RESUMEN
In human, nearly half of the known microRNAs (miRNAs) are encoded within the introns of protein-coding genes. The embedment of these miRNA genes within the sequences of protein-coding genes alludes to a possible functional relationship between intronic miRNAs and their hosting genes. Several studies, using predicted targets, suggested that intronic miRNAs influence their hosts' function either antagonistically or synergistically. New experimental data of miRNA expression patterns and targets enable exploring this putative association by relying on actual data rather than on predictions. Here, our analysis based on currently available experimental data implies that the potential functional association between intronic miRNAs and their hosting genes is limited. For host-miRNA examples where functional associations were detected, it was manifested by either autoregulation, common targets of the miRNA and hosting gene, or through the targeting of transcripts participating in pathways in which the host gene is involved. This low prevalence of functional association is consistent with our observation that many intronic miRNAs have independent transcription start sites and are not coexpressed with the hosting gene. Yet, the intronic miRNAs that do show functional association with their hosts were found to be more evolutionarily conserved compared to other intronic miRNAs. This might suggest a selective pressure to maintain this architecture when it has a functional consequence.
Asunto(s)
Intrones/genética , MicroARNs/genética , Proteínas/genética , Línea Celular Tumoral , Células HEK293 , Humanos , Procesamiento Postranscripcional del ARN/genéticaRESUMEN
The majority of mammalian genes contain one or more alternative polyadenylation sites. Choice of polyadenylation sites was suggested as one of the underlying mechanisms for generating longer/shorter transcript isoforms. Here, we demonstrate that mature mRNA transcripts can undergo additional cleavage and polyadenylation at a proximal internal site in the 3'-UTR, resulting in two stable, autonomous, RNA fragments: a coding sequence with a shorter 3'-UTR (body) and an uncapped 3'-UTR sequence downstream of the cleavage point (tail). Analyses of the human transcriptome has revealed thousands of such cleavage positions, suggesting a widespread post-transcriptional phenomenon producing thousands of stable 3'-UTR RNA tails that exist alongside their transcripts of origin. By analyzing the impact of microRNAs, we observed a significantly stronger effect for microRNA regulation at the body compared to the tail fragments. Our findings open a variety of future research prospects and call for a new perspective on 3'-UTR-dependent gene regulation.
Asunto(s)
Regiones no Traducidas 3'/genética , Isoformas de ARN/genética , Procesamiento Postranscripcional del ARN , ARN Mensajero/genética , Animales , Línea Celular Tumoral , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Células HEK293 , Humanos , Ratones Endogámicos C57BL , MicroARNs/genética , Sistemas de Lectura Abierta/genética , Poliadenilación , Caperuzas de ARNRESUMEN
Competing endogenous RNAs (ceRNAs) were recently introduced as RNA transcripts that affect each other's expression level through competition for their microRNA (miRNA) coregulators. This stems from the bidirectional effects between miRNAs and their target RNAs, where a change in the expression level of one target affects the level of the miRNA regulator, which in turn affects the level of other targets. By the same logic, miRNAs that share targets compete over binding to their common targets and therefore also exhibit ceRNA-like behavior. Taken together, perturbation effects could propagate in the posttranscriptional regulatory network through a path of coregulated targets and miRNAs that share targets, suggesting the existence of distant ceRNAs. Here we study the prevalence of distant ceRNAs and their effect in cellular networks. Analyzing the network of miRNA-target interactions deciphered experimentally in HEK293 cells, we show that it is a dense, intertwined network, suggesting that many nodes can act as distant ceRNAs of one another. Indeed, using gene expression data from a perturbation experiment, we demonstrate small, yet statistically significant, changes in gene expression caused by distant ceRNAs in that network. We further characterize the magnitude of the propagated perturbation effect and the parameters affecting it by mathematical modeling and simulations. Our results show that the magnitude of the effect depends on the generation and degradation rates of involved miRNAs and targets, their interaction rates, the distance between the ceRNAs and the topology of the network. Although demonstrated for a miRNA-mRNA regulatory network, our results offer what to our knowledge is a new view on various posttranscriptional cellular networks, expanding the concept of ceRNAs and implying possible distant cross talk within the network, with consequences for the interpretation of indirect effects of gene perturbation.
