RESUMEN
Variations in DNA methylation patterns in human tissues have been linked to various environmental exposures and infections. Here, we identified the DNA methylation signatures associated with multiple exposures in nine major immune cell types derived from peripheral blood mononuclear cells (PBMCs) at single-cell resolution. We performed methylome sequencing on 111,180 immune cells obtained from 112 individuals who were exposed to different viruses, bacteria, or chemicals. Our analysis revealed 790,662 differentially methylated regions (DMRs) associated with these exposures, which are mostly individual CpG sites. Additionally, we integrated methylation and ATAC-seq data from same samples and found strong correlations between the two modalities. However, the epigenomic remodeling in these two modalities are complementary. Finally, we identified the minimum set of DMRs that can predict exposures. Overall, our study provides the first comprehensive dataset of single immune cell methylation profiles, along with unique methylation biomarkers for various biological and chemical exposures.
RESUMEN
Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited1,2. Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at 9 developmental stages from embryogenesis to adulthood. We identified 1,808,810 genomic regions that showed variations in CG methylation by comparing the methylomes of different tissues or organs from different developmental stages. These DNA elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. During late stages of fetal development, non-CG methylation accumulated within the bodies of key developmental transcription factor genes, coinciding with their transcriptional repression. Integration of genome-wide DNA methylation, histone modification and chromatin accessibility data enabled us to predict 461,141 putative developmental tissue-specific enhancers, the human orthologues of which were enriched for disease-associated genetic variants. These spatiotemporal epigenome maps provide a resource for studies of gene regulation during tissue or organ progression, and a starting point for investigating regulatory elements that are involved in human developmental disorders.
Asunto(s)
Metilación de ADN , Epigenoma , Feto/embriología , Feto/metabolismo , Animales , Animales Recién Nacidos , Cromatina/genética , Cromatina/metabolismo , Enfermedad/genética , Regulación hacia Abajo , Elementos de Facilitación Genéticos/genética , Represión Epigenética , Femenino , Silenciador del Gen , Humanos , Ratones , Ratones Endogámicos C57BL , Modelos Animales , Anotación de Secuencia Molecular , Polimorfismo de Nucleótido Simple , Análisis Espacio-TemporalRESUMEN
Oocyte defects lie at the heart of some forms of infertility and could potentially be addressed therapeutically by alternative routes for oocyte formation. Here, we describe the generation of functional human oocytes following nuclear transfer of first polar body (PB1) genomes from metaphase II (MII) oocytes into enucleated donor MII cytoplasm (PBNT). The reconstructed oocytes supported the formation of de novo meiotic spindles and, after fertilization with sperm, meiosis completion and formation of normal diploid zygotes. While PBNT zygotes developed to blastocysts less frequently (42%) than controls (75%), genome-wide genetic, epigenetic, and transcriptional analyses of PBNT and control ESCs indicated comparable numbers of structural variations and markedly similar DNA methylation and transcriptome profiles. We conclude that rescue of PB1 genetic material via introduction into donor cytoplasm may offer a source of oocytes for infertility treatment or mitochondrial replacement therapy for mtDNA disease.
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Genoma Humano , Técnicas de Transferencia Nuclear , Oocitos/metabolismo , Cuerpos Polares/metabolismo , Adulto , Blastocisto/metabolismo , Metilación de ADN/genética , Desarrollo Embrionario/genética , Epigénesis Genética , Femenino , Fertilización In Vitro , Perfilación de la Expresión Génica , Inestabilidad Genómica , Células Madre Embrionarias Humanas/metabolismo , Humanos , Masculino , Metafase , Ploidias , Análisis de Secuencia de ARN , Espermatozoides/metabolismo , Huso Acromático/metabolismo , Transcripción GenéticaRESUMEN
Understanding the diversity of human tissues is fundamental to disease and requires linking genetic information, which is identical in most of an individual's cells, with epigenetic mechanisms that could have tissue-specific roles. Surveys of DNA methylation in human tissues have established a complex landscape including both tissue-specific and invariant methylation patterns. Here we report high coverage methylomes that catalogue cytosine methylation in all contexts for the major human organ systems, integrated with matched transcriptomes and genomic sequence. By combining these diverse data types with each individuals' phased genome, we identified widespread tissue-specific differential CG methylation (mCG), partially methylated domains, allele-specific methylation and transcription, and the unexpected presence of non-CG methylation (mCH) in almost all human tissues. mCH correlated with tissue-specific functions, and using this mark, we made novel predictions of genes that escape X-chromosome inactivation in specific tissues. Overall, DNA methylation in several genomic contexts varies substantially among human tissues.
