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1.
J Clin Invest ; 132(8)2022 04 15.
Artículo en Inglés | MEDLINE | ID: mdl-35239512

RESUMEN

Y-box-binding protein 1 (YB-1) is a multifunctional RNA binding protein involved in virtually every step of RNA metabolism. However, the functions and mechanisms of YB-1 in one of the most aggressive cancers, glioblastoma, are not well understood. In this study, we found that YB-1 protein was markedly overexpressed in glioblastoma and acted as a critical activator of both mTORC1 and mTORC2 signaling. Mechanistically, YB-1 bound the 5'UTR of CCT4 mRNA to promote the translation of CCT4, a component of the CCT chaperone complex, that in turn activated the mTOR signaling pathway by promoting mLST8 folding. In addition, YB-1 autoregulated its own translation by binding to its 5'UTR, leading to sustained activation of mTOR signaling. In patients with glioblastoma, high protein expression of YB-1 correlated with increased expression of CCT4 and mLST8 and activated mTOR signaling. Importantly, the administration of RNA decoys specifically targeting YB-1 in a mouse xenograft model resulted in slower tumor growth and better survival. Taken together, these findings uncover a disrupted proteostasis pathway involving a YB-1/CCT4/mLST8/mTOR axis in promoting glioblastoma growth, suggesting that YB-1 is a potential therapeutic target for the treatment of glioblastoma.


Asunto(s)
Glioblastoma , Proteína 1 de Unión a la Caja Y , Regiones no Traducidas 5' , Animales , Línea Celular Tumoral , Chaperonina con TCP-1 , Glioblastoma/genética , Humanos , Diana Mecanicista del Complejo 1 de la Rapamicina/genética , Diana Mecanicista del Complejo 1 de la Rapamicina/metabolismo , Ratones , Serina-Treonina Quinasas TOR/genética , Serina-Treonina Quinasas TOR/metabolismo , Factores de Transcripción/genética , Proteína 1 de Unión a la Caja Y/genética , Proteína 1 de Unión a la Caja Y/metabolismo , Homóloga LST8 de la Proteína Asociada al mTOR/genética , Homóloga LST8 de la Proteína Asociada al mTOR/metabolismo
2.
J Cachexia Sarcopenia Muscle ; 13(1): 728-742, 2022 02.
Artículo en Inglés | MEDLINE | ID: mdl-34877814

RESUMEN

BACKGROUND: Most of the microRNAs (MiRs) involved in myogenesis are transcriptional regulated. The role of MiR biogenesis in myogenesis has not been characterized yet. RNA-binding protein Musashi 2 (Msi2) is considered to be one of the major drivers for oncogenesis and stem cell proliferation. The functions of Msi2 in myogenesis have not been explored yet. We sought to investigate Msi2-regulated biogenesis of MiRs in myogenesis and muscle stem cell (MuSC) ageing. METHODS: We detected the expression of Msi2 in MuSCs and differentiated myotubes by quantitative reverse transcription PCR (RT-qPCR) and western blot. Msi2-binding partner human antigen R (HuR) was identified by immunoprecipitation followed by mass spectrometry analysis. The cooperative binding of Msi2 and HuR on MiR7a-1 was analysed by RNA immunoprecipitation and electrophoresis mobility shift assays. The inhibition of the processing of pri-MiR7a-1 mediated by Msi2 and HuR was shown by Msi2 and HuR knockdown. Immunofluorescent staining, RT-qPCR and immunoblotting were used to characterize the function of MiR7a-1 in myogenesis. Msi2 and HuR up-regulate cryptochrome circadian regulator 2 (Cry2) via MiR7a-1 was confirmed by the luciferase assay and western blot. The post-transcriptional regulatory cascade was further confirmed by RNAi and overexpressing of Msi2 and HuR in MuSCs, and the in vivo function was characterized by histopathological and molecular biological methods in Msi2 knockout mice. RESULTS: We identified a post-transcription regulatory cascade governed by a pair of RNA-binding proteins Msi2 and HuR. Msi2 is enriched in differentiated muscle cells and promotes MuSC differentiation despite its pro-proliferation functions in other cell types. Msi2 works synergistically with another RNA-binding protein HuR to repress the biogenesis of MiR7a-1 in an Msi2 dose-dependent manner to regulate the translation of the key component of the circadian core oscillator complex Cry2. Down-regulation of Cry2 (0.6-fold, vs. control, P < 0.05) mediated by MiR7a-1 represses MuSC differentiation. The disruption of this cascade leads to differentiation defects of MuSCs. In aged muscles, Msi2 (0.3-fold, vs. control, P < 0.01) expression declined, and the Cry2 protein level also decreases (0.5-fold, vs. control, P < 0.05), suggesting that the disruption of the Msi2-mediated post-transcriptional regulatory cascade could attribute to the declined ability of muscle regeneration in aged skeletal muscle. CONCLUSIONS: Our findings have identified a new post-transcriptional cascade regulating myogenesis. The cascade is disrupted in skeletal muscle ageing, which leads to declined muscle regeneration ability.


