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1.
iScience ; 21: 706-719, 2019 Nov 22.
Artículo en Inglés | MEDLINE | ID: mdl-31733516

RESUMEN

RNA-binding proteins (RBPs) are key players of post-transcriptional regulation of gene expression, relying on competitive and cooperative interactions to fine-tune their action. Several studies have described individual interactions of RBPs with RBP mRNAs. Here we present a systematic network investigation of fifty thousand interactions between RBPs and the UTRs of RBP mRNAs. We identified two structural features in this network. RBP clusters are groups of densely interconnected RBPs co-binding their targets, suggesting a tight control of cooperative and competitive behaviors. RBP chains are hierarchical structures connecting RBP clusters and driven by evolutionarily ancient RBPs. These features suggest that RBP chains may coordinate the different cell programs controlled by RBP clusters. Under this model, the regulatory signal flows through chains from one cluster to another, implementing elaborate regulatory plans. This work thus suggests RBP-RBP interactions as a backbone driving post-transcriptional regulation of gene expression to control RBPs action on their targets.

2.
EBioMedicine ; 46: 79-93, 2019 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-31303496

RESUMEN

BACKGROUND: Metastatic colorectal cancer (CRC) remains a deadly disease. Identifying locally advanced CRC patients with high risk of developing metastasis and improving outcome of metastatic CRC patients require discovering master regulators of metastasis. In this context, the non-coding part of the human genome is still largely unexplored. METHODS: To interrogate the non-coding part of the human genome and disclose regulators of CRC metastasis, we combined a transposon-based forward genetic screen with a novel in vitro assay, which forces cells to grow deprived of cell-substrate and cell-cell contacts (i.e. forced single cell suspension assay - fSCS). FINDINGS: We proved that fSCS selects CRC cells with mesenchymal and pro-metastatic traits. Moreover, we found that the transposon insertions conferred CRC cells resistance to fSCS and thus metastatic advantage. Among the retrieved transposon insertions, we demonstrated that the one located in the 3'UTR of BTBD7 disrupts miR-23b::BTBD7 interaction and contributes to pro-metastatic traits. In addition, miR-23b and BTBD7 correlate with CRC metastasis both in preclinical experiments and in clinical samples. INTERPRETATION: fSCS is a simple and scalable in vitro assay to investigate pro-metastatic traits and transposon-based genetic screens can interrogate the non-coding part of the human genome (e.g. miRNA::target interactions). Finally, both Btbd7 and miR-23b represent promising prognostic biomarkers and therapeutic targets in CRC. FUND: This work was supported by Marie Curie Actions (CIG n. 303877) and Friuli Venezia Giulia region (Grant Agreement n°245574), Italian Association for Cancer Research (AIRC, MFAG n°13589), Italian Ministry of Health (GR-2010-2319387 and PE-2016-02361040) and 5x1000 to CRO Aviano.


Asunto(s)
Proteínas Adaptadoras Transductoras de Señales/genética , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/patología , Regulación Neoplásica de la Expresión Génica , MicroARNs/genética , Interferencia de ARN , Comunicación Celular , Línea Celular Tumoral , Proliferación Celular , Transición Epitelial-Mesenquimal/genética , Matriz Extracelular/metabolismo , Pruebas Genéticas , Humanos , Metástasis de la Neoplasia , Estadificación de Neoplasias
3.
Int J Mol Sci ; 19(9)2018 Aug 24.
Artículo en Inglés | MEDLINE | ID: mdl-30149579