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Metilación de ADN , Epigénesis Genética , Factores de Edad , Alelos , Mapeo Cromosómico , Femenino , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Variación Genética , Humanos , Masculino , Especificidad de ÓrganosRESUMEN
Allelic differences between the two homologous chromosomes can affect the propensity of inheritance in humans; however, the extent of such differences in the human genome has yet to be fully explored. Here we delineate allelic chromatin modifications and transcriptomes among a broad set of human tissues, enabled by a chromosome-spanning haplotype reconstruction strategy. The resulting large collection of haplotype-resolved epigenomic maps reveals extensive allelic biases in both chromatin state and transcription, which show considerable variation across tissues and between individuals, and allow us to investigate cis-regulatory relationships between genes and their control sequences. Analyses of histone modification maps also uncover intriguing characteristics of cis-regulatory elements and tissue-restricted activities of repetitive elements. The rich data sets described here will enhance our understanding of the mechanisms by which cis-regulatory elements control gene expression programs.
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Alelos , Epigénesis Genética/genética , Epigenómica , Haplotipos/genética , Acetilación , Cromatina/genética , Cromatina/metabolismo , Cromosomas Humanos/genética , Conjuntos de Datos como Asunto , Elementos de Facilitación Genéticos/genética , Variación Genética/genética , Histonas/metabolismo , Humanos , Motivos de Nucleótidos , Especificidad de Órganos/genética , Transcripción Genética/genéticaRESUMEN
Human pluripotent stem cells hold potential for regenerative medicine, but available cell types have significant limitations. Although embryonic stem cells (ES cells) from in vitro fertilized embryos (IVF ES cells) represent the 'gold standard', they are allogeneic to patients. Autologous induced pluripotent stem cells (iPS cells) are prone to epigenetic and transcriptional aberrations. To determine whether such abnormalities are intrinsic to somatic cell reprogramming or secondary to the reprogramming method, genetically matched sets of human IVF ES cells, iPS cells and nuclear transfer ES cells (NT ES cells) derived by somatic cell nuclear transfer (SCNT) were subjected to genome-wide analyses. Both NT ES cells and iPS cells derived from the same somatic cells contained comparable numbers of de novo copy number variations. In contrast, DNA methylation and transcriptome profiles of NT ES cells corresponded closely to those of IVF ES cells, whereas iPS cells differed and retained residual DNA methylation patterns typical of parental somatic cells. Thus, human somatic cells can be faithfully reprogrammed to pluripotency by SCNT and are therefore ideal for cell replacement therapies.