Asunto(s)
MicroARNs , Desarrollo de Músculos , Proteínas de Unión al ARN/metabolismo , Animales , Diferenciación Celular/genética , Ratones , MicroARNs/genética , MicroARNs/metabolismo , Desarrollo de Músculos/genética , Fibras Musculares Esqueléticas/metabolismo , Mioblastos/metabolismo
3.
Nat Commun ; 12(1): 5767, 2021 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-34599184

RESUMEN

Rett syndrome (RTT) is a severe neurological disorder and a leading cause of intellectual disability in young females. RTT is mainly caused by mutations found in the X-linked gene encoding methyl-CpG binding protein 2 (MeCP2). Despite extensive studies, the molecular mechanism underlying RTT pathogenesis is still poorly understood. Here, we report MeCP2 as a key subunit of a higher-order multiunit protein complex Rbfox/LASR. Defective MeCP2 in RTT mouse models disrupts the assembly of the MeCP2/Rbfox/LASR complex, leading to reduced binding of Rbfox proteins to target pre-mRNAs and aberrant splicing of Nrxns and Nlgn1 critical for synaptic plasticity. We further show that MeCP2 disease mutants display defective condensate properties and fail to promote phase-separated condensates with Rbfox proteins in vitro and in cultured cells. These data link an impaired function of MeCP2 with disease mutation in splicing control to its defective properties in mediating the higher-order assembly of the MeCP2/Rbfox/LASR complex.


Asunto(s)
Proteína 2 de Unión a Metil-CpG/metabolismo , Complejos Multiproteicos/metabolismo , Factores de Empalme de ARN/metabolismo , Síndrome de Rett/genética , Empalme Alternativo/genética , Animales , Núcleo Celular/metabolismo , Modelos Animales de Enfermedad , Exones/genética , Femenino , Células HEK293 , Ribonucleoproteínas Nucleares Heterogéneas/metabolismo , Humanos , Proteína 2 de Unión a Metil-CpG/química , Ratones , Mutación/genética , Proteínas del Tejido Nervioso/genética , Dominios Proteicos , Subunidades de Proteína/metabolismo
4.
Elife ; 102021 06 29.
Artículo en Inglés | MEDLINE | ID: mdl-34184986

RESUMEN

The congenital intellectual disability (ID)-causing gene mutations remain largely unclear, although many genetic variations might relate to ID. We screened gene mutations in Chinese Han children suffering from severe ID and found a single-nucleotide polymorphism (SNP) in the 5'-untranslated region (5'-UTR) of fibroblast growth factor 13 (FGF13) mRNA (NM_001139500.1:c.-32c>G) shared by three male children. In both HEK293 cells and patient-derived induced pluripotent stem cells, this SNP reduced the translation of FGF13, which stabilizes microtubules in developing neurons. Mice carrying the homologous point mutation in 5'-UTR of Fgf13 showed delayed neuronal migration during cortical development, and weakened learning and memory. Furthermore, this SNP reduced the interaction between FGF13 5'-UTR and polypyrimidine-tract-binding protein 2 (PTBP2), which was required for FGF13 translation in cortical neurons. Thus, this 5'-UTR SNP of FGF13 interferes with the translational process of FGF13 and causes deficits in brain development and cognitive functions.


Asunto(s)
Regiones no Traducidas 5'/genética , Factores de Crecimiento de Fibroblastos/genética , Discapacidad Intelectual/genética , Mutación Puntual , Polimorfismo de Nucleótido Simple , Adolescente , Animales , Niño , Preescolar , Factores de Crecimiento de Fibroblastos/metabolismo , Células HEK293 , Humanos , Aprendizaje , Masculino , Memoria , Ratones , Ratones Endogámicos C57BL
5.
Genome Biol ; 22(1): 77, 2021 03 09.
Artículo en Inglés | MEDLINE | ID: mdl-33685485

RESUMEN

BACKGROUND: A-to-I RNA editing diversifies the transcriptome and has multiple downstream functional effects. Genetic variation contributes to RNA editing variability between individuals and has the potential to impact phenotypic variability. RESULTS: We analyze matched genetic and transcriptomic data in 49 tissues across 437 individuals to identify RNA editing events that are associated with genetic variation. Using an RNA editing quantitative trait loci (edQTL) mapping approach, we identify 3117 unique RNA editing events associated with a cis genetic polymorphism. Fourteen percent of these edQTL events are also associated with genetic variation in their gene expression. A subset of these events are associated with genome-wide association study signals of complex traits or diseases. We determine that tissue-specific levels of ADAR and ADARB1 are able to explain a subset of tissue-specific edQTL events. We find that certain microRNAs are able to differentiate between the edited and unedited isoforms of their targets. Furthermore, microRNAs can generate an expression quantitative trait loci (eQTL) signal from an edQTL locus by microRNA-mediated transcript degradation in an editing-specific manner. By integrative analyses of edQTL, eQTL, and microRNA expression profiles, we computationally discover and experimentally validate edQTL-microRNA pairs for which the microRNA may generate an eQTL signal from an edQTL locus in a tissue-specific manner. CONCLUSIONS: Our work suggests a mechanism in which RNA editing variability can influence the phenotypes of complex traits and diseases by altering the stability and steady-state level of critical RNA molecules.