RESUMEN

High-grade serous epithelial ovarian cancer (HGSOC) is the fifth leading cause of cancer death in women and the first among gynecological malignancies. Despite an initial response to standard chemotherapy, most HGSOC patients relapse. To improve treatment options, we must continue investigating tumor biology. Tumor characteristics (e.g., risk factors and epidemiology) are valuable clues to accomplish this task. The two most frequent risk factors for HGSOC are the lifetime number of ovulations, which is associated with increased oxidative stress in the pelvic area caused by ovulation fluid, and a positive family history due to genetic factors. In the attempt to identify novel genetic factors (i.e., genes) associated with HGSOC, we observed that several genes in linkage with HGSOC are expressed in the ciliated cells of the fallopian tube. This finding made us hypothesize that ciliated cells, despite not being the cell of origin for HGSOC, may take part in HGSOC tumor initiation. Specifically, malfunction of the ciliary beat impairs the laminar fluid flow above the fallopian tube epithelia, thus likely reducing the clearance of oxidative stress caused by follicular fluid. Herein, we review the up-to-date findings dealing with HGSOC predisposition with the hypothesis that fallopian ciliated cells take part in HGSOC onset. Finally, we review the up-to-date literature concerning genes that are located in genomic loci associated with epithelial ovarian cancer (EOC) predisposition that are expressed by the fallopian ciliated cells.


Asunto(s)
Cistadenocarcinoma Seroso/etiología , Cistadenocarcinoma Seroso/metabolismo , Trompas Uterinas/metabolismo , Membrana Mucosa/metabolismo , Neoplasias Ováricas/etiología , Neoplasias Ováricas/metabolismo , Animales , Biomarcadores , Carcinoma Epitelial de Ovario/diagnóstico , Carcinoma Epitelial de Ovario/etiología , Carcinoma Epitelial de Ovario/metabolismo , Cistadenocarcinoma Seroso/diagnóstico , Susceptibilidad a Enfermedades , Trompas Uterinas/patología , Femenino , Predisposición Genética a la Enfermedad , Variación Genética , Humanos , Membrana Mucosa/patología , Clasificación del Tumor , Células Madre Neoplásicas/metabolismo , Oncogenes , Neoplasias Ováricas/diagnóstico
4.
Sci Rep ; 8(1): 10476, 2018 Jul 11.
Artículo en Inglés | MEDLINE | ID: mdl-29992994

RESUMEN

The dysbiosis of the oral microbiome is associated with both localized and systemic diseases. Modulating the resident microbial communities by the dietary consumption of probiotics has become an appealing means to promote host health by either restoring host-microbe balance or preventing dysbiosis. Most probiotics strategies target the intestinal microbiome, but little is known about their impact on the oral microbiome. We analyzed here the saliva microbiome from 21 volunteers, longitudinally collected before, during, and after consumption of a commercial probiotic and a standard yoghurt using 16S amplicon sequencing. The alpha diversity of the saliva microbiome had a statistically significant increase (P-value = 0.0011) in one of the groups that consumed the probiotic. The overall structure of the microbiome was however not significantly impacted by the probiotic, although oligotyping analysis revealed that both Streptococci and Lactobacilli present in the probiotic product persisted in the saliva microbiome. In contrast, non-probiotic yoghurt consumption had a lesser impact on the overall diversity and Lactobacillus and Streptococcus persistence. Our results suggest that consumption of commercial probiotics in healthy subjects increase the overall diversity of the oral cavity microbiome in the short term, but such dietary interventions are not able to substantially modify the structure of the microbiome.


Asunto(s)
Microbiota/efectos de los fármacos , Boca/microbiología , Probióticos/farmacología , Saliva/microbiología , Biodiversidad , Femenino , Voluntarios Sanos , Humanos , Estudios Longitudinales , Masculino , Probióticos/administración & dosificación , ARN Ribosómico 16S/genética , Factores de Tiempo , Adulto Joven
5.
Front Mol Biosci ; 4: 67, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-29034245

