RESUMEN

Among vertebrates that can be kept in captivity, the annual fish Nothobranchius furzeri possesses the shortest known lifespan. It also shows typical signs of aging and is therefore an ideal model to assess the role of different physiological and environmental parameters on aging and lifespan determination. Here, we used Nothobranchius furzeri to study whether aging is associated with mitochondrial DNA (mtDNA) alterations and changes in mitochondrial function. We sequenced the complete mitochondrial genome of N. furzeri and found an extended control region. Large-scale mtDNA deletions have been frequently described to accumulate in other organisms with age, but there was no evidence for the presence of detectable age-related mtDNA deletions in N. furzeri. However, mtDNA copy number significantly decreased with age in skeletal muscle, brain, liver, skin and dorsal fin. Consistent with this finding, expression of Pgc-1α that encodes a transcriptional coactivator of mitochondrial biogenesis and expression of Tfam and mtSsbp both encoding mtDNA binding factors was downregulated with age. The investigation of possible changes in mitochondrial function revealed that the content of respiratory chain complexes III and IV was reduced in skeletal muscle with age. In addition, ADP-stimulated and succinate-dependent respiration was decreased in mitochondria of old fish. These findings suggest that despite the short lifespan, aging in N. furzeri is associated with a decline in mtDNA copy number, the downregulation of mtDNA-associated genes and an impairment of mitochondrial function.

Asunto(s)

Ciprinodontiformes/genética , Variaciones en el Número de Copia de ADN , ADN Mitocondrial/análisis , Mitocondrias/genética , Envejecimiento/genética , Envejecimiento/metabolismo , Envejecimiento/fisiología , Animales , Respiración de la Célula , Ciprinodontiformes/metabolismo , Ciprinodontiformes/fisiología , ADN Mitocondrial/genética , Electroforesis en Gel Bidimensional , Regulación del Desarrollo de la Expresión Génica , Genoma Mitocondrial , Longevidad , Mitocondrias/metabolismo , Mitocondrias/fisiología , Proteínas Mitocondriales/genética , Proteínas Mitocondriales/metabolismo , Modelos Teóricos , Músculo Esquelético/citología , Músculo Esquelético/metabolismo , Músculo Esquelético/fisiología , Factores de Transcripción/genética , Factores de Transcripción/metabolismo

RESUMEN

BACKGROUND: Melanin-concentrating hormone receptor 1 (MCHR1) plays a significant role in regulation of energy balance, food intake, physical activity and body weight in humans and rodents. Several association studies for human obesity showed contrary results concerning the SNPs rs133072 (G/A) and rs133073 (T/C), which localize to the first exon of MCHR1. The variations constitute two main haplotypes (GT, AC). Both SNPs affect CpG dinucleotides, whereby each haplotype contains a potential methylation site at one of the two SNP positions. In addition, 15 CpGs in close vicinity of these SNPs constitute a weak CpG island. Here, we studied whether DNA methylation in this sequence context may contribute to population- and age-specific effects of MCHR1 alleles in obesity. PRINCIPAL FINDINGS: We analyzed DNA methylation of a 315 bp region of MCHR1 encompassing rs133072 and rs133073 and the CpG island in blood samples of 49 individuals by bisulfite sequencing. The AC haplotype shows a significantly higher methylation level than the GT haplotype. This allele-specific methylation is age-dependent. In young individuals (20-30 years) the difference in DNA methylation between haplotypes is significant; whereas in individuals older than 60 years it is not detectable. Interestingly, the GT allele shows a decrease in methylation status with increasing BMI, whereas the methylation of the AC allele is not associated with this phenotype. Heterozygous lymphoblastoid cell lines show the same pattern of allele-specific DNA methylation. The cell line, which exhibits the highest difference in methylation levels between both haplotypes, also shows allele-specific transcription of MCHR1, which can be abolished by treatment with the DNA methylase inhibitor 5-aza-2'-deoxycytidine. CONCLUSIONS: We show that DNA methylation at MCHR1 is allele-specific, age-dependent, BMI-associated and affects transcription. Conceivably, this epigenetic regulation contributes to the age- and/or population specific effects reported for MCHR1 in several human obesity studies.