Asunto(s)
Marcación de Gen , Variación Genética , MicroARNs/genética , Edición de ARN , RNA-Seq/métodos , Transcriptoma , Alelos , Biología Computacional/métodos , Marcación de Gen/métodos , Estudio de Asociación del Genoma Completo/métodos , Humanos , Desequilibrio de Ligamiento , Herencia Multifactorial , Especificidad de Órganos/genética , Polimorfismo de Nucleótido Simple , Sitios de Carácter Cuantitativo , Interferencia de ARN , Estabilidad del ARN
6.
J Mol Cell Biol ; 13(5): 347-360, 2021 08 18.
Artículo en Inglés | MEDLINE | ID: mdl-33196842

RESUMEN

Accumulating evidence indicates that the alternative splicing program undergoes extensive changes during cancer development and progression. The RNA-binding protein QKI-5 is frequently downregulated and exhibits anti-tumor activity in lung cancer. Howeve-r, little is known about the functional targets and regulatory mechanism of QKI-5. Here, we report that upregulation of exon 14 inclusion of cytoskeletal gene Adducin 3 (ADD3) significantly correlates with a poor prognosis in lung cancer. QKI-5 inhibits cell proliferation and migration in part through suppressing the splicing of ADD3 exon 14. Through genome-wide mapping of QKI-5 binding sites in vivo at nucleotide resolution by iCLIP-seq analysis, we found that QKI-5 regulates alternative splicing of its target mRNAs in a binding position-dependent manner. By binding to multiple sites in an upstream intron region, QKI-5 represses the splicing of ADD3 exon 14. We also identified several QKI mutations in tumors, which cause dysregulation of the splicing of QKI targets ADD3 and NUMB. Taken together, our results reveal that QKI-mediated alternative splicing of ADD3 is a key lung cancer-associated splicing event, which underlies in part the tumor suppressor function of QKI.


Asunto(s)
Empalme Alternativo/genética , Proteínas de Unión a Calmodulina/genética , Citoesqueleto/genética , Neoplasias Pulmonares/genética , Proteínas de Unión al ARN/genética , Células A549 , Línea Celular , Línea Celular Tumoral , Movimiento Celular/genética , Proliferación Celular/genética , Regulación hacia Abajo/genética , Exones/genética , Genes Supresores de Tumor/fisiología , Células HEK293 , Humanos , Intrones/genética , Neoplasias Pulmonares/patología , ARN Mensajero/genética , Regulación hacia Arriba/genética
7.
Mol Cell ; 77(5): 999-1013.e6, 2020 03 05.
Artículo en Inglés | MEDLINE | ID: mdl-32017896

RESUMEN

U6 snRNA, as an essential component of the catalytic core of the pre-mRNA processing spliceosome, is heavily modified post-transcriptionally, with 2'-O-methylation being most common. The role of these modifications in pre-mRNA splicing as well as their physiological function in mammals have remained largely unclear. Here we report that the La-related protein LARP7 functions as a critical cofactor for 2'-O-methylation of U6 in mouse male germ cells. Mechanistically, LARP7 promotes U6 loading onto box C/D snoRNP, facilitating U6 2'-O-methylation by box C/D snoRNP. Importantly, ablation of LARP7 in the male germline causes defective U6 2'-O-methylation, massive alterations in pre-mRNA splicing, and spermatogenic failure in mice, which can be rescued by ectopic expression of wild-type LARP7 but not an U6-loading-deficient mutant LARP7. Our data uncover a novel role of LARP7 in regulating U6 2'-O-methylation and demonstrate the functional requirement of such modification for splicing fidelity and spermatogenesis in mice.


Asunto(s)
Precursores del ARN/metabolismo , Empalme del ARN , ARN Mensajero/metabolismo , ARN Nuclear Pequeño/metabolismo , Proteínas de Unión al ARN/metabolismo , Espermatogénesis , Espermatozoides/metabolismo , Empalmosomas/metabolismo , Animales , Fertilidad , Regulación del Desarrollo de la Expresión Génica , Células HEK293 , Humanos , Masculino , Metilación , Ratones Endogámicos C57BL , Ratones Noqueados , Precursores del ARN/genética , ARN Mensajero/genética , ARN Nuclear Pequeño/genética , Proteínas de Unión al ARN/genética , Ribonucleoproteínas Nucleolares Pequeñas/genética , Ribonucleoproteínas Nucleolares Pequeñas/metabolismo , Transducción de Señal , Espermatogénesis/genética , Empalmosomas/genética
8.
J Biol Chem ; 294(28): 10998-11010, 2019 07 12.
Artículo en Inglés | MEDLINE | ID: mdl-31160337

