5 tri-small nuclear ribonucleoprotein complex and several splicing factors that are commonly mutated in cancer. The interaction between cohesin and splicing factors/RBPs was RNA- and DNA-independent, occurred in chromatin, was enhanced during mitosis, and required RAD21. Furthermore, cohesin-interacting splicing factors and RBPs followed the cohesin cycle and prophase pathway of cell cycle-regulated interactions with chromatin. Depletion of cohesin-interacting splicing factors and RBPs resulted in aberrant mitotic progression. These results provide a comprehensive view of the endogenous human cohesin interactome and identify splicing factors and RBPs as functionally significant cohesin-interacting proteins.


Assuntos
Proteínas de Ciclo Celular/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , Mitose , Proteômica , Fatores de Processamento de RNA/metabolismo , Proteínas de Ligação a RNA/metabolismo , Proteínas de Ciclo Celular/antagonistas & inibidores , Proteínas de Ciclo Celular/genética , Linhagem Celular Tumoral , Cromatina/metabolismo , Proteínas Cromossômicas não Histona/genética , Proteínas de Ligação a DNA/antagonistas & inibidores , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Humanos , Microscopia de Fluorescência , Ligação Proteica , Mapas de Interação de Proteínas , Interferência de RNA , Fatores de Processamento de RNA/antagonistas & inibidores , Fatores de Processamento de RNA/genética , RNA Interferente Pequeno/metabolismo , Proteínas de Ligação a RNA/antagonistas & inibidores , Proteínas de Ligação a RNA/genética
17.
Biomolecules ; 9(4)2019 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-30939845

RESUMO

Although inhibition of the androgen⁻androgen receptor (AR) axis effectively represses the growth of prostate cancer, most of all cases eventually become castration-resistant prostate cancers (CRPCs). Enhancement of the expression of AR and its variants along with the downstream signals is important for disease progression. AR-V7, a constitutive active form of AR, is generated as a result of RNA splicing. RNA splicing creates multiple transcript variants from one pre-messenger RNA (mRNA) by removing introns/exons to allow mRNA translation. The molecular mechanisms leading to marked increases of AR and generation of AR-V7 have been unclear. However, recent papers highlighted the roles of RNA splicing factors which promote AR expression and production of variants. Notably, a broad range of splicing components were aberrantly regulated in CRPC tissues. Interestingly, expression of various spliceosome genes is enhanced by RNA-binding protein splicing factor proline- and glutamine-rich (PSF/SFPQ), leading to changes in the expression of AR transcript variants. Moreover, inhibition of several splicing factors repressed tumor growth in vivo. Altered expression of splicing factors is correlated to biochemical recurrence in prostate cancer patients. Thus, these findings suggest that splicing factors would be a potential therapeutic target. This review focuses on the emerging roles of splicing factors in prostate cancer progression and AR signaling.


Assuntos
Neoplasias da Próstata/metabolismo , Neoplasias da Próstata/patologia , Fatores de Processamento de RNA/metabolismo , Receptores Androgênicos/metabolismo , Transdução de Sinais , Animais , Humanos , Masculino , Neoplasias da Próstata/genética , Fatores de Processamento de RNA/genética , Transdução de Sinais/genética
18.
RNA ; 25(7): 813-824, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30988101

RESUMO

Splicing of precursor mRNA (pre-mRNA) is an important regulatory step in gene expression. Recent evidence points to a regulatory role of chromatin-related proteins in alternative splicing regulation. Using an unbiased approach, we have identified the acetyltransferase p300 as a key chromatin-related regulator of alternative splicing. p300 promotes genome-wide exon inclusion in both a transcription-dependent and -independent manner. Using CD44 as a paradigm, we found that p300 regulates alternative splicing by modulating the binding of splicing factors to pre-mRNA. Using a tethering strategy, we found that binding of p300 to the CD44 promoter region promotes CD44v exon inclusion independently of RNAPII transcriptional elongation rate. Promoter-bound p300 regulates alternative splicing by acetylating splicing factors, leading to exclusion of hnRNP M from CD44 pre-mRNA and activation of Sam68. p300-mediated CD44 alternative splicing reduces cell motility and promotes epithelial features. Our findings reveal a chromatin-related mechanism of alternative splicing regulation and demonstrate its impact on cellular function.