Asunto(s)

Envejecimiento/genética , Alelos , Índice de Masa Corporal , Metilación de ADN/genética , Receptores de Somatostatina/genética , Adulto , Anciano , Envejecimiento/efectos de los fármacos , Azacitidina/farmacología , Línea Celular , Islas de CpG/genética , Metilación de ADN/efectos de los fármacos , Regulación de la Expresión Génica/efectos de los fármacos , Genoma Humano/genética , Humanos , Masculino , Persona de Mediana Edad , ARN Mensajero/genética , ARN Mensajero/metabolismo , Receptores de Somatostatina/metabolismo , Adulto Joven

RESUMEN

BACKGROUND: Subtle alternative splicing events involving tandem splice sites separated by a short (2-12 nucleotides) distance are frequent and evolutionarily widespread in eukaryotes, and a major contributor to the complexity of transcriptomes and proteomes. However, these events have been either omitted altogether in databases on alternative splicing, or only the cases of experimentally confirmed alternative splicing have been reported. Thus, a database which covers all confirmed cases of subtle alternative splicing as well as the numerous putative tandem splice sites (which might be confirmed once more transcript data becomes available), and allows to search for tandem splice sites with specific features and download the results, is a valuable resource for targeted experimental studies and large-scale bioinformatics analyses of tandem splice sites. Towards this goal we recently set up TassDB (Tandem Splice Site DataBase, version 1), which stores data about alternative splicing events at tandem splice sites separated by 3 nt in eight species. DESCRIPTION: We have substantially revised and extended TassDB. The currently available version 2 contains extensive information about tandem splice sites separated by 2-12 nt for the human and mouse transcriptomes including data on the conservation of the tandem motifs in five vertebrates. TassDB2 offers a user-friendly interface to search for specific genes or for genes containing tandem splice sites with specific features as well as the possibility to download result datasets. For example, users can search for cases of alternative splicing where the proportion of EST/mRNA evidence supporting the minor isoform exceeds a specific threshold, or where the difference in splice site scores is specified by the user. The predicted impact of each event on the protein is also reported, along with information about being a putative target for the nonsense-mediated decay (NMD) pathway. Links are provided to the UCSC genome browser and other external resources. CONCLUSION: TassDB2, available via http://www.tassdb.info, provides comprehensive resources for researchers interested in both targeted experimental studies and large-scale bioinformatics analyses of short distance tandem splice sites.

Asunto(s)

Empalme Alternativo , Genómica/métodos , Programas Informáticos , Animales , Bases de Datos Factuales , Genoma , Humanos , Internet , Sitios de Empalme de ARN , Empalme del ARN

RESUMEN

BACKGROUND: Due to the rapid data accumulation on pathogenesis and progression of chronic inflammation, there is an increasing demand for approaches to analyse the underlying regulatory networks. For example, rheumatoid arthritis (RA) is a chronic inflammatory disease, characterised by joint destruction and perpetuated by activated synovial fibroblasts (SFB). These abnormally express and/or secrete pro-inflammatory cytokines, collagens causing joint fibrosis, or tissue-degrading enzymes resulting in destruction of the extra-cellular matrix (ECM).We applied three methods to analyse ECM regulation: data discretisation to filter out noise and to reduce complexity, Boolean network construction to implement logic relationships, and formal concept analysis (FCA) for the formation of minimal, but complete rule sets from the data. RESULTS: First, we extracted literature information to develop an interaction network containing 18 genes representing ECM formation and destruction. Subsequently, we constructed an asynchronous Boolean network with biologically plausible time intervals for mRNA and protein production, secretion, and inactivation. Experimental gene expression data was obtained from SFB stimulated by TGFbeta1 or by TNFalpha and discretised thereafter. The Boolean functions of the initial network were improved iteratively by the comparison of the simulation runs to the experimental data and by exploitation of expert knowledge. This resulted in adapted networks for both cytokine stimulation conditions. The simulations were further analysed by the attribute exploration algorithm of FCA, integrating the observed time series in a fine-tuned and automated manner. The resulting temporal rules yielded new contributions to controversially discussed aspects of fibroblast biology (e.g., considerable expression of TNF and MMP9 by fibroblasts stimulation) and corroborated previously known facts (e.g., co-expression of collagens and MMPs after TNFalpha stimulation), but also revealed some discrepancies to literature knowledge (e.g., MMP1 expression in the absence of FOS). CONCLUSION: The newly developed method successfully and iteratively integrated expert knowledge at different steps, resulting in a promising solution for the in-depth understanding of regulatory pathways in disease dynamics. The knowledge base containing all the temporal rules may be queried to predict the functional consequences of observed or hypothetical gene expression disturbances. Furthermore, new hypotheses about gene relations were derived which await further experimental validation.