RESUMEN

What drives the flow of signals controlling the outcome of post-transcriptional regulation of gene expression? This regulatory layer, presiding to processes ranging from splicing to mRNA stability and localization, is a key determinant of protein levels and thus cell phenotypes. RNA-binding proteins (RBPs) form a remarkable army of post-transcriptional regulators, strong of more than 1,500 genes implementing this expression fine-tuning plan and implicated in both cell physiology and pathology. RBPs can bind and control a wide array of RNA targets. This sheer amount of interactions form complex regulatory networks (PTRNs) where the action of individual RBPs cannot be easily untangled from each other. While past studies have mostly focused on the action of individual RBPs on their targets, we are now observing an increasing amount of evidence describing the occurrence of interactions between RBPs, defining how common target RNAs are regulated. This suggests that the flow of signals in PTRNs is driven by the intertwined contribution of multiple RBPs, concurrently acting on each of their targets. Understanding how RBPs cooperate and compete is thus of paramount importance to chart the wiring of PTRNs and their impact on cell phenotypes. Here we review the current knowledge about patterns of RBP interaction and attempt at describing their general principles. We also discuss future directions which should be taken to reach a comprehensive understanding of this fundamental aspect of gene expression regulation.

6.
Nucleic Acids Res ; 45(16): 9514-9527, 2017 Sep 19.
Artículo en Inglés | MEDLINE | ID: mdl-28934484

RESUMEN

The Human antigen R protein (HuR) is an RNA-binding protein that recognizes U/AU-rich elements in diverse RNAs through two RNA-recognition motifs, RRM1 and RRM2, and post-transcriptionally regulates the fate of target RNAs. The natural product dihydrotanshinone-I (DHTS) prevents the association of HuR and target RNAs in vitro and in cultured cells by interfering with the binding of HuR to RNA. Here, we report the structural determinants of the interaction between DHTS and HuR and the impact of DHTS on HuR binding to target mRNAs transcriptome-wide. NMR titration and Molecular Dynamics simulation identified the residues within RRM1 and RRM2 responsible for the interaction between DHTS and HuR. RNA Electromobility Shifts and Alpha Screen Assays showed that DHTS interacts with HuR through the same binding regions as target RNAs, stabilizing HuR in a locked conformation that hampers RNA binding competitively. HuR ribonucleoprotein immunoprecipitation followed by microarray (RIP-chip) analysis showed that DHTS treatment of HeLa cells paradoxically enriched HuR binding to mRNAs with longer 3'UTR and with higher density of U/AU-rich elements, suggesting that DHTS inhibits the association of HuR to weaker target mRNAs. In vivo, DHTS potently inhibited xenograft tumor growth in a HuR-dependent model without systemic toxicity.


Asunto(s)
Proteína 1 Similar a ELAV/química , Fenantrenos/química , Fenantrenos/farmacología , Regiones no Traducidas 3' , Elementos Ricos en Adenilato y Uridilato , Animales , Antineoplásicos Fitogénicos/química , Antineoplásicos Fitogénicos/farmacología , Proteína 1 Similar a ELAV/antagonistas & inhibidores , Proteína 1 Similar a ELAV/genética , Proteína 1 Similar a ELAV/metabolismo , Humanos , Espectroscopía de Resonancia Magnética , Ratones Mutantes Neurológicos , Simulación de Dinámica Molecular , Fenantrenos/metabolismo , Mutación Puntual , Conformación Proteica , Dominios Proteicos , ARN Mensajero/metabolismo , Ensayos Antitumor por Modelo de Xenoinjerto
7.
Nucleic Acids Res ; 44(10): 4988, 2016 06 02.
Artículo en Inglés | MEDLINE | ID: mdl-26895890
8.
Methods Mol Biol ; 1358: v-viii, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-26744759
9.
Nucleic Acids Res ; 44(1): e2, 2016 Jan 08.
Artículo en Inglés | MEDLINE | ID: mdl-26253738

RESUMEN

De-novo motif search is a frequently applied bioinformatics procedure to identify and prioritize recurrent elements in sequences sets for biological investigation, such as the ones derived from high-throughput differential expression experiments. Several algorithms have been developed to perform motif search, employing widely different approaches and often giving divergent results. In order to maximize the power of these investigations and ultimately be able to draft solid biological hypotheses, there is the need for applying multiple tools on the same sequences and merge the obtained results. However, motif reporting formats and statistical evaluation methods currently make such an integration task difficult to perform and mostly restricted to specific scenarios. We thus introduce here the Dynamic Motif Integration Toolkit (DynaMIT), an extremely flexible platform allowing to identify motifs employing multiple algorithms, integrate them by means of a user-selected strategy and visualize results in several ways; furthermore, the platform is user-extendible in all its aspects. DynaMIT is freely available at http://cibioltg.bitbucket.org.