RESUMEN

The Y-box binding protein 1 (YB-1) is a member of the cold shock domain (CSD) protein family and is recognized as an oncogenic factor in several solid tumors. By binding to RNA, YB-1 participates in several steps of posttranscriptional regulation of gene expression, including mRNA splicing, stability, and translation; microRNA processing; and stress granule assembly. However, the mechanisms in YB-1-mediated regulation of RNAs are unclear. Previously, we used both systematic evolution of ligands by exponential enrichment (SELEX) and individual-nucleotide resolution UV cross-linking and immunoprecipitation coupled RNA-Seq (iCLIP-Seq) analyses, which defined the RNA-binding consensus sequence of YB-1 as CA(U/C)C. We also reported that through binding to its core motif CAUC in primary transcripts, YB-1 regulates the alternative splicing of a CD44 variable exon and the biogenesis of miR-29b-2 during both Drosha and Dicer steps. To elucidate the molecular basis of the YB-1-RNA interactions, we report high-resolution crystal structures of the YB-1 CSD in complex with different RNA oligos at 1.7 Å resolution. The structure revealed that CSD interacts with RNA mainly through π-π stacking interactions assembled by four highly conserved aromatic residues. Interestingly, YB-1 CSD forms a homodimer in solution, and we observed that two residues, Tyr-99 and Asp-105, at the dimer interface are important for YB-1 CSD dimerization. Substituting these two residues with Ala reduced CSD's RNA-binding activity and abrogated the splicing activation of YB-1 targets. The YB-1 CSD-RNA structures presented here at atomic resolution provide mechanistic insights into gene expression regulated by CSD-containing proteins.


Asunto(s)
Proteína 1 de Unión a la Caja Y/metabolismo , Proteína 1 de Unión a la Caja Y/ultraestructura , Empalme Alternativo/fisiología , Proteínas de Unión al ADN/metabolismo , Exones/genética , Exones/fisiología , Humanos , Unión Proteica , ARN/metabolismo , ARN Mensajero/metabolismo , Proteínas de Unión al ARN/metabolismo , Proteínas de Unión al ARN/ultraestructura , Proteína 1 de Unión a la Caja Y/genética
9.
J Mol Cell Biol ; 11(10): 930-939, 2019 10 25.
Artículo en Inglés | MEDLINE | ID: mdl-31152582

RESUMEN

RNA-binding proteins (RBPs) are key regulators in post-transcriptional control of gene expression. Mutations that alter their activity or abundance have been implicated in numerous diseases such as neurodegenerative disorders and various types of cancer. This highlights the importance of RBP proteostasis and the necessity to tightly control the expression levels and activities of RBPs. In many cases, RBPs engage in an auto-regulatory feedback by directly binding to and influencing the fate of their own mRNAs, exerting control over their own expression. For this feedback control, RBPs employ a variety of mechanisms operating at all levels of post-transcriptional regulation of gene expression. Here we review RBP-mediated autogenous feedback regulation that either serves to maintain protein abundance within a physiological range (by negative feedback) or generates binary, genetic on/off switches important for e.g. cell fate decisions (by positive feedback).


Asunto(s)
Proteínas de Unión al ARN/metabolismo , Regulación de la Expresión Génica , Humanos , Procesamiento Postranscripcional del ARN , ARN Mensajero/genética , ARN Mensajero/metabolismo , Proteínas de Unión al ARN/genética
10.
EMBO Rep ; 19(6)2018 06.
Artículo en Inglés | MEDLINE | ID: mdl-29735517

RESUMEN

Alternative pre-mRNA splicing plays important roles in regulating self-renewal and differentiation of embryonic stem cells (ESCs). However, how specific alternative splicing programs are established in ESCs remains elusive. Here, we show that a subset of alternative splicing events in ESCs is dependent on miR-294 expression. Remarkably, roughly 60% of these splicing events are affected by the depletion of Muscleblind-Like Splicing Regulator 1 and 2 (Mbnl1/2). Distinct from canonical miRNA function, miR-294 represses Mbnl1/2 through both posttranscriptional and epigenetic mechanisms. Furthermore, we uncover non-canonical functions of MBNL proteins that bind and promote the expression of miR-294 targets, including Cdkn1a and Tgfbr2, thereby opposing the role of miR-294 in regulating cell proliferation, apoptosis, and epithelial-mesenchymal transition (EMT). Our study reveals extensive interactions between miRNAs and splicing factors, highlighting their roles in regulating cell type-specific alternative splicing and defining gene expression programs during development and cellular differentiation.