Asunto(s)
Redes Reguladoras de Genes , MicroARNs/genética , ARN/genética , Células HEK293 , Humanos , Modelos Genéticos , ARN Mensajero/genéticaRESUMEN
In studies of inflammatory bowel diseases (IBD), research has so far focused mainly on the role of T cells. Despite evidence suggesting that B cells and the production of autoantibodies may play a significant role in IBD pathogenesis, the role of B cells in gut inflammation has not yet been thoroughly investigated. In the present study we used the new approach of lineage tree analysis for studying immunoglobulin variable region gene diversification in B cells found in the inflamed intestinal tissue of two ulcerative colitis patients as well as B cells from mucosa-associated lymph nodes (LN) in the same patients. Healthy intestinal tissue of three patients with carcinoma of the colon was used as normal control. Lineage tree shapes revealed active immune clonal diversification processes occurring in ulcerative colitis patients, which were quantitatively similar to those in healthy controls. B cells from intestinal tissues and the associated LN are shown here to be clonally related, thus supplying the first direct evidence supporting B-cell trafficking between gut and associated LN in IBD and control tissues.
Asunto(s)
Linfocitos B/inmunología , Colitis Ulcerosa/inmunología , Colon/inmunología , Genes de Inmunoglobulinas , Región Variable de Inmunoglobulina/inmunología , Mucosa Intestinal/inmunología , Ganglios Linfáticos/inmunología , Adulto , Anciano de 80 o más Años , Movimiento Celular , Colitis Ulcerosa/genética , Femenino , Humanos , Región Variable de Inmunoglobulina/genética , Masculino , Persona de Mediana EdadRESUMEN
Lineage trees have frequently been drawn to illustrate diversification, via somatic hypermutation (SHM), of immunoglobulin variable-region (IGV) genes. In order to extract more information from IGV sequences, we developed a novel mathematical method for analyzing the graphical properties of IgV gene lineage trees, allowing quantification of the differences between the dynamics of SHM and antigen-driven selection in different lymphoid tissues, species, and disease situations. Here, we investigated trees generated from published IGV sequence data from B cell clones participating in autoimmune responses in patients with Myasthenia Gravis (MG), Rheumatoid Arthritis (RA), and Sjögren's Syndrome (SS). At present, as no standards exist for cell sampling and sequence extraction methods, data obtained by different research groups from two studies of the same disease often vary considerably. Nevertheless, based on comparisons of data groups within individual studies, we show here that lineage trees from different individual patients are often similar and can be grouped together, as can trees from two different tissues in the same patient, and even from IgG- and IgA-expressing B cell clones. Additionally, lineage trees from most studies reflect the chronic character of autoimmune diseases.
Asunto(s)
Enfermedades Autoinmunes/genética , Enfermedades Autoinmunes/inmunología , Región Variable de Inmunoglobulina/genética , Región Variable de Inmunoglobulina/inmunología , Mutación , Linaje , Artritis Reumatoide/genética , Artritis Reumatoide/inmunología , Linfocitos B/inmunología , Biología Computacional/métodos , Análisis Mutacional de ADN , Genes de Inmunoglobulinas/genética , Genes de Inmunoglobulinas/inmunología , Técnicas Genéticas , Humanos , Miastenia Gravis/genética , Miastenia Gravis/inmunología , Síndrome de Sjögren/genética , Síndrome de Sjögren/inmunología , Hipermutación Somática de Inmunoglobulina/genética , Hipermutación Somática de Inmunoglobulina/inmunologíaRESUMEN
Autoimmune diseases show high diversity in the affected organs, clinical manifestations and disease dynamics. Yet they all share common features, such as the ectopic germinal centers found in many affected tissues. Lineage trees depict the diversification, via somatic hypermutation (SHM), of immunoglobulin variable-region (IGV) genes. We previously developed an algorithm for quantifying the graphical properties of IGV gene lineage trees, allowing evaluation of the dynamical interplay between SHM and antigen-driven selection in different lymphoid tissues, species, and disease situations. Here, we apply this method to ectopic GC B cell clones from patients with Myasthenia Gravis, Rheumatoid Arthritis, and Sjögren's Syndrome, using data scaling to minimize the effects of the large variability due to methodological differences between groups. Autoimmune trees were found to be significantly larger relative to normal controls. In contrast, comparison of the measurements for tree branching indicated that similar selection pressure operates on autoimmune and normal control clones.