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Reprogramación Celular , Células Madre Pluripotentes/metabolismo , Animales , Línea Celular , Aberraciones Cromosómicas , Cromosomas Humanos X/genética , Cromosomas Humanos X/metabolismo , Variaciones en el Número de Copia de ADN , Metilación de ADN , Estudio de Asociación del Genoma Completo , Impresión Genómica , Humanos , Técnicas de Transferencia Nuclear/normas , Células Madre Pluripotentes/citología , TranscriptomaRESUMEN
BACKGROUND: MicroRNAs (miRNAs) are non-uniformly distributed in genomes and ~30% of the miRNAs in the human genome are clustered. In this study we have focused on the imprinted miRNA cluster miR-379/miR-656 on 14q32.31 (hereafter C14) to test their coordinated function. We have analyzed expression profile of >1000 human miRNAs in >1400 samples representing seven different human tissue types obtained from cancer patients along with matched and unmatched controls. RESULTS: We found 68% of the miRNAs in this cluster to be significantly downregulated in glioblastoma multiforme (GBM), 61% downregulated in kidney renal clear cell carcinoma (KIRC), 46% in breast invasive carcinoma (BRCA) and 14% in ovarian serous cystadenocarcinoma (OV). On a genome-wide scale C14 miRNAs accounted for 12-30% of the total downregulated miRNAs in different cancers. Pathway enrichment for the predicted targets of C14 miRNA was significant for cancer pathways, especially Glioma (p< 3.77x10â»6, FDR<0.005). The observed downregulation was confirmed in GBM patients by real-time PCR, where 79% of C14 miRNAs (34/43) showed downregulation. In GBM samples, hypermethylation at C14 locus (p<0.003) and downregulation of MEF2, a crucial transcription factor for the cluster was observed which likely contribute to the observed downregulation of the entire miRNA cluster. CONCLUSION: We provide compelling evidence that the entire C14 miRNA cluster is a tumor suppressor locus involved in multiple cancers, especially in GBM, and points toward a general mechanism of coordinated function for clustered miRNAs.
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Regulación Neoplásica de la Expresión Génica/fisiología , MicroARNs/genética , Neoplasias/genética , Neoplasias de la Mama/genética , Femenino , Regulación Neoplásica de la Expresión Génica/genética , Glioma/genética , Humanos , Técnicas In Vitro , Masculino , Neoplasias Ováricas/genética , Reacción en Cadena en Tiempo Real de la PolimerasaRESUMEN
Advances in genome sequencing have progressed at a rapid pace, with increased throughput accompanied by plunging costs. But these advances go far beyond faster and cheaper. High-throughput sequencing technologies are now routinely being applied to a wide range of important topics in biology and medicine, often allowing researchers to address important biological questions that were not possible before. In this review, we discuss these innovative new approaches-including ever finer analyses of transcriptome dynamics, genome structure and genomic variation-and provide an overview of the new insights into complex biological systems catalyzed by these technologies. We also assess the impact of genotyping, genome sequencing and personal omics profiling on medical applications, including diagnosis and disease monitoring. Finally, we review recent developments in single-cell sequencing, and conclude with a discussion of possible future advances and obstacles for sequencing in biology and health.
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Investigación Biomédica/métodos , Genoma , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Epigenómica , Perfilación de la Expresión Génica , Variación Genética , Histonas/metabolismo , Humanos , Análisis de la Célula IndividualRESUMEN
As the sequencing of healthy and disease genomes becomes more commonplace, detailed annotation provides interpretation for individual variation responsible for normal and disease phenotypes. Current approaches focus on direct changes in protein coding genes, particularly nonsynonymous mutations that directly affect the gene product. However, most individual variation occurs outside of genes and, indeed, most markers generated from genome-wide association studies (GWAS) identify variants outside of coding segments. Identification of potential regulatory changes that perturb these sites will lead to a better localization of truly functional variants and interpretation of their effects. We have developed a novel approach and database, RegulomeDB, which guides interpretation of regulatory variants in the human genome. RegulomeDB includes high-throughput, experimental data sets from ENCODE and other sources, as well as computational predictions and manual annotations to identify putative regulatory potential and identify functional variants. These data sources are combined into a powerful tool that scores variants to help separate functional variants from a large pool and provides a small set of putative sites with testable hypotheses as to their function. We demonstrate the applicability of this tool to the annotation of noncoding variants from 69 full sequenced genomes as well as that of a personal genome, where thousands of functionally associated variants were identified. Moreover, we demonstrate a GWAS where the database is able to quickly identify the known associated functional variant and provide a hypothesis as to its function. Overall, we expect this approach and resource to be valuable for the annotation of human genome sequences.