Asunto(s)
Proteínas de Unión al ADN/fisiología , Células Madre Embrionarias/fisiología , MicroARNs/fisiología , Proteínas de Unión al ARN/fisiología , Empalme Alternativo , Animales , Apoptosis/genética , Línea Celular , Proliferación Celular/genética , Transición Epitelial-Mesenquimal/genética , Regulación del Desarrollo de la Expresión Génica , Redes Reguladoras de Genes , MicroARNs/genética
11.
J Clin Invest ; 127(9): 3375-3391, 2017 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-28825595

RESUMEN

The histone H3K36 methyltransferase SETD2 is frequently mutated or deleted in a variety of human tumors. Nevertheless, the role of SETD2 loss in oncogenesis remains largely undefined. Here, we found that SETD2 counteracts Wnt signaling and its inactivation promotes intestinal tumorigenesis in mouse models of colorectal cancer (CRC). SETD2 was not required for intestinal homeostasis under steady state; however, upon irradiation, genetic inactivation of Setd2 in mouse intestinal epithelium facilitated the self-renewal of intestinal stem/progenitor cells as well as tissue regeneration. Furthermore, depletion of SETD2 enhanced the susceptibility to tumorigenesis in the context of dysregulated Wnt signaling. Mechanistic characterizations indicated that SETD2 downregulation affects the alternative splicing of a subset of genes implicated in tumorigenesis. Importantly, we uncovered that SETD2 ablation reduces intron retention of dishevelled segment polarity protein 2 (DVL2) pre-mRNA, which would otherwise be degraded by nonsense-mediated decay, thereby augmenting Wnt signaling. The signaling cascades mediated by SETD2 were further substantiated by a CRC patient cohort analysis. Together, our studies highlight SETD2 as an integral regulator of Wnt signaling through epigenetic regulation of RNA processing during tissue regeneration and tumorigenesis.


Asunto(s)
Empalme Alternativo , Carcinogénesis/genética , Neoplasias Colorrectales/genética , N-Metiltransferasa de Histona-Lisina/genética , Animales , Diferenciación Celular , Transformación Celular Neoplásica , Modelos Animales de Enfermedad , Proteínas Dishevelled/genética , Epigénesis Genética , Regulación Neoplásica de la Expresión Génica , Humanos , Intrones , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Desnudos , Regeneración , Transducción de Señal , Células Madre/citología , Proteínas Wnt/metabolismo
12.
Cell Res ; 27(3): 416-439, 2017 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-28244490

RESUMEN

MicroRNA (miRNA) biogenesis is finely controlled by complex layers of post-transcriptional regulators, including RNA-binding proteins (RBPs). Here, we show that an RBP, QKI5, activates the processing of primary miR-124-1 (pri-124-1) during erythropoiesis. QKI5 recognizes a distal QKI response element and recruits Microprocessor through interaction with DGCR8. Furthermore, the recruited Microprocessor is brought to pri-124-1 stem loops by a spatial RNA-RNA interaction between two complementary sequences. Thus, mutations disrupting their base-pairing affect the strength of QKI5 activation. When erythropoiesis proceeds, the concomitant decrease of QKI5 releases Microprocessor from pri-124-1 and reduces mature miR-124 levels to facilitate erythrocyte maturation. Mechanistically, miR-124 targets TAL1 and c-MYB, two transcription factors involved in normal erythropoiesis. Importantly, this QKI5-mediated regulation also gives rise to a unique miRNA signature, which is required for erythroid differentiation. Taken together, these results demonstrate the pivotal role of QKI5 in primary miRNA processing during erythropoiesis and provide new insights into how a distal element on primary transcripts affects miRNA biogenesis.


Asunto(s)
Eritropoyesis/genética , MicroARNs/genética , Motivos de Nucleótidos/genética , Procesamiento Postranscripcional del ARN/genética , Proteínas de Unión al ARN/metabolismo , ARN/genética , Animales , Secuencia de Bases , Diferenciación Celular/genética , Células Eritroides/citología , Células Eritroides/metabolismo , Regulación de la Expresión Génica , Células HEK293 , Xenoinjertos , Humanos , Células K562 , Ratones , MicroARNs/metabolismo , Unión Proteica/genética , Proteínas Proto-Oncogénicas c-myb , ARN/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , Proteína 1 de la Leucemia Linfocítica T Aguda/metabolismo
13.
Cell Res ; 27(4): 540-558, 2017 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-28084329

RESUMEN

Extracellular signals have been shown to impact on alternative pre-mRNA splicing; however, the molecular mechanisms and biological significance of signal-induced splicing regulation remain largely unknown. Here, we report that epidermal growth factor (EGF) induces splicing changes through ubiquitylation of a well-known splicing regulator, hnRNP A1. EGF signaling upregulates an E3 ubiquitin (Ub) ligase adaptor, SPRY domain-containing SOCS box protein 1 (SPSB1), which recruits Elongin B/C-Cullin complexes to conjugate lysine 29-linked polyUb chains onto hnRNP A1. Importantly, SPSB1 and ubiquitylation of hnRNP A1 have a critical role in EGF-driven cell migration. Mechanistically, EGF-induced ubiquitylation of hnRNP A1 together with the activation of SR protein kinases (SRPKs) results in the upregulation of a Rac1 splicing isoform, Rac1b, to promote cell motility. These findings unravel a novel crosstalk between protein ubiquitylation and alternative splicing in EGF/EGF receptor signaling, and identify a new EGF/SPSB1/hnRNP A1/Rac1 axis in modulating cell migration, which may have important implications for cancer treatment.


