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1.
PLoS Genet ; 19(10): e1010988, 2023 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-37831730

RESUMEN

Alternative splicing (AS) appears to be altered in Huntington's disease (HD), but its significance for early, pre-symptomatic disease stages has not been inspected. Here, taking advantage of Htt CAG knock-in mouse in vitro and in vivo models, we demonstrate a correlation between Htt CAG repeat length and increased aberrant linear AS, specifically affecting neural progenitors and, in vivo, the striatum prior to overt behavioral phenotypes stages. Remarkably, a significant proportion (36%) of the aberrantly spliced isoforms are not-functional and meant to non-sense mediated decay (NMD). The expanded Htt CAG repeats further reflect on a previously neglected, global impairment of back-splicing, leading to decreased circular RNAs production in neural progenitors. Integrative transcriptomic analyses unveil a network of transcriptionally altered micro-RNAs and RNA-binding proteins (Celf, hnRNPs, Ptbp, Srsf, Upf1, Ythd2) which might influence the AS machinery, primarily in neural cells. We suggest that this unbalanced expression of linear and circular RNAs might alter neural fitness, contributing to HD pathogenesis.


Asunto(s)
Enfermedad de Huntington , Ratones , Animales , Enfermedad de Huntington/genética , Enfermedad de Huntington/patología , ARN Circular/genética , Empalme del ARN , Empalme Alternativo/genética , Perfilación de la Expresión Génica , Expansión de Repetición de Trinucleótido/genética , Proteína Huntingtina/genética
2.
Nucleic Acids Res ; 50(22): 12809-12828, 2022 12 09.
Artículo en Inglés | MEDLINE | ID: mdl-36537238

RESUMEN

Disruptive mutations in the chromodomain helicase DNA-binding protein 8 gene (CHD8) have been recurrently associated with autism spectrum disorders (ASDs). Here we investigated how chromatin reacts to CHD8 suppression by analyzing a panel of histone modifications in induced pluripotent stem cell-derived neural progenitors. CHD8 suppression led to significant reduction (47.82%) in histone H3K36me3 peaks at gene bodies, particularly impacting on transcriptional elongation chromatin states. H3K36me3 reduction specifically affects highly expressed, CHD8-bound genes and correlates with altered alternative splicing patterns of 462 genes implicated in 'regulation of RNA splicing' and 'mRNA catabolic process'. Mass spectrometry analysis uncovered a novel interaction between CHD8 and the splicing regulator heterogeneous nuclear ribonucleoprotein L (hnRNPL), providing the first mechanistic insights to explain the CHD8 suppression-derived splicing phenotype, partly implicating SETD2, a H3K36me3 methyltransferase. In summary, our results point toward broad molecular consequences of CHD8 suppression, entailing altered histone deposition/maintenance and RNA processing regulation as important regulatory processes in ASD.


Asunto(s)
Empalme Alternativo , Cadherinas , Histonas , Cromatina , Histonas/metabolismo , Lisina/metabolismo , ARN/metabolismo , Cadherinas/genética , Humanos , Células Madre Pluripotentes Inducidas , Células-Madre Neurales , Trastorno del Espectro Autista/genética
3.
PLoS Genet ; 15(3): e1007765, 2019 03.
Artículo en Inglés | MEDLINE | ID: mdl-30897080

RESUMEN

Rare individuals with inactivating mutations in the Huntington's disease gene (HTT) exhibit variable abnormalities that imply essential HTT roles during organ development. Here we report phenotypes produced when increasingly severe hypomorphic mutations in the murine HTT orthologue Htt, (HdhneoQ20, HdhneoQ50, HdhneoQ111), were placed over a null allele (Hdhex4/5). The most severe hypomorphic allele failed to rescue null lethality at gastrulation, while the intermediate, though still severe, alleles yielded recessive perinatal lethality and a variety of fetal abnormalities affecting body size, skin, skeletal and ear formation, and transient defects in hematopoiesis. Comparative molecular analysis of wild-type and Htt-null retinoic acid-differentiated cells revealed gene network dysregulation associated with organ development that nominate polycomb repressive complexes and miRNAs as molecular mediators. Together these findings demonstrate that Htt is required both pre- and post-gastrulation to support normal development.