Asunto(s)
Biología Computacional/métodos , Motivos de Nucleótidos , Programas Informáticos , Animales , Sitios de Unión , Humanos , Ratones , Posición Específica de Matrices de Puntuación , Unión Proteica , Reproducibilidad de los Resultados
10.
Methods Mol Biol ; 1358: 3-28, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-26463374

RESUMEN

Untranslated regions (UTRs) and, to a lesser extent, coding sequences of mRNAs are involved in defining the fate of the mature transcripts through the modulation of three primary control processes, mRNA localization, degradation and translation; the action of trans-factors such as RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) combined with the presence of defined sequence and structural cis-elements ultimately determines translation levels. Identifying functional regions in UTRs and uncovering post-transcriptional regulators acting upon these regions is thus of paramount importance to understand the spectrum of regulatory possibilities for any given mRNA. This tasks can now be approached computationally, to reduce the space of testable hypotheses and to drive experimental validation.This chapter focuses on presenting databases and tools allowing to study the various aspects of post-transcriptional regulation, including motif search (sequence and secondary structure), prediction of regulatory networks (e.g., RBP and ncRNA binding sites), profiling of the mRNAs translational state, and other aspects of this level of gene expression regulation. Two analysis pipelines are also presented as practical examples of how the described tools could be integrated and effectively employed.


Asunto(s)
Biología Computacional/métodos , Regulación de la Expresión Génica/genética , ARN Mensajero/genética , ARN Mensajero/biosíntesis , ARN no Traducido/genética , Proteínas de Unión al ARN/genética , Regiones no Traducidas/genética
11.
Genom Data ; 6: 285-7, 2015 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-26697401

RESUMEN

Neuroblastoma is the most common pediatric cancer, arising from the neural crest cells of the sympathetic nervous system. Its most aggressive subtype, characterized by the amplification of the MYCN oncogene, has a dismal prognosis and no effective treatment is available. Understanding the alterations induced by the tumor on the various layers of gene expression is therefore important for a complete characterization of this neuroblastoma subtype and for the discovery of new therapeutic opportunities. Here we describe the profiling of 13 MYCN-amplified neuroblastoma cell lines at the genome (copy number), transcriptome, translatome and miRome levels (GEO series GSE56654, GSE56552 and GSE56655). We provide detailed experimental and data analysis procedures by means of which we derived the results described in [1].

12.
Eur J Med Genet ; 58(11): 597-602, 2015 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-26420031

RESUMEN

In the present study we describe the exome sequencing and analysis of a patient with Catel-Manzke-like phenotype showing bilateral hyperphalangism of the second finger and thumb clinodactyly due to a unilateral delta phalanx, associated with growth, cardiac and vertebral defects. The exome sequencing analysis excluded pathogenetic mutations in the genes known to cause syndromes with hyperphalangism and did not identify any alteration in the X-chromosome or de novo mutations in likely candidate genes. Under the assumption of an autosomal recessive mode of inheritance and based on the frequency of the single nucleotide variants found in homozygous or double heterozygous states and the results of computer prediction programs, only one gene, DNAH10, emerged as a candidate in the pathogenesis of the disease in our patient. However, the differences among the known biological functions of DNAH10 and the genes involved in the other syndromes with hyperphalangism, suggest caution in the interpretation of the results.