Asunto(s)
Empalme Alternativo/genética , Movimiento Celular , Factor de Crecimiento Epidérmico/farmacología , Ribonucleoproteína Nuclear Heterogénea A1/metabolismo , Transducción de Señal , Proteínas Supresoras de la Señalización de Citocinas/metabolismo , Ubiquitinación , Movimiento Celular/efectos de los fármacos , Núcleo Celular/efectos de los fármacos , Núcleo Celular/metabolismo , Proteínas Cullin/metabolismo , Elonguina/metabolismo , Receptores ErbB/metabolismo , Células HEK293 , Células HeLa , Humanos , Lisina/metabolismo , Poliubiquitina/metabolismo , Unión Proteica/efectos de los fármacos , Precursores del ARN/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , Transducción de Señal/efectos de los fármacos , Ubiquitinación/efectos de los fármacos , Proteína de Unión al GTP rac1/metabolismo
14.
Oncotarget ; 7(22): 32821-34, 2016 May 31.
Artículo en Inglés | MEDLINE | ID: mdl-27092877

RESUMEN

Alternative pre-mRNA splicing is a key mechanism for increasing proteomic diversity and modulating gene expression. Emerging evidence indicated that the splicing program is frequently dysregulated during tumorigenesis. Cancer cells produce protein isoforms that can promote growth and survival. The RNA-binding protein QKI5 is a critical regulator of alternative splicing in expanding lists of primary human tumors and tumor cell lines. However, its biological role and regulatory mechanism are poorly defined in gastric cancer (GC) development and progression. In this study, we demonstrated that the downregulation of QKI5 was associated with pTNM stage and pM state of GC patients. Re-introduction of QKI5 could inhibit GC cell proliferation, migration, and invasion in vitro and in vivo, which might be due to the altered splicing pattern of macroH2A1 pre-mRNA, leading to the accumulation of macroH2A1.1 isoform. Furthermore, QKI5 could inhibit cyclin L1 expression via promoting macroH2A1.1 production. Thus, this study identified a novel regulatory axis involved in gastric tumorigenesis and provided a new strategy for GC therapy.


Asunto(s)
Empalme Alternativo , Histonas/metabolismo , Precursores del ARN/metabolismo , ARN Mensajero/metabolismo , Proteínas de Unión al ARN/metabolismo , Neoplasias Gástricas/metabolismo , Proteínas Supresoras de Tumor/metabolismo , Animales , Línea Celular Tumoral , Movimiento Celular , Proliferación Celular , Ciclinas/genética , Ciclinas/metabolismo , Femenino , Xenoinjertos , Histonas/genética , Humanos , Ratones Endogámicos BALB C , Ratones Desnudos , Invasividad Neoplásica , Estadificación de Neoplasias , Isoformas de Proteínas , Precursores del ARN/genética , ARN Mensajero/genética , Proteínas de Unión al ARN/genética , Neoplasias Gástricas/genética , Neoplasias Gástricas/patología , Factores de Tiempo , Transfección , Carga Tumoral , Proteínas Supresoras de Tumor/genética
15.
Nucleic Acids Res ; 43(17): 8516-28, 2015 Sep 30.
Artículo en Inglés | MEDLINE | ID: mdl-26240386

RESUMEN

Altered miRNA expression is believed to play a crucial role in a variety of human cancers; however, the mechanisms leading to the dysregulation of miRNA expression remain elusive. In this study, we report that the human Y box-binding protein (YB-1), a major mRNA packaging protein, is a novel modulator of miRNA processing in glioblastoma multiforme (GBM). Using individual nucleotide-resolution crosslinking immunoprecipitation coupled to deep sequencing (iCLIP-seq), we performed the first genome-wide analysis of the in vivo YB-1-RNA interactions and found that YB-1 preferentially recognizes a UYAUC consensus motif and binds to the majority of coding gene transcripts including pre-mRNAs and mature mRNAs. Remarkably, our data show that YB-1 also binds extensively to the terminal loop region of pri-/pre-miR-29b-2 and regulates the biogenesis of miR-29b-2 by blocking the recruitment of microprocessor and Dicer to its precursors. Furthermore, we show that down-regulation of miR-29b by YB-1, which is up-regulated in GBM, is important for cell proliferation. Together, our findings reveal a novel function of YB-1 in regulating non-coding RNA expression, which has important implications in tumorigenesis.