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Bases de Datos Genéticas , Variación Genética , Genoma Humano , Anotación de Secuencia Molecular , Proteínas de Unión al ADN/genética , Estudio de Asociación del Genoma Completo , Genotipo , Humanos , Internet , Péptidos y Proteínas de Señalización Intracelular/genética , Lupus Eritematoso Sistémico/genética , Proteínas Nucleares/genética , Sistemas de Lectura Abierta , Polimorfismo de Nucleótido Simple , Secuencias Reguladoras de Ácidos Nucleicos , Proteína 3 Inducida por el Factor de Necrosis Tumoral alfaRESUMEN
Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes; the ensemble of these binding events forms a regulatory network, constituting the wiring diagram for a cell. To examine the principles of the human transcriptional regulatory network, we determined the genomic binding information of 119 transcription-related factors in over 450 distinct experiments. We found the combinatorial, co-association of transcription factors to be highly context specific: distinct combinations of factors bind at specific genomic locations. In particular, there are significant differences in the binding proximal and distal to genes. We organized all the transcription factor binding into a hierarchy and integrated it with other genomic information (for example, microRNA regulation), forming a dense meta-network. Factors at different levels have different properties; for instance, top-level transcription factors more strongly influence expression and middle-level ones co-regulate targets to mitigate information-flow bottlenecks. Moreover, these co-regulations give rise to many enriched network motifs (for example, noise-buffering feed-forward loops). Finally, more connected network components are under stronger selection and exhibit a greater degree of allele-specific activity (that is, differential binding to the two parental alleles). The regulatory information obtained in this study will be crucial for interpreting personal genome sequences and understanding basic principles of human biology and disease.
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ADN/genética , Enciclopedias como Asunto , Redes Reguladoras de Genes/genética , Genoma Humano/genética , Anotación de Secuencia Molecular , Secuencias Reguladoras de Ácidos Nucleicos/genética , Factores de Transcripción/metabolismo , Alelos , Línea Celular , Factor de Transcripción GATA1/metabolismo , Perfilación de la Expresión Génica , Genómica , Humanos , Células K562 , Especificidad de Órganos , Fosforilación/genética , Polimorfismo de Nucleótido Simple/genética , Mapas de Interacción de Proteínas , ARN no Traducido/genética , ARN no Traducido/metabolismo , Selección Genética/genética , Sitio de Iniciación de la TranscripciónRESUMEN
To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome.
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Bases de Datos de Ácidos Nucleicos , Genómica , Ratones/genética , Anotación de Secuencia Molecular , Animales , Genoma , Genoma Humano , Humanos , InternetRESUMEN
The importance of microRNA (miRNA) in modulating gene expression at the post-transcriptional level is well known. Such regulation has been shown to influence the dynamics of several regulatory networks including the cell cycle. In this study we incorporated regulatory effects of intronic miRNA into an existing mathematical model of the cell cycle through the use of an existing 'proxy' protein--the host protein. It was observed that the incorporation of intronic miRNA mediated regulation improved the performance of the model resulting in a closer match to experimental results. To test the universality of this approach we compared the effects of intronic miRNA mediated regulation and host protein mediated regulation. Further, we compared miRNA mediated and protein mediated positive and negative feedback regulations of the target protein. We found that the target protein profiles were predominantly similar. These observations show the applicability of our method for incorporating intronic miRNA mediated dynamic effects in models for regulation of gene expression.