Asunto(s)
Dineínas/genética , Exoma , Deformidades Congénitas de la Mano/genética , Síndrome de Pierre Robin/genética , Secuencia de Aminoácidos , Deformidades Congénitas de la Mano/diagnóstico , Heterocigoto , Humanos , Masculino , Datos de Secuencia Molecular , Mutación , Síndrome de Pierre Robin/diagnóstico , Polimorfismo de Nucleótido Simple , Adulto Joven
13.
Sci Rep ; 5: 14364, 2015 Sep 24.
Artículo en Inglés | MEDLINE | ID: mdl-26399178

RESUMEN

Cancer-associated gene expression imbalances are conventionally studied at the genomic, epigenomic and transcriptomic levels. Given the relevance of translational control in determining cell phenotypes, we evaluated the translatome, i.e., the transcriptome engaged in translation, as a descriptor of the effects of genetic instability in cancer. We performed this evaluation in high-risk neuroblastomas, which are characterized by a low frequency of point mutations or known cancer-driving genes and by the presence of several segmental chromosomal aberrations that produce gene-copy imbalances that guide aggressiveness. We thus integrated genome, transcriptome, translatome and miRome profiles in a representative panel of high-risk neuroblastoma cell lines. We identified a number of genes whose genomic imbalance was corrected by compensatory adaptations in translational efficiency. The transcriptomic level of these genes was predictive of poor prognosis in more than half of cases, and the genomic imbalances found in their loci were shared by 27 other tumor types. This homeostatic process is also not limited to copy number-altered genes, as we showed the translational stoichiometric rebalance of histone genes. We suggest that the translational buffering of fluctuations in these dose-sensitive transcripts is a potential driving process of neuroblastoma evolution.


Asunto(s)
Regulación Neoplásica de la Expresión Génica , Inestabilidad Genómica , Neuroblastoma/genética , Biosíntesis de Proteínas , Línea Celular Tumoral , Hibridación Genómica Comparativa , Variaciones en el Número de Copia de ADN , Amplificación de Genes , Perfilación de la Expresión Génica , Genes myc , Histonas/metabolismo , Humanos , Neuroblastoma/metabolismo
14.
Invest Ophthalmol Vis Sci ; 56(8): 4846-56, 2015 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-26218913

RESUMEN

PURPOSE: Mutations in CACNA2D4 exon 25 cause photoreceptor dysfunction in humans (c.2406C→A mutation) and mice (c.2451insC mutation). We investigated the feasibility of an exon-skipping therapeutic approach by evaluating the splicing patterns and functional role of targeted exons. METHODS: Splicing of the targeted α2δ4 (CACNA2D4) exons in presence and absence of the mutation was assessed by RT-PCR in vivo on mouse retinae and in vitro in HEK293T cells using splicing-reporter minigenes. Whole-cell patch-clamp recordings were performed to evaluate the impact of different Cacna2d4 variants on the biophysical properties of Cav1.4 L-type calcium channels (CACNA1F). RESULTS: Splicing analysis revealed the presence of a previously unknown splicing isoform of α2δ4 in the retina that truncates the gene open reading frame (ORF) in a similar way as the c.2451insC mutation. This isoform originates from alternative splicing of exon 25 (E25) with a new exon (E25b). Moreover, the c.2451insC mutation has an effect on splicing and increases the proportion of transcripts including E25b. Our electrophysiological analyses showed that only full-length α2δ4 was able to increase Cav1.4/ß3-mediated currents while all other α2δ4 variants did not mediate such effect. CONCLUSIONS: The designed exon-skipping strategy is not applicable because the resulting skipped α2δ4 are nonfunctional. α2δ4 E25b splicing variant is normally present in mouse retina and mimics the effect of c.2451insC mutation. Since this variant does not promote significant Cav1.4-mediated calcium current, it could possibly mediate a different function, unrelated to modulation of calcium channel properties at the photoreceptor terminals.