Asunto(s)
Regulación Neoplásica de la Expresión Génica , Glioblastoma/genética , MicroARNs/metabolismo , Procesamiento Postranscripcional del ARN , Proteína 1 de Unión a la Caja Y/metabolismo , Sitios de Unión , Línea Celular Tumoral , Proliferación Celular , Genoma Humano , Genómica , Glioblastoma/enzimología , Glioblastoma/metabolismo , Células HEK293 , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , MicroARNs/química , Unión Proteica , ARN/metabolismo , Proteínas de Unión al ARN/metabolismo , Ribonucleasa III/antagonistas & inhibidores , Análisis de Secuencia de ARN
16.
Mol Cell ; 56(2): 298-310, 2014 Oct 23.
Artículo en Inglés | MEDLINE | ID: mdl-25263594

RESUMEN

BS69 (also called ZMYND11) contains tandemly arranged PHD, BROMO, and PWWP domains, which are chromatin recognition modalities. Here, we show that BS69 selectively recognizes histone variant H3.3 lysine 36 trimethylation (H3.3K36me3) via its chromatin-binding domains. We further identify BS69 association with RNA splicing regulators, including the U5 snRNP components of the spliceosome, such as EFTUD2. Remarkably, RNA sequencing shows that BS69 mainly regulates intron retention (IR), which is the least understood RNA alternative splicing event in mammalian cells. Biochemical and genetic experiments demonstrate that BS69 promotes IR by antagonizing EFTUD2 through physical interactions. We further show that regulation of IR by BS69 also depends on its binding to H3K36me3-decorated chromatin. Taken together, our study identifies an H3.3K36me3-specific reader and a regulator of IR and reveals that BS69 connects histone H3.3K36me3 to regulated RNA splicing, providing significant, important insights into chromatin regulation of pre-mRNA processing.


Asunto(s)
Empalme Alternativo , Proteínas Portadoras/metabolismo , Cromatina/metabolismo , Histonas/metabolismo , Precursores del ARN/genética , ARN Mensajero/genética , Secuencia de Bases , Proteínas Portadoras/genética , Proteínas de Ciclo Celular , Línea Celular Tumoral , Cromatina/genética , Proteínas Co-Represoras , Metilación de ADN/genética , Proteínas de Unión al ADN , Células HeLa , N-Metiltransferasa de Histona-Lisina/genética , N-Metiltransferasa de Histona-Lisina/metabolismo , Histonas/genética , Humanos , Intrones/genética , Lisina/genética , Lisina/metabolismo , Factores de Elongación de Péptidos/antagonistas & inhibidores , Factores de Elongación de Péptidos/genética , Factores de Elongación de Péptidos/metabolismo , Unión Proteica , Estructura Terciaria de Proteína , Interferencia de ARN , Procesamiento Postranscripcional del ARN/genética , ARN Interferente Pequeño , Ribonucleoproteína Nuclear Pequeña U5/antagonistas & inhibidores , Ribonucleoproteína Nuclear Pequeña U5/genética , Ribonucleoproteína Nuclear Pequeña U5/metabolismo , Análisis de Secuencia de ARN , Empalmosomas/genética
17.
PLoS Genet ; 10(4): e1004289, 2014 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-24722255

RESUMEN

Lung cancer is the leading cause of cancer-related death worldwide. Aberrant splicing has been implicated in lung tumorigenesis. However, the functional links between splicing regulation and lung cancer are not well understood. Here we identify the RNA-binding protein QKI as a key regulator of alternative splicing in lung cancer. We show that QKI is frequently down-regulated in lung cancer, and its down-regulation is significantly associated with a poorer prognosis. QKI-5 inhibits the proliferation and transformation of lung cancer cells both in vitro and in vivo. Our results demonstrate that QKI-5 regulates the alternative splicing of NUMB via binding to two RNA elements in its pre-mRNA, which in turn suppresses cell proliferation and prevents the activation of the Notch signaling pathway. We further show that QKI-5 inhibits splicing by selectively competing with a core splicing factor SF1 for binding to the branchpoint sequence. Taken together, our data reveal QKI as a critical regulator of splicing in lung cancer and suggest a novel tumor suppression mechanism involving QKI-mediated regulation of the Notch signaling pathway.


Asunto(s)
Empalme Alternativo/genética , Neoplasias Pulmonares/genética , Empalme del ARN/genética , Proteínas de Unión al ARN/genética , Proteínas Supresoras de Tumor/genética , Línea Celular Tumoral , Proliferación Celular , Transformación Celular Neoplásica/genética , Regulación hacia Abajo/genética , Genes Supresores de Tumor , Humanos , Proteínas de la Membrana/genética , Proteínas del Tejido Nervioso/genética , ARN/genética , Precursores del ARN/genética , ARN Mensajero/genética , Receptores Notch/genética , Transducción de Señal/genética
18.
Nucleic Acids Res ; 40(17): 8622-36, 2012 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-22730292