Assuntos
Processamento Alternativo , Neoplasias da Mama/genética , Cromatina/metabolismo , Proteína p300 Associada a E1A/metabolismo , Regulação Neoplásica da Expressão Gênica , Receptores de Hialuronatos/genética , Fatores de Processamento de RNA/química , Acetilação , Neoplasias da Mama/metabolismo , Neoplasias da Mama/patologia , Cromatina/genética , Proteína p300 Associada a E1A/genética , Éxons , Feminino , Humanos , Receptores de Hialuronatos/metabolismo , Regiões Promotoras Genéticas , Fatores de Processamento de RNA/genética , Fatores de Processamento de RNA/metabolismo , Transcrição Genética , Células Tumorais Cultivadas
19.
DNA Cell Biol ; 38(7): 627-638, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31025877

RESUMO

Head and neck squamous cell carcinoma (HNSC) is a common malignancy with high mortality and poor prognosis. Alternative splicing (AS) is a transcriptional regulation mechanism that generates multiple transcripts from same genes, and aberrant AS signatures of cancers can be predictive for prognosis. We identified the survival-related AS events and splicing factors (SFs) from the RNA sequencing data and the corresponding clinical information of an HNSC cohort downloaded from The Cancer Genome Atlas (TCGA) and SpliceSeq. The independent prognostic predictors were assessed by Cox proportional regression analysis, and the regulatory network of SFs and AS events was analyzed by Spearman's test and constructed. A total of 4626 survival-related AS events in 3280 genes were identified, and most were protective factors. Among the different types of splicing events, exon skip was the most frequent. The prognostic models were constructed for each type of AS, and the area under the curve of the receiver operating characteristic curve of the combined prognostic model was 0.765, indicating good predictive performance. Finally, a correlation network between SF and AS events was constructed. We identified prognostic predictors based on AS events that stratified HNSC patients into the high- and low-risk groups, and revealed splicing networks that provide insights into the underlying mechanisms.


Assuntos
Processamento Alternativo , Biomarcadores Tumorais/genética , Carcinoma de Células Escamosas/genética , Neoplasias de Cabeça e Pescoço/genética , Fatores de Processamento de RNA/genética , RNA Mensageiro/genética , Adulto , Idoso , Carcinoma de Células Escamosas/patologia , Feminino , Neoplasias de Cabeça e Pescoço/patologia , Humanos , Masculino , Pessoa de Meia-Idade , Fatores de Processamento de RNA/metabolismo , RNA Mensageiro/metabolismo
20.
Proc Natl Acad Sci U S A ; 116(13): 6172-6180, 2019 03 26.
Artigo em Inglês | MEDLINE | ID: mdl-30867288

RESUMO

Heart performance relies on highly coordinated excitation-contraction (EC) coupling, and defects in this critical process may be exacerbated by additional genetic defects and/or environmental insults to cause eventual heart failure. Here we report a regulatory pathway consisting of the RNA binding protein RBFox2, a stress-induced microRNA miR-34a, and the essential EC coupler JPH2. In this pathway, initial cardiac defects diminish RBFox2 expression, which induces transcriptional repression of miR-34a, and elevated miR-34a targets Jph2 to impair EC coupling, which further manifests heart dysfunction, leading to progressive heart failure. The key contribution of miR-34a to this process is further established by administrating its mimic, which is sufficient to induce cardiac defects, and by using its antagomir to alleviate RBFox2 depletion-induced heart dysfunction. These findings elucidate a potential feed-forward mechanism to account for a critical transition to cardiac decompensation and suggest a potential therapeutic avenue against heart failure.


Assuntos
Insuficiência Cardíaca/metabolismo , Coração/fisiopatologia , Proteínas de Membrana/metabolismo , MicroRNAs/metabolismo , Proteínas Musculares/metabolismo , Fatores de Processamento de RNA/metabolismo , Animais , Regulação para Baixo , Insuficiência Cardíaca/fisiopatologia , Humanos , Camundongos , Camundongos Knockout , Miócitos Cardíacos/metabolismo , Miócitos Cardíacos/fisiologia
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