Asunto(s)
Canales de Calcio Tipo L/genética , Mutación , ARN/genética , Retina/metabolismo , Distrofias Retinianas/genética , Empalme Alternativo , Animales , Western Blotting , Canales de Calcio Tipo L/metabolismo , Modelos Animales de Enfermedad , Exones , Células HEK293 , Humanos , Ratones , Ratones Endogámicos C57BL , Ratones Mutantes , Técnicas de Placa-Clamp , Empalme del ARN , Retina/patología , Distrofias Retinianas/metabolismo , Distrofias Retinianas/patología , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa
15.
Nucleic Acids Res ; 43(W1): W589-98, 2015 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-25897122

RESUMEN

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.


Asunto(s)
Sistemas de Administración de Bases de Datos , Genómica , Humanos , Internet , Neoplasias/genética , Proteómica
16.
Front Cell Dev Biol ; 2: 39, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25364746

RESUMEN

The recent explosion of high-throughput sequencing methods applied to RNA molecules is allowing us to go beyond the description of sequence variants and their relative abundances, as measured by RNA-seq. We can now probe for RNA engagement in polysomes, for ribosomes, RNA binding proteins and microRNAs binding sites, for RNA secondary structure and for RNA methylation. These descriptors produce a steadily growing multidimensional array of positional information on RNA sequences, whose effective integration only would bring to decipher the regulatory interplay occurring between proteins, RNAs and their modifications on the transcriptome. This interplay ultimately dictates the degree of mRNA availability to translation, and thus the occurrence of cell phenotypes. However, several issues in data presentation are slowing down effective integration. A standardization effort for new dataset types produced should be urgently undertaken to solve these issues. Providing uniformed experimental details along with datasets processed to be directly usable and employing shared formats would greatly simplify integration efforts, strengthening hypotheses stemming from correlative observations and eventually bringing to mechanistic understanding.

17.
J Biotechnol ; 190: 30-9, 2014 Nov 20.
Artículo en Inglés | MEDLINE | ID: mdl-24670254

RESUMEN

Microbial communities populating several human body habitats are important determinants of human health. Cultivation-free community-wide approaches like bacterial 16S rRNA sequencing recently revolutionized the study of such human-associated microbial diversity, and the continuously decreasing cost/throughput ratio of current sequencing platforms is further enhancing the availability and effectiveness of microbiome research. The IonTorrent PGM platform is among the latest available commercial high-throughput sequencing tools, but it is just starting to be used for 16S rRNA surveys with only episodic assessments of its performance. We present here the first IonTorrent profiling of the human saliva microbiome collected from 12 healthy individuals. In this cohort, a subset of the volunteers was asked to assume a probiotic product, in order to investigate its impact on the composition and the structure of the saliva microbiome. Analysis of the generated dataset suggests the suitability of the IonTorrent platform for 16S rRNA surveys, even though some platform-specific choices are required to optimize the consistency of the obtained bacterial profiles. Interestingly, we found a marked and statistically significant increase of the overall bacterial diversity in the saliva of individuals who received the probiotic product compared to the control group, suggesting a short-term effect of probiotic product administration on oral microbiome composition.


Asunto(s)
ADN Bacteriano/química , Secuenciación de Nucleótidos de Alto Rendimiento , Microbiota/genética , Probióticos/administración & dosificación , ARN Ribosómico 16S/genética , Saliva/microbiología , Adulto , Bacterias/clasificación , Bacterias/genética , Femenino , Humanos , Masculino , Análisis de Secuencia de ADN/métodos
18.
Bioinformatics ; 30(2): 289-91, 2014 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-24222209

RESUMEN

UNLABELLED: High-throughput technologies have led to an explosion of genomic data available for automated analysis. The consequent possibility to simultaneously sample multiple layers of variation along the gene expression flow requires computational methods integrating raw information from different '-omics'. It has been recently demonstrated that translational control is a widespread phenomenon, with profound and still underestimated regulation capabilities. Although detecting changes in the levels of total messenger RNAs (mRNAs; the transcriptome), of polysomally loaded mRNAs (the translatome) and of proteins (the proteome) is experimentally feasible in a high-throughput way, the integration of these levels is still far from being robustly approached. Here we introduce tRanslatome, a new R/Bioconductor package, which is a complete platform for the simultaneous pairwise analysis of transcriptome, translatome and proteome data. The package includes most of the available statistical methods developed for the analysis of high-throughput data, allowing the parallel comparison of differentially expressed genes and the corresponding differentially enriched biological themes. Notably, it also enables the prediction of translational regulatory elements on mRNA sequences. The utility of this tool is demonstrated with two case studies. AVAILABILITY AND IMPLEMENTATION: tRanslatome is available in Bioconductor.