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Biología Computacional/métodos , Intrones/genética , MicroARNs/genética , Ciclo Celular/genética , Perfilación de la Expresión Génica , Redes Reguladoras de Genes/genética , Humanos , Proteínas/genética , Proteínas/metabolismoRESUMEN
Personalized medicine is expected to benefit from combining genomic information with regular monitoring of physiological states by multiple high-throughput methods. Here, we present an integrative personal omics profile (iPOP), an analysis that combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. Our iPOP analysis revealed various medical risks, including type 2 diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. Extremely high-coverage genomic and transcriptomic data, which provide the basis of our iPOP, revealed extensive heteroallelic changes during healthy and diseased states and an unexpected RNA editing mechanism. This study demonstrates that longitudinal iPOP can be used to interpret healthy and diseased states by connecting genomic information with additional dynamic omics activity.
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Genoma Humano , Genómica , Medicina de Precisión , Diabetes Mellitus Tipo 2/genética , Femenino , Perfilación de la Expresión Génica , Humanos , Masculino , Metabolómica , Persona de Mediana Edad , Mutación , Proteómica , Virus Sincitiales Respiratorios/aislamiento & purificación , Rhinovirus/aislamiento & purificaciónRESUMEN
A critical problem in biology is understanding how cells choose between self-renewal and differentiation. To generate a comprehensive view of the mechanisms controlling early hematopoietic precursor self-renewal and differentiation, we used systems-based approaches and murine EML multipotential hematopoietic precursor cells as a primary model. EML cells give rise to a mixture of self-renewing Lin-SCA+CD34+ cells and partially differentiated non-renewing Lin-SCA-CD34- cells in a cell autonomous fashion. We identified and validated the HMG box protein TCF7 as a regulator in this self-renewal/differentiation switch that operates in the absence of autocrine Wnt signaling. We found that Tcf7 is the most down-regulated transcription factor when CD34+ cells switch into CD34- cells, using RNA-Seq. We subsequently identified the target genes bound by TCF7, using ChIP-Seq. We show that TCF7 and RUNX1 (AML1) bind to each other's promoter regions and that TCF7 is necessary for the production of the short isoforms, but not the long isoforms of RUNX1, suggesting that TCF7 and the short isoforms of RUNX1 function coordinately in regulation. Tcf7 knock-down experiments and Gene Set Enrichment Analyses suggest that TCF7 plays a dual role in promoting the expression of genes characteristic of self-renewing CD34+ cells while repressing genes activated in partially differentiated CD34- state. Finally a network of up-regulated transcription factors of CD34+ cells was constructed. Factors that control hematopoietic stem cell (HSC) establishment and development, cell growth, and multipotency were identified. These studies in EML cells demonstrate fundamental cell-intrinsic properties of the switch between self-renewal and differentiation, and yield valuable insights for manipulating HSCs and other differentiating systems.
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Diferenciación Celular , Proliferación Celular , Subunidad alfa 2 del Factor de Unión al Sitio Principal , Células Madre Hematopoyéticas/metabolismo , Factor 1 de Transcripción de Linfocitos T/genética , Factor 1 de Transcripción de Linfocitos T/metabolismo , Animales , Antígenos CD34/metabolismo , Línea Celular , Subunidad alfa 2 del Factor de Unión al Sitio Principal/genética , Subunidad alfa 2 del Factor de Unión al Sitio Principal/metabolismo , Regulación del Desarrollo de la Expresión Génica , Técnicas de Silenciamiento del Gen , Células Madre Hematopoyéticas/citología , Factor Nuclear 1-alfa del Hepatocito , Humanos , Ratones , Regiones Promotoras Genéticas , Unión Proteica , ARN Interferente Pequeño , Análisis de Secuencia de ARN , Factor 1 de Transcripción de Linfocitos T/antagonistas & inhibidores , Factores de Transcripción/clasificación , Factores de Transcripción/metabolismoRESUMEN
Cholesterol is highly enriched in the brain, and plays a key role in synapse formation and function. The brain does not derive cholesterol from the circulation; instead, the majority of cholesterol is made in glia and secreted in form of lipoproteins. Neurons can synthesize cholesterol, but the extent of neuronal cholesterol biosynthesis in the adult brain is unknown. Cholesterol biosynthesis inhibitors of the statin family are widely used to lower circulating cholesterol and cardiovascular risk. Lipophilic statins can cross the blood brain barrier and inhibit brain cholesterol biosynthesis with possible consequences for synaptic cholesterol homeostasis. We have investigated the effects of lovastatin on synapse maturation and synaptic vesicle release. Treatment of primary hippocampal neurons with low levels of lovastatin for one week reduced synapse density and impaired synaptic vesicle release. Neither lipoproteins nor geranylgeraniol fully counteracted the lovastatin-induced decrease of synaptic vesicle exocytosis, even when cholesterol depletion was prevented. In contrast, restoration of neuronal cholesterol synthesis with mevalonate prevented defects in vesicle exocytosis without fully normalizing neuronal cholesterol content. These results raise the possibility that chronic exposure of neurons to lipophilic statins may affect synaptic transmission, and indicate that hippocampal neurons need a certain level of endogenous cholesterol biosynthesis.