Asunto(s)
Proteína Huntingtina/genética , Enfermedad de Huntington/genética , Alelos , Animales , Diferenciación Celular/genética , Modelos Animales de Enfermedad , Frecuencia de los Genes/genética , Genotipo , Proteína Huntingtina/fisiología , Ratones/embriología , Mutación , Proteínas del Tejido Nervioso/genética , Fenotipo
4.
Nature ; 491(7424): 454-7, 2012 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-23064229

RESUMEN

Most of the mammalian genome is transcribed. This generates a vast repertoire of transcripts that includes protein-coding messenger RNAs, long non-coding RNAs (lncRNAs) and repetitive sequences, such as SINEs (short interspersed nuclear elements). A large percentage of ncRNAs are nuclear-enriched with unknown function. Antisense lncRNAs may form sense-antisense pairs by pairing with a protein-coding gene on the opposite strand to regulate epigenetic silencing, transcription and mRNA stability. Here we identify a nuclear-enriched lncRNA antisense to mouse ubiquitin carboxy-terminal hydrolase L1 (Uchl1), a gene involved in brain function and neurodegenerative diseases. Antisense Uchl1 increases UCHL1 protein synthesis at a post-transcriptional level, hereby identifying a new functional class of lncRNAs. Antisense Uchl1 activity depends on the presence of a 5' overlapping sequence and an embedded inverted SINEB2 element. These features are shared by other natural antisense transcripts and can confer regulatory activity to an artificial antisense to green fluorescent protein. Antisense Uchl1 function is under the control of stress signalling pathways, as mTORC1 inhibition by rapamycin causes an increase in UCHL1 protein that is associated to the shuttling of antisense Uchl1 RNA from the nucleus to the cytoplasm. Antisense Uchl1 RNA is then required for the association of the overlapping sense protein-coding mRNA to active polysomes for translation. These data reveal another layer of gene expression control at the post-transcriptional level.


Asunto(s)
Biosíntesis de Proteínas/genética , ARN sin Sentido/metabolismo , Elementos de Nucleótido Esparcido Corto/genética , Ubiquitina Tiolesterasa/genética , Ubiquitina Tiolesterasa/metabolismo , Animales , Antibacterianos/farmacología , Línea Celular , Humanos , Masculino , Ratones , Biosíntesis de Proteínas/efectos de los fármacos , ARN sin Sentido/genética , Inversión de Secuencia , Sirolimus/farmacología
5.
Hum Mol Genet ; 24(9): 2442-57, 2015 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-25574027

RESUMEN

The CAG repeat expansion in the Huntington's disease gene HTT extends a polyglutamine tract in mutant huntingtin that enhances its ability to facilitate polycomb repressive complex 2 (PRC2). To gain insight into this dominant gain of function, we mapped histone modifications genome-wide across an isogenic panel of mouse embryonic stem cell (ESC) and neuronal progenitor cell (NPC) lines, comparing the effects of Htt null and different size Htt CAG mutations. We found that Htt is required in ESC for the proper deposition of histone H3K27me3 at a subset of 'bivalent' loci but in NPC it is needed at 'bivalent' loci for both the proper maintenance and the appropriate removal of this mark. In contrast, Htt CAG size, though changing histone H3K27me3, is prominently associated with altered histone H3K4me3 at 'active' loci. The sets of ESC and NPC genes with altered histone marks delineated by the lack of huntingtin or the presence of mutant huntingtin, though distinct, are enriched in similar pathways with apoptosis specifically highlighted for the CAG mutation. Thus, the manner by which huntingtin function facilitates PRC2 may afford mutant huntingtin with multiple opportunities to impinge upon the broader machinery that orchestrates developmentally appropriate chromatin status.


Asunto(s)
Cromatina/genética , Cromatina/metabolismo , Mutación , Proteínas del Tejido Nervioso/genética , Proteínas del Tejido Nervioso/metabolismo , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Expansión de Repetición de Trinucleótido , Alelos , Animales , Ensamble y Desensamble de Cromatina , Inmunoprecipitación de Cromatina , Análisis por Conglomerados , Células Madre Embrionarias/metabolismo , Eliminación de Gen , Regulación de la Expresión Génica , Estudio de Asociación del Genoma Completo , Genotipo , Secuenciación de Nucleótidos de Alto Rendimiento , Histonas/metabolismo , Proteína Huntingtina , Ratones , Ratones Transgénicos , Proteínas del Tejido Nervioso/química , Células-Madre Neurales/metabolismo , Proteínas Nucleares/química , Complejo Represivo Polycomb 2/genética
6.
Adv Exp Med Biol ; 978: 277-299, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28523552