Asunto(s)

Matriz Extracelular/genética , Expresión Génica , Femenino , Humanos , Masculino , Persona de Mediana Edad , Modelos Biológicos , Transducción de Señal/efectos de los fármacos , Membrana Sinovial/efectos de los fármacos , Membrana Sinovial/metabolismo , Biología de Sistemas , Factor de Crecimiento Transformador alfa/farmacología , Factor de Crecimiento Transformador beta1/farmacología

RESUMEN

BACKGROUND: The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal laboratory conditions, show explosive growth, early sexual maturation and age-dependent physiological and behavioral decline, and express aging related biomarkers. Treatment with resveratrol and low temperature significantly extends the maximum life span. These features make N. furzeri a promising new vertebrate model for age research. RESULTS: To contribute to establishing N. furzeri as a new model organism, we provide a first insight into its genome and a comparison to medaka, stickleback, tetraodon and zebrafish. The N. furzeri genome contains 19 chromosomes (2n = 38). Its genome of between 1.6 and 1.9 Gb is the largest among the analyzed fish species and has, at 45%, the highest repeat content. Remarkably, tandem repeats comprise 21%, which is 4-12 times more than in the other four fish species. In addition, G+C-rich tandem repeats preferentially localize to centromeric regions. Phylogenetic analysis based on coding sequences identifies medaka as the closest relative. Genotyping of an initial set of 27 markers and multi-locus fingerprinting of one microsatellite provides the first molecular evidence that the GRZ strain is highly inbred. CONCLUSIONS: Our work presents a first basis for systematic genomic and genetic analyses aimed at understanding the mechanisms of life span determination in N. furzeri.

Asunto(s)

Envejecimiento/genética , Genoma/genética , Longevidad/genética , Secuencias Repetidas en Tándem , Animales , Antioxidantes/farmacología , Frío , Peces , Marcadores Genéticos , Modelos Animales , Filogenia , Resveratrol , Estilbenos/farmacología

RESUMEN

BACKGROUND: Alternative splicing is a major contributor to the diversity of eukaryotic transcriptomes and proteomes. Currently, large scale detection of alternative splicing using expressed sequence tags (ESTs) or microarrays does not capture all alternative splicing events. Moreover, for many species genomic data is being produced at a far greater rate than corresponding transcript data, hence in silico methods of predicting alternative splicing have to be improved. RESULTS: Here, we show that the use of Bayesian networks (BNs) allows accurate prediction of evolutionary conserved exon skipping events. At a stringent false positive rate of 0.5%, our BN achieves an improved true positive rate of 61%, compared to a previously reported 50% on the same dataset using support vector machines (SVMs). Incorporating several novel discriminative features such as intronic splicing regulatory elements leads to the improvement. Features related to mRNA secondary structure increase the prediction performance, corroborating previous findings that secondary structures are important for exon recognition. Random labelling tests rule out overfitting. Cross-validation on another dataset confirms the increased performance. When using the same dataset and the same set of features, the BN matches the performance of an SVM in earlier literature. Remarkably, we could show that about half of the exons which are labelled constitutive but receive a high probability of being alternative by the BN, are in fact alternative exons according to the latest EST data. Finally, we predict exon skipping without using conservation-based features, and achieve a true positive rate of 29% at a false positive rate of 0.5%. CONCLUSION: BNs can be used to achieve accurate identification of alternative exons and provide clues about possible dependencies between relevant features. The near-identical performance of the BN and SVM when using the same features shows that good classification depends more on features than on the choice of classifier. Conservation based features continue to be the most informative, and hence distinguishing alternative exons from constitutive ones without using conservation based features remains a challenging problem.