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Anticolesterolemiantes/toxicidad , Colesterol/metabolismo , Diterpenos/farmacología , Lipoproteínas/fisiología , Lovastatina/toxicidad , Neuronas/metabolismo , Transmisión Sináptica/fisiología , Vesículas Sinápticas/metabolismo , Animales , Animales Recién Nacidos , Astrocitos/citología , Astrocitos/efectos de los fármacos , Astrocitos/metabolismo , Línea Celular , Colesterol/biosíntesis , Ratones , Inhibición Neural/fisiología , Neuronas/citología , Neuronas/efectos de los fármacos , Terminales Presinápticos/efectos de los fármacos , Terminales Presinápticos/fisiología , Cultivo Primario de Células , Ratas , Ratas Sprague-Dawley , Transmisión Sináptica/efectos de los fármacos , Vesículas Sinápticas/efectos de los fármacosRESUMEN
Differences in gene expression may play a major role in speciation and phenotypic diversity. We examined genome-wide differences in transcription factor (TF) binding in several humans and a single chimpanzee by using chromatin immunoprecipitation followed by sequencing. The binding sites of RNA polymerase II (PolII) and a key regulator of immune responses, nuclear factor kappaB (p65), were mapped in 10 lymphoblastoid cell lines, and 25 and 7.5% of the respective binding regions were found to differ between individuals. Binding differences were frequently associated with single-nucleotide polymorphisms and genomic structural variants, and these differences were often correlated with differences in gene expression, suggesting functional consequences of binding variation. Furthermore, comparing PolII binding between humans and chimpanzee suggests extensive divergence in TF binding. Our results indicate that many differences in individuals and species occur at the level of TF binding, and they provide insight into the genetic events responsible for these differences.
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Regulación de la Expresión Génica , Polimorfismo de Nucleótido Simple , ARN Polimerasa II/metabolismo , Factor de Transcripción ReIA/metabolismo , Animales , Sitios de Unión , Línea Celular , Inmunoprecipitación de Cromatina , Variaciones en el Número de Copia de ADN , ADN Intergénico , Femenino , Humanos , Masculino , Pan troglodytes/genética , Unión Proteica , ARN Polimerasa II/genética , Análisis de Secuencia de ADN , Especificidad de la Especie , Factor de Transcripción ReIA/genética , Sitio de Iniciación de la TranscripciónRESUMEN
Eukaryotic gene expression is controlled at the post-transcriptional level by small noncoding RNAs called microRNAs (miRNA). miRNAs play important roles during early development and participate in gene regulatory circuits in the cell. Different high-throughput expression analysis methods including microarrays, bead-based detection, and small RNA cloning have been applied to quantitatively detect miRNAs in various tissues, cell types, and biological conditions. High-throughput expression data was collected from public repositories and processed to create a database of miRNA expression profiles. Several commonly used normalization methods were compared to identify suitable methods for cross-platform comparison of high-throughput miRNA expression data. The database provides interlaboratory and interplatform validated reference expression levels for miRNAs. The normalized expression profiles were validated by querying for well-established features of miRNA expression. Firstly, expression profiles of several tissue-specific miRNAs showed good agreement between the database and previously reported profiles. We have also identified a set of miRNAs that are constitutively expressed across mammalian tissues. Secondly, we used the database to compare the expression patterns of miRNAs belonging to the let-7 family, where the divergence in expression patterns implies that they may have diversified functionally. Lastly, we compared expression profiles of intronic and clustered miRNAs. Expression profiles of intronic miRNAs and clustered miRNAs showed either very good, or in certain cases, very poor correlation with the host gene. Interplatform comparison of miRNA expression profiles thus provides a resource of consensus expression profiles that can be used in the future for studying miRNA function and regulation.