RESUMEN

Huntington's disease (HD) is a genetic, fatal autosomal dominant neurodegenerative disorder typically occurring in midlife with symptoms ranging from chorea, to dementia, to personality disturbances (Philos Trans R Soc Lond Ser B Biol Sci 354:957-961, 1999). HD is inherited in a dominant fashion, and the underlying mutation in all cases is a CAG trinucleotide repeat expansion within exon 1 of the HD gene (Cell 72:971-983, 1993). The expanded CAG repeat, translated into a lengthened glutamine tract at the amino terminus of the huntingtin protein, affects its structural properties and functional activities. The effects are pleiotropic, as huntingtin is broadly expressed in different cellular compartments (i.e., cytosol, nucleus, mitochondria) as well as in all cell types of the body at all developmental stages, such that HD pathogenesis likely starts at conception and is a lifelong process (Front Neurosci 9:509, 2015). The rate-limiting mechanism(s) of neurodegeneration in HD still remains elusive: many different processes are commonly disrupted in HD cell lines and animal models, as well as in HD patient cells (Eur J Neurosci 27:2803-2820, 2008); however, epigenetic-chromatin deregulation, as determined by the analysis of DNA methylation, histone modifications, and noncoding RNAs, has now become a prevailing feature. Thus, the overarching goal of this chapter is to discuss the current status of the literature, reviewing how an aberrant epigenetic landscape can contribute to altered gene expression and neuronal dysfunction in HD.


Asunto(s)
Epigénesis Genética/genética , Proteína Huntingtina/genética , Enfermedad de Huntington/genética , Acetilación , Animales , Línea Celular , Ensamble y Desensamble de Cromatina/genética , Ensayos Clínicos como Asunto , Metilación de ADN/genética , Modelos Animales de Enfermedad , Regulación de la Expresión Génica/genética , Código de Histonas/genética , Inhibidores de Histona Desacetilasas/uso terapéutico , Histona Desacetilasas/fisiología , Histona Metiltransferasas , N-Metiltransferasa de Histona-Lisina/antagonistas & inhibidores , N-Metiltransferasa de Histona-Lisina/fisiología , Homeostasis , Humanos , Enfermedad de Huntington/tratamiento farmacológico , Enfermedad de Huntington/metabolismo , Metilación , Proteína de la Leucemia Mieloide-Linfoide/fisiología , Proteínas del Tejido Nervioso/genética , Proteínas del Tejido Nervioso/fisiología , Proteínas del Grupo Polycomb/fisiología , Procesamiento Proteico-Postraduccional/genética , ARN no Traducido/genética
7.
Proc Natl Acad Sci U S A ; 111(42): E4468-77, 2014 Oct 21.
Artículo en Inglés | MEDLINE | ID: mdl-25294932

RESUMEN

Truncating mutations of chromodomain helicase DNA-binding protein 8 (CHD8), and of many other genes with diverse functions, are strong-effect risk factors for autism spectrum disorder (ASD), suggesting multiple mechanisms of pathogenesis. We explored the transcriptional networks that CHD8 regulates in neural progenitor cells (NPCs) by reducing its expression and then integrating transcriptome sequencing (RNA sequencing) with genome-wide CHD8 binding (ChIP sequencing). Suppressing CHD8 to levels comparable with the loss of a single allele caused altered expression of 1,756 genes, 64.9% of which were up-regulated. CHD8 showed widespread binding to chromatin, with 7,324 replicated sites that marked 5,658 genes. Integration of these data suggests that a limited array of direct regulatory effects of CHD8 produced a much larger network of secondary expression changes. Genes indirectly down-regulated (i.e., without CHD8-binding sites) reflect pathways involved in brain development, including synapse formation, neuron differentiation, cell adhesion, and axon guidance, whereas CHD8-bound genes are strongly associated with chromatin modification and transcriptional regulation. Genes associated with ASD were strongly enriched among indirectly down-regulated loci (P < 10(-8)) and CHD8-bound genes (P = 0.0043), which align with previously identified coexpression modules during fetal development. We also find an intriguing enrichment of cancer-related gene sets among CHD8-bound genes (P < 10(-10)). In vivo suppression of chd8 in zebrafish produced macrocephaly comparable to that of humans with inactivating mutations. These data indicate that heterozygous disruption of CHD8 precipitates a network of gene-expression changes involved in neurodevelopmental pathways in which many ASD-associated genes may converge on shared mechanisms of pathogenesis.