Asunto(s)
Biología Computacional , Biosíntesis de Proteínas , Proteoma/análisis , Secuencias Reguladoras de Ácidos Nucleicos/genética , Programas Informáticos , Transcriptoma , Diferenciación Celular , Bases de Datos Factuales , Genómica , Hepatocitos/citología , Hepatocitos/metabolismo , Humanos , ARN Mensajero/genética
19.
Translation (Austin) ; 2(1): e27738, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-26779400

RESUMEN

Post-transcriptional regulation (PTR) of gene expression is now recognized as a major determinant of cell phenotypes. The recent availability of methods to map protein-RNA interactions in entire transcriptomes such as RIP, CLIP and their variants, together with global polysomal and ribosome profiling techniques, are driving the exponential accumulation of vast amounts of data on mRNA contacts in cells, and of corresponding predictions of PTR events. However, this exceptional quantity of information cannot be exploited at its best to reconstruct potential PTR networks, as it still lies scattered throughout several databases and in isolated reports of single interactions. To address this issue, we developed the second and vastly enhanced version of the Atlas of UTR Regulatory Activity (AURA 2), a meta-database centered on mapping interaction of trans-factors with human and mouse UTRs. AURA 2 includes experimentally demonstrated binding sites for RBPs, ncRNAs, thousands of cis-elements, variations, RNA epigenetics data and more. Its user-friendly interface offers various data-mining features including co-regulation search, network generation and regulatory enrichment testing. Gene expression profiles for many tissues and cell lines can be also combined with these analyses to display only the interactions possible in the system under study. AURA 2 aims at becoming a valuable toolbox for PTR studies and at tracing the road for how PTR network-building tools should be designed. AURA 2 is available at http://aura.science.unitn.it.

20.
Mol Autism ; 4(1): 51, 2013 Dec 19.
Artículo en Inglés | MEDLINE | ID: mdl-24355397

RESUMEN

BACKGROUND: Transcriptome analysis has been used in autism spectrum disorder (ASD) to unravel common pathogenic pathways based on the assumption that distinct rare genetic variants or epigenetic modifications affect common biological pathways. To unravel recurrent ASD-related neuropathological mechanisms, we took advantage of the En2-/- mouse model and performed transcriptome profiling on cerebellar and hippocampal adult tissues. METHODS: Cerebellar and hippocampal tissue samples from three En2-/- and wild type (WT) littermate mice were assessed for differential gene expression using microarray hybridization followed by RankProd analysis. To identify functional categories overrepresented in the differentially expressed genes, we used integrated gene-network analysis, gene ontology enrichment and mouse phenotype ontology analysis. Furthermore, we performed direct enrichment analysis of ASD-associated genes from the SFARI repository in our differentially expressed genes. RESULTS: Given the limited number of animals used in the study, we used permissive criteria and identified 842 differentially expressed genes in En2-/- cerebellum and 862 in the En2-/- hippocampus. Our functional analysis revealed that the molecular signature of En2-/- cerebellum and hippocampus shares convergent pathological pathways with ASD, including abnormal synaptic transmission, altered developmental processes and increased immune response. Furthermore, when directly compared to the repository of the SFARI database, our differentially expressed genes in the hippocampus showed enrichment of ASD-associated genes significantly higher than previously reported. qPCR was performed for representative genes to confirm relative transcript levels compared to those detected in microarrays. CONCLUSIONS: Despite the limited number of animals used in the study, our bioinformatic analysis indicates the En2-/- mouse is a valuable tool for investigating molecular alterations related to ASD.

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