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Secuencia de Consenso/genética , Interpretación Estadística de Datos , Perfilación de la Expresión Génica/normas , MicroARNs/genética , Análisis de Secuencia por Matrices de Oligonucleótidos/normas , Algoritmos , Animales , Perfilación de la Expresión Génica/instrumentación , Perfilación de la Expresión Génica/métodos , Humanos , Metaanálisis como Asunto , MicroARNs/análisis , MicroARNs/metabolismo , Neoplasias/genética , Análisis de Secuencia por Matrices de Oligonucleótidos/instrumentación , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Especificidad de Órganos/genética , Valores de ReferenciaRESUMEN
Incomplete penetrance and variable expressivity are non-Mendelian phenomena resulting in the lack of correlation between genotype and phenotype. Not withstanding the diversity in mechanisms, differential expression of homologous alleles within cells manifests as variations in penetrance and expressivity of mutations between individuals of the same genotype. These phenomena are seen most often in dominantly inherited diseases, implying that they are sensitive to concentration of the gene product. In this framework and the advances in understanding the role of microRNA (miRNA) in fine-tuning gene expression at translational level, we propose miRNA-mediated regulation as a mechanism for incomplete penetrance and variable expressivity. The presence of miRNA binding sites at 3' UTR, co-expression of target gene-miRNA pairs for genes showing incomplete penetrance and variable expressivity derived from available data lend support to our hypothesis. Single nucleotide polymorphisms in the miRNA target site facilitate the implied differential targeting of the transcripts from homologous alleles.
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Expresión Génica , MicroARNs/genética , Penetrancia , Alelos , Animales , Humanos , Polimorfismo GenéticoRESUMEN
miRNAs have emerged as important players in the regulation of gene expression and their deregulation is a common feature in a variety of diseases, especially cancer. Currently, many efforts are focused on studying miRNA expression patterns, as well as miRNA target validation. Here, we show that the over expression of miR-23a approximately 27a approximately 24-2 cluster in HEK293T cells induces apoptosis by caspase-dependent as well as caspase-independent pathway as proved by the annexin assay, caspase activation, release of cytochrome-c and AIF (apoptosis inducing factor) from mitochondria. Furthermore, the over expressed cluster modulates the expression of a number of genes involved in apoptosis including FADD (Fas Associated protein with Death Domain). Bioinformatically, FADD is predicted to be the target of hsa-miR-27a and interestingly, FADD protein was found to be up regulated consistent with very less expression of hsa-miR-27a in HEK293T cells. This effect was direct, as hsa-miR-27a negatively regulated the expression of FADD 3'UTR based reporter construct. Moreover, we also showed that over expression of miR-23a approximately 27a approximately 24-2 sensitized HEK293T cells to TNF-alpha cytotoxicity. Taken together, our study demonstrates that enhanced TNF-alpha induced apoptosis in HEK293T cells by over expression of miR-23a approximately 27a approximately 24-2 cluster provides new insights in the development of novel therapeutics for cancer.