Asunto(s)
Trastornos Generalizados del Desarrollo Infantil/genética , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/fisiología , Regulación del Desarrollo de la Expresión Génica , Células-Madre Neurales/fisiología , Factores de Transcripción/genética , Factores de Transcripción/fisiología , Proteínas de Pez Cebra/fisiología , Animales , Axones/metabolismo , Sitios de Unión , Trastornos Generalizados del Desarrollo Infantil/metabolismo , Cromatina/metabolismo , ADN Helicasas/metabolismo , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Redes Reguladoras de Genes , Genoma , Heterocigoto , Humanos , Megalencefalia/metabolismo , Mutación , Neoplasias/metabolismo , Neuronas/metabolismo , Unión Proteica , Factores de Riesgo , Análisis de Secuencia de ARN , Programas Informáticos , Pez Cebra , Proteínas de Pez Cebra/genética
8.
Am J Hum Genet ; 91(6): 1128-34, 2012 Dec 07.
Artículo en Inglés | MEDLINE | ID: mdl-23217328

RESUMEN

Large intergenic noncoding (linc) RNAs represent a newly described class of ribonucleic acid whose importance in human disease remains undefined. We identified a severely developmentally delayed 16-year-old female with karyotype 46,XX,t(2;11)(p25.1;p15.1)dn in the absence of clinically significant copy number variants (CNVs). DNA capture followed by next-generation sequencing of the translocation breakpoints revealed disruption of a single noncoding gene on chromosome 2, LINC00299, whose RNA product is expressed in all tissues measured, but most abundantly in brain. Among a series of additional, unrelated subjects referred for clinical diagnostic testing who showed CNV affecting this locus, we identified four with exon-crossing deletions in association with neurodevelopmental abnormalities. No disruption of the LINC00299 coding sequence was seen in almost 14,000 control subjects. Together, these subjects with disruption of LINC00299 implicate this particular noncoding RNA in brain development and raise the possibility that, as a class, abnormalities of lincRNAs may play a significant role in human developmental disorders.


Asunto(s)
Discapacidades del Desarrollo/genética , Mutación , ARN Largo no Codificante/genética , Adolescente , Empalme Alternativo , Secuencia de Bases , Puntos de Rotura del Cromosoma , Cromosomas Humanos Par 11 , Cromosomas Humanos Par 2 , Femenino , Orden Génico , Humanos , Linfocitos/metabolismo , Datos de Secuencia Molecular , Células-Madre Neurales/metabolismo , Translocación Genética
9.
Mol Ther Nucleic Acids ; 35(3): 102234, 2024 Sep 10.
Artículo en Inglés | MEDLINE | ID: mdl-38974999

RESUMEN

Circular RNA (circRNA) molecules have critical functions during brain development and in brain-related disorders. Here, we identified and validated a circRNA, circHTT(2,3,4,5,6), stemming from the Huntington's disease (HD) gene locus that is most abundant in the central nervous system (CNS). We uncovered its evolutionary conservation in diverse mammalian species, and a correlation between circHTT(2,3,4,5,6) levels and the length of the CAG-repeat tract in exon-1 of HTT in human and mouse HD model systems. The mouse orthologue, circHtt(2,3,4,5,6), is expressed during embryogenesis, increases during nervous system development, and is aberrantly upregulated in the presence of the expanded CAG tract. While an IRES-like motif was predicted in circH TT (2,3,4,5,6), the circRNA does not appear to be translated in adult mouse brain tissue. Nonetheless, a modest, but consistent fraction of circHtt(2,3,4,5,6) associates with the 40S ribosomal subunit, suggesting a possible role in the regulation of protein translation. Finally, circHtt(2,3,4,5,6) overexpression experiments in HD-relevant STHdh striatal cells revealed its ability to modulate CAG expansion-driven cellular defects in cell-to-substrate adhesion, thus uncovering an unconventional modifier of HD pathology.

10.
J Biol Chem ; 286(28): 25108-17, 2011 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-21454471

RESUMEN

Huntington disease (HD) is a neurodegenerative disorder caused by an expansion of polyglutamines in the first exon of huntingtin (HTT), which confers aggregation-promoting properties to amino-terminal fragments of the protein (N-HTT). Mutant N-HTT aggregates are enriched for ubiquitin and contain ubiquitin E3 ligases, thus suggesting a role for ubiquitination in aggregate formation. Here, we report that tumor necrosis factor receptor-associated factor 6 (TRAF6) binds to WT and polyQ-expanded N-HTT in vitro as well as to endogenous full-length proteins in mouse and human brain in vivo. Endogenous TRAF6 is recruited to cellular inclusions formed by mutant N-HTT. Transient overexpression of TRAF6 promotes WT and mutant N-HTT atypical ubiquitination with Lys(6), Lys(27), and Lys(29) linkage formation. Both interaction and ubiquitination seem to be independent from polyQ length. In cultured cells, TRAF6 enhances mutant N-HTT aggregate formation, whereas it has no effect on WT N-HTT protein localization. Mutant N-HTT inclusions are enriched for ubiquitin staining only when TRAF6 and Lys(6), Lys(27), and Lys(29) ubiquitin mutants are expressed. Finally, we show that TRAF6 is up-regulated in post-mortem brains from HD patients where it is found in the insoluble fraction. These results suggest that TRAF6 atypical ubiquitination warrants investigation in HD pathogenesis.