RESUMEN

The human Y box-binding protein-1 (YB-1) is a deoxyribonucleic acid (DNA)/ribonucleic acid (RNA)-binding protein with pleiotropic functions. Besides its roles in the regulation of transcription and translation, several recent studies indicate that YB-1 is a spliceosome-associated protein and is involved in alternative splicing, but the underlying mechanism has remained elusive. Here, we define both CAUC and CACC as high-affinity binding motifs for YB-1 by systematic evolution of ligands by exponential enrichment (SELEX) and demonstrate that these newly defined motifs function as splicing enhancers. Interestingly, on the endogenous CD44 gene, YB-1 appears to mediate a network interaction to activate exon v5 inclusion via multiple CAUC motifs in both the alternative exon and its upstream polypyrimidine tract. We provide evidence that YB-1 activates splicing by facilitating the recruitment of U2AF65 to weak polypyrimidine tracts through direct protein-protein interactions. Together, these findings suggest a vital role of YB-1 in activating a subset of weak 3' splice sites in mammalian cells.


Asunto(s)
Empalme Alternativo , Exones , Intrones , Proteínas Nucleares/metabolismo , Proteínas de Unión al ARN/metabolismo , Ribonucleoproteínas/metabolismo , Proteína 1 de Unión a la Caja Y/metabolismo , Sitios de Unión , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Células HEK293 , Humanos , Receptores de Hialuranos/genética , Receptores de Hialuranos/metabolismo , Proteínas Nucleares/química , Motivos de Nucleótidos , Dominios y Motivos de Interacción de Proteínas , ARN/química , ARN/metabolismo , Precursores del ARN/metabolismo , ARN Mensajero/metabolismo , Proteínas de Unión al ARN/química , Ribonucleoproteínas/química , Técnica SELEX de Producción de Aptámeros , Factor de Empalme U2AF , Proteína 1 de Unión a la Caja Y/química
19.
Mol Cell ; 45(4): 459-69, 2012 Feb 24.
Artículo en Inglés | MEDLINE | ID: mdl-22264826

RESUMEN

Mediator complex is an integrative hub for transcriptional regulation. Here we show that Mediator regulates alternative mRNA processing via its MED23 subunit. Combining tandem affinity purification and mass spectrometry, we identified a number of mRNA processing factors that bind to a soluble recombinant Mediator subunit, MED23, but not to several other Mediator components. One of these factors, hnRNP L, specifically interacts with MED23 in vitro and in vivo. Consistently, Mediator partially colocalizes with hnRNP L and the splicing machinery in the cell. Functionally, MED23 regulates a subset of hnRNP L-targeted alternative splicing (AS) and alternative cleavage and polyadenylation (APA) events, as shown by minigene reporters and exon array analysis. ChIP-seq analysis revealed that MED23 can regulate hnRNP L occupancy at their coregulated genes. Taken together, these results demonstrate a crosstalk between Mediator and the splicing machinery, providing a molecular basis for coupling mRNA processing to transcription.


Asunto(s)
Empalme Alternativo , Complejo Mediador/fisiología , ARN Mensajero/metabolismo , Animales , Células Cultivadas , Ribonucleoproteína Heterogénea-Nuclear Grupo L/metabolismo , Ribonucleoproteína Heterogénea-Nuclear Grupo L/fisiología , Ratones , Modelos Genéticos , Poliadenilación
20.
Hum Mol Genet ; 19(7): 1153-64, 2010 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-20053671

RESUMEN

The loss of HBII-52 and related C/D box small nucleolar RNA (snoRNA) expression units have been implicated as a cause for the Prader-Willi syndrome (PWS). We recently found that the C/D box snoRNA HBII-52 changes the alternative splicing of the serotonin receptor 2C pre-mRNA, which is different from the traditional C/D box snoRNA function in non-mRNA methylation. Using bioinformatic predictions and experimental verification, we identified five pre-mRNAs (DPM2, TAF1, RALGPS1, PBRM1 and CRHR1) containing alternative exons that are regulated by MBII-52, the mouse homolog of HBII-52. Analysis of a single member of the MBII-52 cluster of snoRNAs by RNase protection and northern blot analysis shows that the MBII-52 expressing unit generates shorter RNAs that originate from the full-length MBII-52 snoRNA through additional processing steps. These novel RNAs associate with hnRNPs and not with proteins associated with canonical C/D box snoRNAs. Our data indicate that not a traditional C/D box snoRNA MBII-52, but a processed version lacking the snoRNA stem is the predominant MBII-52 RNA missing in PWS. This processed snoRNA functions in alternative splice-site selection. Its substitution could be a therapeutic principle for PWS.


Asunto(s)
Empalme Alternativo , Síndrome de Prader-Willi/genética , ARN Nucleolar Pequeño , Receptor de Serotonina 5-HT2C/genética , Animales , Regulación de la Expresión Génica , Ribonucleoproteínas Nucleares Heterogéneas/metabolismo , Ratones , Edición de ARN , Precursores del ARN
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