Asunto(s)

Algoritmos , Empalme Alternativo/genética , Biología Computacional/métodos , Exones/genética , Inteligencia Artificial , Teorema de Bayes , Conformación de Ácido Nucleico , ARN Mensajero/química

RESUMEN

INTRODUCTION: Rheumatoid arthritis (RA) is a chronic inflammatory and destructive joint disease characterized by overexpression of pro-inflammatory/pro-destructive genes and other activating genes (for example, proto-oncogenes) in the synovial membrane (SM). The gene expression in disease is often characterized by significant inter-individual variances via specific synchronization/desynchronization of gene expression. To elucidate the contribution of the variance to the pathogenesis of disease, expression variances were tested in SM samples of RA patients, osteoarthritis (OA) patients, and normal controls (NCs). METHOD: Analysis of gene expression in RA, OA, and NC samples was carried out using Affymetrix U133A/B oligonucleotide arrays, and the results were validated by real-time reverse transcription-polymerase chain reaction. For the comparison between RA and NC, 568 genes with significantly different variances in the two groups (P

Asunto(s)

Artritis Reumatoide/genética , Artritis Reumatoide/metabolismo , Perfilación de la Expresión Génica , Variación Genética/genética , ARN Mensajero/metabolismo , Transducción de Señal/genética , Membrana Sinovial/metabolismo , Adulto , Anciano , Proteínas Reguladoras de la Apoptosis/genética , Proteínas Reguladoras de la Apoptosis/metabolismo , Artritis Reumatoide/etiología , Estudios de Casos y Controles , Supervivencia Celular/genética , Femenino , Humanos , Inflamación/genética , Masculino , Persona de Mediana Edad , Neovascularización Patológica/genética , Osteoartritis/etiología , Osteoartritis/genética , Osteoartritis/metabolismo , ARN Mensajero/genética , Receptores de Citocinas/genética , Receptores de Citocinas/metabolismo , Factor de Crecimiento Transformador beta/genética , Factor de Crecimiento Transformador beta/metabolismo , Factor A de Crecimiento Endotelial Vascular/genética , Factor A de Crecimiento Endotelial Vascular/metabolismo

RESUMEN

GenColors (gencolors.fli-leibniz.de) is a new web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes considering information on related genomes and making extensive use of genome comparison. It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained from GenBank. A variety of export/import filters manages an effective data flow from sequence assembly and manipulation programs (e.g., GAP4) to GenColors and back as well as to standard GenBank file(s). The genome comparison tools include best bidirectional hits, gene conservation, syntenies, and gene core sets. Precomputed UniProt matches allow annotation and analysis in an effective manner. In addition to these analysis options, base-specific quality data (coverage and confidence) can also be handled if available. The GenColors system can be used both for annotation purposes in ongoing genome projects and as an analysis tool for finished genomes. GenColors comes in two types, as dedicated genome browsers and as the Jena Prokaryotic Genome Viewer (JPGV). Dedicated genome browsers contain genomic information on a set of related genomes and offer a large number of options for genome comparison. The system has been efficiently used in the genomic sequencing of Borrelia garinii and is currently applied to various ongoing genome projects on Borrelia, Legionella, Escherichia, and Pseudomonas genomes. One of these dedicated browsers, the Spirochetes Genome Browser (sgb.fli-leibniz.de) with Borrelia, Leptospira, and Treponema genomes, is freely accessible. The others will be released after finalization of the corresponding genome projects. JPGV (jpgv.fli-leibniz.de) offers information on almost all finished bacterial genomes, as compared to the dedicated browsers with reduced genome comparison functionality, however. As of January 2006, this viewer includes 632 genomic elements (e.g., chromosomes and plasmids) of 293 species. The system provides versatile quick and advanced search options for all currently known prokaryotic genomes and generates circular and linear genome plots. Gene information sheets contain basic gene information, database search options, and links to external databases. GenColors is also available on request for local installation.