Asunto(s)
Encéfalo/metabolismo , Proteínas del Tejido Nervioso/metabolismo , Proteínas Nucleares/metabolismo , Péptidos/metabolismo , Factor 6 Asociado a Receptor de TNF/metabolismo , Ubiquitinación , Animales , Encéfalo/patología , Células HEK293 , Humanos , Proteína Huntingtina , Enfermedad de Huntington/genética , Enfermedad de Huntington/metabolismo , Enfermedad de Huntington/patología , Cuerpos de Inclusión/genética , Cuerpos de Inclusión/metabolismo , Cuerpos de Inclusión/patología , Ratones , Mutación , Proteínas del Tejido Nervioso/genética , Proteínas Nucleares/genética , Péptidos/genética , Unión Proteica , Transporte de Proteínas/genética , Factor 6 Asociado a Receptor de TNF/genética
11.
Hum Mol Genet ; 19(19): 3759-70, 2010 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-20634198

RESUMEN

Parkinson's disease (PD) is a neurodegenerative disorder characterized by loss of dopaminergic neurons in the Substantia Nigra and the formation of ubiquitin- and alpha-synuclein (aSYN)-positive cytoplasmic inclusions called Lewy bodies (LBs). Although most PD cases are sporadic, families with genetic mutations have been found. Mutations in PARK7/DJ-1 have been associated with autosomal recessive early-onset PD, while missense mutations or duplications of aSYN (PARK1, PARK4) have been linked to dominant forms of the disease. In this study, we identify the E3 ubiquitin ligase tumor necrosis factor-receptor associated factor 6 (TRAF6) as a common player in genetic and sporadic cases. TRAF6 binds misfolded mutant DJ-1 and aSYN. Both proteins are substrates of TRAF6 ligase activity in vivo. Interestingly, rather than conventional K63 assembly, TRAF6 promotes atypical ubiquitin linkage formation to both PD targets that share K6-, K27- and K29- mediated ubiquitination. Importantly, TRAF6 stimulates the accumulation of insoluble and polyubiquitinated mutant DJ-1 into cytoplasmic aggregates. In human post-mortem brains of PD patients, TRAF6 protein colocalizes with aSYN in LBs. These results reveal a novel role for TRAF6 and for atypical ubiquitination in PD pathogenesis.


Asunto(s)
Encéfalo/patología , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Cuerpos de Lewy/metabolismo , Proteínas Mutantes/metabolismo , Proteínas Oncogénicas/metabolismo , Enfermedad de Parkinson/metabolismo , Factor 6 Asociado a Receptor de TNF/metabolismo , alfa-Sinucleína/metabolismo , Encéfalo/metabolismo , Células HEK293 , Humanos , Péptidos y Proteínas de Señalización Intracelular/química , Cuerpos de Lewy/patología , Proteínas Mutantes/química , Proteínas Oncogénicas/química , Enfermedad de Parkinson/patología , Unión Proteica , Proteína Desglicasa DJ-1 , Pliegue de Proteína , Estructura Cuaternaria de Proteína , Transporte de Proteínas , Especificidad por Sustrato , Ubiquitinación
12.
Proc Natl Acad Sci U S A ; 106(36): 15454-9, 2009 Sep 08.
Artículo en Inglés | MEDLINE | ID: mdl-19717439

RESUMEN

The mesencephalic dopaminergic (mDA) cell system is composed of two major groups of projecting cells in the substantia nigra (SN) (A9 neurons) and the ventral tegmental area (VTA) (A10 cells). A9 neurons form the nigrostriatal pathway and are involved in regulating voluntary movements and postural reflexes. Their selective degeneration leads to Parkinson's disease. Here, we report that gene expression analysis of A9 dopaminergic neurons (DA) identifies transcripts for alpha- and beta-chains of hemoglobin (Hb). Globin immunoreactivity decorates the majority of A9 DA, a subpopulation of cortical and hippocampal astrocytes and mature oligodendrocytes. This pattern of expression was confirmed in different mouse strains and in rat and human. We show that Hb is expressed in the SN of human postmortem brain. By microarray analysis of dopaminergic cell lines overexpressing alpha- and beta-globin chains, changes in genes involved in O(2) homeostasis and oxidative phopshorylation were observed, linking Hb expression to mitochondrial function. Our data suggest that the most famed oxygen-carrying globin is not exclusively restricted to the blood, but it may play a role in the normal physiology of the brain and neurodegenerative diseases.


Asunto(s)
Neuroglía/metabolismo , Neuronas/metabolismo , Sustancia Negra/citología , Área Tegmental Ventral/citología , Globinas alfa/metabolismo , Globinas beta/metabolismo , Animales , Citometría de Flujo , Proteínas Fluorescentes Verdes , Humanos , Ratones , Análisis de Secuencia por Matrices de Oligonucleótidos , Ratas
13.
Genes (Basel) ; 13(11)2022 11 03.
Artículo en Inglés | MEDLINE | ID: mdl-36360254

RESUMEN

Whether as a cause or a symptom, RNA transcription is recurrently altered in pathologic conditions. This is also true for non-coding RNAs, with regulatory functions in a variety of processes such as differentiation, cell identity and metabolism. In line with their increasingly recognized roles in cellular pathways, RNAs are also currently evaluated as possible disease biomarkers. They could be informative not only to follow disease progression and assess treatment efficacy in clinics, but also to aid in the development of new therapeutic approaches. This is especially important for neurological and genetic disorders, where the administration of appropriate treatment during the disease prodromal stage could significantly delay, if not halt, disease progression. In this review we focus on the current status of biomarkers in Huntington's Disease (HD), a fatal hereditary and degenerative disease condition. First, we revise the sources and type of wet biomarkers currently in use. Then, we explore the feasibility of different RNA types (miRNA, ncRNA, circRNA) as possible biomarker candidates, discussing potential advantages, disadvantages, sources of origin and the ongoing investigations on this topic.


Asunto(s)
Enfermedad de Huntington , MicroARNs , Humanos , Enfermedad de Huntington/diagnóstico , Enfermedad de Huntington/genética , ARN no Traducido/genética , ARN no Traducido/metabolismo , Biomarcadores/metabolismo , Progresión de la Enfermedad
14.
Methods Mol Biol ; 2434: 63-87, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35213010

RESUMEN

SINEUP is a new class of long non-coding RNAs (lncRNAs) which contain an inverted Short Interspersed Nuclear Element (SINE) B2 element (invSINEB2) necessary to specifically upregulate target gene translation. Originally identified in the mouse AS-Uchl1 (antisense Ubiquitin carboxyl-terminal esterase L1) locus, natural SINEUP molecules are oriented head to head to their sense protein coding, target gene (Uchl1, in this example). Peculiarly, SINEUP is able to augment, in a specific and controlled way, the expression of the target protein, with no alteration of target mRNA levels. SINEUP is characterized by a modular structure with the Binding Domain (BD) providing specificity to the target transcript and an effector domain (ED)-containing the invSINEB2 element-able to promote the loading to the heavy polysomes of the target mRNA. Since the understanding of its modular structure in the endogenous AS-Uchl1 ncRNA, synthetic SINEUP molecules have been developed by creating a specific BD for the gene of interest and placing it upstream the invSINEB2 ED. Synthetic SINEUP is thus a novel molecular tool that potentially may be used for any industrial or biomedical application to enhance protein production, also as possible therapeutic strategy in haploinsufficiency-driven disorders.Here, we describe a detailed protocol to (1) design a specific BD directed to a gene of interest and (2) assemble and clone it with the ED to obtain a functional SINEUP molecule. Then, we provide guidelines to efficiently deliver SINEUP into mammalian cells and evaluate its ability to effectively upregulate target protein translation.


Asunto(s)
Biosíntesis de Proteínas , ARN Largo no Codificante , Animales , Ratones , ARN sin Sentido/genética , ARN Largo no Codificante/genética , ARN Largo no Codificante/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , Elementos de Nucleótido Esparcido Corto
15.
J Biol Chem ; 285(24): 18565-74, 2010 Jun 11.
Artículo en Inglés | MEDLINE | ID: mdl-20395301

RESUMEN

Mutations in PARK7/DJ-1 are associated with autosomal recessive, early onset Parkinson disease (PD). DJ-1 is an atypical peroxiredoxin-like peroxidase that may act as a redox-dependent chaperone and a regulator of transcription. Here we show that DJ-1 plays an essential role in the expression of rearranged during transfection (RET), a receptor for the glial cell line-derived neurotrophic factor, a neuroprotective molecule for dopaminergic neurons, the main target of degeneration in PD. The inducible loss of DJ-1 triggers the establishment of hypoxia and the production of reactive oxygen species that stabilize the hypoxia-inducible factor-1alpha (HIF-1a). HIF-1a expression is required for RET down-regulation. This study establishes for the first time a molecular link between the lack of functional DJ-1 and the glial cell line-derived neurotrophic factor signaling pathway that may explain the adult-onset loss of dopaminergic neurons. Furthermore, it suggests that hypoxia may play an important role in PD.