Asunto(s)

Bases de Datos Genéticas , Genómica , Internet

RESUMEN

Careful manual annotation of the human reference sequence provides a solid basis for the identification of disease-associated genes. Toward this end, we focused on a medically relevant 2.6-Mb region of the human chromosome Xp11.4 between markers DXS9851 and DXS9751 and identified 16 transcription units according to the Vertebrate Genome Annotation (Vega) rules. In order to validate these annotations, we performed a comprehensive RT-PCR expression analysis and a human-mouse comparison. This revealed, despite the high overall genomic conservation of the region, remarkable differences of the gene content between human and mouse. Whereas 12 of 16 annotations were confirmed by RT-PCR in human tissues, for only seven genes mouse orthologs could be identified and found to be expressed. This indicates that a comprehensive and experimentally supported annotation effort of the human genome simultaneously highlights regions with striking differences in gene organization to other species and may indicate evolutionary events specific to the human lineage demanding further functional analyses.

Asunto(s)

Cromosomas Humanos X , Animales , Mapeo Cromosómico , Secuencia Conservada , Bases de Datos como Asunto , Etiquetas de Secuencia Expresada , Predicción , Perfilación de la Expresión Génica , Humanos , Ratones , ARN Mensajero , Reproducibilidad de los Resultados , Alineación de Secuencia , Especificidad de la Especie

RESUMEN

The molecular mechanisms underlying the regulation of interleukin (IL)-10 transcription in monocytic cells by various stimuli during inflammation and the stress reaction are not fully understood. Recently, we provided evidence that stress-induced IL-10 promoter activation in monocytic cells is mediated by catecholamines via a cAMP-dependent signaling pathway including CREB/ATF (cAMP-responsive element binding protein/activating transcription factor) binding to two CRE motifs. However, the mutation of these sites diminished cAMP responsiveness by only 50%, suggesting a role for additional transcription factors and elements in the cAMP-dependent regulation of the human IL-10 promoter. Here, we analyze the functional role of one such factor, C/EBP, in two cell lines of myelomonocytic origin, THP-1 and HL-60, which are known to differ in their differentiation status and C/EBP protein content. We show that the level of basal as well as cAMP-stimulated IL-10 transcription depends on the expression of C/EBP alpha and beta and their binding to three motifs in the promoter/enhancer region. The C/EBP5 motif, which is located between the TATA-box and the translation start point, is essential for the C/EBP-mediated constitutive and most of the cAMP-stimulated expression as its mutation nearly abolished IL-10 promoter activity. Our results suggest a dominant role of C/EBP transcription factors relative to CREB/ATF in tissue-specific and differentiation-dependent IL-10 transcription.

Asunto(s)

Bucladesina/farmacología , Proteínas Potenciadoras de Unión a CCAAT/genética , Proteínas Potenciadoras de Unión a CCAAT/metabolismo , AMP Cíclico/fisiología , Regulación de la Expresión Génica/inmunología , Interleucina-10/genética , Monocitos/citología , Regiones Promotoras Genéticas , Transcripción Genética/inmunología , Animales , Secuencia de Bases , Diferenciación Celular , Codón Iniciador , Regulación de la Expresión Génica/efectos de los fármacos , Células HL-60 , Humanos , Ratones , Datos de Secuencia Molecular , Monocitos/inmunología , Muridae , Oligodesoxirribonucleótidos , Biosíntesis de Proteínas , Proteínas Recombinantes/inmunología , TATA Box , Transfección