Asunto(s)
Regulación Neoplásica de la Expresión Génica , Péptidos y Proteínas de Señalización Intracelular/fisiología , Mutación , Neuroblastoma/metabolismo , Proteínas Oncogénicas/fisiología , Proteínas Proto-Oncogénicas c-ret/metabolismo , Línea Celular Tumoral , Citometría de Flujo , Humanos , Hipoxia , Subunidad alfa del Factor 1 Inducible por Hipoxia/metabolismo , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Neuroglía/citología , Análisis de Secuencia por Matrices de Oligonucleótidos , Proteínas Oncogénicas/metabolismo , Oxidación-Reducción , Proteína Desglicasa DJ-1 , Especies Reactivas de Oxígeno , Transducción de Señal
16.
Front Cell Neurosci ; 15: 628010, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33642998

RESUMEN

Huntington's disease (HD) is a devastating neurodegenerative disorder caused by an aberrant expansion of the CAG tract within the exon 1 of the HD gene, HTT. HD progressively impairs motor and cognitive capabilities, leading to a total loss of autonomy and ultimate death. Currently, no cure or effective treatment is available to halt the disease. Although the HTT gene is ubiquitously expressed, the striatum appears to be the most susceptible district to the HD mutation with Medium-sized Spiny Neurons (MSNs) (D1R and D2R) representing 95% of the striatal neuronal population. Why are striatal MSNs so vulnerable to the HD mutation? Particularly, why do D1R- and D2R-MSNs display different susceptibility to HD? Here, we highlight significant differences between D1R- and D2R-MSNs subpopulations, such as morphology, electrophysiology, transcriptomic, functionality, and localization in the striatum. We discuss possible reasons for their selective degeneration in the context of HD. Our review suggests that a better understanding of cell type-specific gene expression dysregulation within the striatum might reveal new paths to therapeutic intervention or prevention to ameliorate HD patients' life expectancy.

17.
Front Genet ; 12: 745229, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34880900

RESUMEN

CHD8 represents one of the highest confidence genetic risk factors implied in Autism Spectrum Disorders, with most mutations leading to CHD8 haploinsufficiency and the insurgence of specific phenotypes, such as macrocephaly, facial dysmorphisms, intellectual disability, and gastrointestinal complaints. While extensive studies have been conducted on the possible consequences of CHD8 suppression and protein coding RNAs dysregulation during neuronal development, the effects of transcriptional changes of long non-coding RNAs (lncRNAs) remain unclear. In this study, we focused on a peculiar class of natural antisense lncRNAs, SINEUPs, that enhance translation of a target mRNA through the activity of two RNA domains, an embedded transposable element sequence and an antisense region. By looking at dysregulated transcripts following CHD8 knock down (KD), we first identified RAB11B-AS1 as a potential SINEUP RNA for its domain configuration. Then we demonstrated that such lncRNA is able to increase endogenous RAB11B protein amounts without affecting its transcriptional levels. RAB11B has a pivotal role in vesicular trafficking, and mutations on this gene correlate with intellectual disability and microcephaly. Thus, our study discloses an additional layer of molecular regulation which is altered by CHD8 suppression. This represents the first experimental confirmation that naturally occurring SINEUP could be involved in ASD pathogenesis and underscores the importance of dysregulation of functional lncRNAs in neurodevelopment.

18.
Cell Calcium ; 43(2): 184-95, 2008 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-17588656

RESUMEN

Cadmium, a toxic environmental contaminant, exerts adverse effects on different cellular pathways such as cell proliferation, DNA damage and apoptosis. In particular, the modulation of Ca(2+) homeostasis seems to have an important role during Cd(2+) injury, but the precise assessment of Ca(2+) signalling still remains poorly understood. We used aequorin-based probes specifically directed to intracellular organelles to study Ca(2+) changes during cadmium injury. We observed that cadmium decreased agonist-evoked endoplasmic reticulum (ER) Ca(2+) signals and caused a 40% inhibition of sarcoplasmic-ER calcium ATPases activity. Moreover, time course experiments correlate morphological alterations, processing of xbp-1 mRNA and caspase-12 activation during cadmium administration. Finally, the time response of ER to cadmium injury was compared with that of mitochondria. In conclusion, we highlighted a novel pathway of cadmium-induced cell death triggered by ER stress and involving caspase-12. Mitochondria and ER pathways seemed to share common time courses and a parallel activation of caspase-12 and caspase-9 seemed likely to be involved in acute cadmium toxicity.


Asunto(s)
Apoptosis/efectos de los fármacos , Cadmio/toxicidad , Señalización del Calcio/fisiología , Retículo Endoplásmico/fisiología , Aequorina/efectos de los fármacos , Aequorina/metabolismo , Animales , Bradiquinina/farmacología , Calcio/metabolismo , Señalización del Calcio/efectos de los fármacos , Caspasa 12/metabolismo , Citocromos c/metabolismo , Proteínas de Unión al ADN/metabolismo , Retículo Endoplásmico/efectos de los fármacos , Retículo Endoplásmico/ultraestructura , Activación Enzimática , Homeostasis/efectos de los fármacos , Ratones , Mitocondrias/efectos de los fármacos , Mitocondrias/ultraestructura , Células 3T3 NIH , Pliegue de Proteína , Factores de Transcripción del Factor Regulador X , Factores de Transcripción/metabolismo , Transfección , Proteína 1 de Unión a la X-Box
19.
Toxins (Basel) ; 9(11)2017 11 03.
Artículo en Inglés | MEDLINE | ID: mdl-29469820

RESUMEN

Pathogenic bacteria produce powerful virulent factors, such as pore-forming toxins, that promote their survival and cause serious damage to the host. Host cells reply to membrane stresses and ionic imbalance by modifying gene expression at the epigenetic, transcriptional and translational level, to recover from the toxin attack. The fact that the majority of the human transcriptome encodes for non-coding RNAs (ncRNAs) raises the question: do host cells deploy non-coding transcripts to rapidly control the most energy-consuming process in cells-i.e., host translation-to counteract the infection? Here, we discuss the intriguing possibility that membrane-damaging toxins induce, in the host, the expression of toxin-specific long non-coding RNAs (lncRNAs), which act as sponges for other molecules, encoding small peptides or binding target mRNAs to depress their translation efficiency. Unravelling the function of host-produced lncRNAs upon bacterial infection or membrane damage requires an improved understanding of host lncRNA expression patterns, their association with polysomes and their function during this stress. This field of investigation holds a unique opportunity to reveal unpredicted scenarios and novel approaches to counteract antibiotic-resistant infections.


Asunto(s)
Infecciones Bacterianas/genética , Interacciones Huésped-Patógeno , ARN Largo no Codificante , Fenómenos Fisiológicos Bacterianos , Toxinas Bacterianas/metabolismo , Expresión Génica , Humanos , Biosíntesis de Proteínas
20.
Environ Health Perspect ; 110 Suppl 5: 865-7, 2002 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-12426148

RESUMEN

In various mammalian cells, two group IIb metals, cadmium and zinc, induce several morphological and biochemical effects that are salient features of programmed cell death. In C6 rat glioma cells, cadmium caused externalization of phosphatidylserine, breakdown of the mitochondrial membrane potential, activation of caspase-9, internucleosomal DNA fragmentation, chromatin condensation, and nuclear fragmentation. In NIH3T3 murine fibroblasts, cadmium-induced apoptosis was inhibited by overexpression of the antiapoptotic protein Bcl-2. Cadmium-induced DNA fragmentation in C6 cells was independent of inhibition of protein kinase A (PKA), protein kinase C (PKC), mitogen-activated protein kinase (MAPK), phosphatidylinositol-3-kinase, Ca-calmodulin-dependent protein kinase, and protein kinase G. Zinc at moderate concentrations (10-50 microM) protected against programmed cell death induced by cadmium, whereas deprivation of zinc by the membrane-permeable chelator N,N,N',N-terakis-(2-pyridylmethyl)ethylenediamine (TPEN) caused cell death with features characteristic of apoptosis. On the other hand, at elevated extracellular levels (150-200 microM), zinc alone caused programmed cell death in C6 cells. Zinc-induced apoptosis was independent of inhibition of PKA, PKC, guanylate cyclase and MAPK, but it was suppressed in the presence of 100 microM lanthanum chloride.


Asunto(s)
Apoptosis/efectos de los fármacos , Cadmio/efectos adversos , Zinc/efectos adversos , Animales , Cadmio/farmacología , Proteínas Quinasas Dependientes de AMP Cíclico/efectos de los fármacos , Proteínas Quinasas Dependientes de AMP Cíclico/farmacología , Fibroblastos , Glioma/patología , Guanilato Ciclasa/efectos de los fármacos , Guanilato Ciclasa/farmacología , Ratones , Proteínas Quinasas Activadas por Mitógenos/efectos de los fármacos , Proteínas Quinasas Activadas por Mitógenos/farmacología , Proteína Quinasa C/efectos de los fármacos , Proteína Quinasa C/farmacología , Ratas , Células Tumorales Cultivadas , Zinc/farmacología
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